CYIY is supported by FAPESP (2012/14421-5) and FMV is supported by a fellowship from FAPESP (2009/53695-0). We thank the DNA Technologies Core at University of California, Davis for preparation and sequencing of the RNA-Seq libraries used in this work, the Galaxy team for providing an excellent and free interface for high-throughput sequencing data analysis tools and Dr. Marianne Bronner for allowing us to film in her laboratory space.

1. Electroporate HH12-13 닭 배아의 신경 튜브 OVO의 관심의 구조물 형질 전환의 만족 수준이 개인의 빠른 식별을 가능하게하기 위해, 바람직하게는 시스 트론 성적 증명서, 형광 기자를 사용하거나 인터 바이러스 2A 펩타이드 (11)와 함께 관심의 단백질에 융합. 참고 :이 단계에 대한 일반적인 배양 시간은 37.8 ° C에서 약 48 시간이다. <ol><li> 18 G X 1 1/2 바늘에 연결된 주사기와 알부민의 3 ㎖를 제거한 후 계란에있는 작은 창을 엽니 다. 배아 시각화를 향상시키기 위해, 배아 1-4 아래 멸균 링거액에서 1:50 희석 인도 소량의 잉크를 분사. </li><li> 멸균 링거액과 배아를 커버 한 후, 2.5 μg의이 신경관의 후방 말까지 DNA가 채우기 / 때까지 μL를 포함하는 10 mM 트리스 - 염산, pH를 8.2 및 0.1 % 식품 염료 (F, D &amp; C) 솔루션을 주입후뇌 지역까지. 상기 측면 영역을 따라 4mm (1)에 의해 분리 된 위치 백금 전극 (직경 0.5 mm)를 electroporate하고 (4) 사이의 100 밀리 초 간격으로 5 내지 50 밀리 초 펄스 및 20 V를 제공한다. </li><li> 전기 후, 그들은 무대 HH23에 도달 할 때까지 더 48 시간 동안 조작 배아를 배양시키고, 형광 실체 현미경을 이용하여 측면 지역에서 형질의 높은 수준을 제시 개인을 식별 할 수 있습니다. NOTE : 일렉트로 후 배양 기간은 실험의 목적에 의존한다. 일렉트로 플라스미드는 2 시간이 후에 상당한 발현 수준을 생성 할 수있다. 관심 조발성 유전자에 놓여 있다면 따라서, 이후 일렉트로 잠복기가 감소 될 수있다. </li></ol> 2. 수확 성공적으로 배아 형질과 일렉트릭 척수 반쪽을 해부하다 참고 :이 절차는 각 10 배아 및 수익률 1 ~ 3 시간까지 지속-2 배아 당 μg의 총 RNA. 신경 튜브의 해부는 좋은 움직임을 필요로하고 연습 세션은 실험 시료에 적용하기 전에해야 할 수 있습니다. <ol><li> 의 RNase의 오염 제거 용액 또는 4 시간 12 150 ℃에서 소성하여 금속 해부 도구의 오염을 제거하고 DEPC 처리 된 PBS를 준비합니다. 만 새로운 인증의 RNase없는 plasticware에 사용합니다. NOTE : 수확 후에는 박리시의 RNase 오염을 방지하기 위해 표준 치료를 수행하는 것이 중요하다. </li><li> 미세 해부 가위와 정립 수집 숟가락을 사용하여 배아를 수확. 100mm 페트리 접시에 차가운 DEPC 처리 된 PBS에서 배아를 보관하십시오. </li><li> 미세 핀셋으로 (전방 사지 꽃 봉 오리와 후방 사지 새싹의 전방 한계의 후방 한계 사이의) 전체 측면 영역을 잘라 차가운 DEPC 처리 된 PBS를 포함하는 새로운 요리에이 부분을 전송할 수 있습니다. </li><li> 세 가지를 관통하는 두 개의 미세 유리 바늘을 사용하여신경 튜브와 근축 중배엽 사이의 배아 각각의 배 외측면에 가리 킵니다. </li><li> 중앙 구멍에 두 개의 유리 바늘을 소개하고 천천히 신경관 전후방 축을 따라 그 중 하나를 멀리 이동합니다. 첫 번째 움직임에 의해 도달되지 않은 구멍에 대해이 단계를 반복합니다. 미세 핀셋으로 분리 된 근축 중배엽를 제거합니다. </li><li> 옆으로 배아를 돌려 신경관과 척색 사이의 핀셋의 끝을 삽입하고 두 개의 구조를 분리하는 전후방 축 방향의 반대 방향으로 그들을 밀어 넣습니다. 참고 :이 또한 중배엽의 대부분은 여전히​​ 신경 튜브에 부착 제거해야합니다. </li><li> 필요한 경우 가볍게 핀셋의 또 다른 쌍의 신경 튜브를 잡고 핀셋으로 잡아 당겨 부착 된 상태로 유지 mesodermic 조직의 더 큰 조각을 제거합니다. 완료되면, 부드럽게를 사용하여 추운 DEPC 처리 된 PBS를 포함하는 다른 요리에 신경 튜브를 전송의 RNase없는 유리 파스퇴르 피펫은 수동 피펫 펌프에 연결된 모든 튜브 해부 될 때까지 얼음에 보관하십시오. </li><li> 두 부분으로 신경 튜브를 나눈다. 이를 위해, 루멘에 핀셋의 폐쇄 된 한 쌍의 날카로운 끝을 삽입하고 그것을 통해 핀셋을 이동하여 지붕 판을 엽니 다. 그 후, 핀셋 팁 바닥 판을 절단하여 절반을 분리. </li><li> 정렬 얼음처럼 차가운 DEPC 처리 된 PBS로 가득 1.5 ML 튜브에 형광 해부 범위 및 전송에서 비 일렉트로 반쪽에서 일렉트로. 필요한 경우, 플라스틱 벽에 부착 된 조직을 분리하고 튜브의 침전을 촉진하기 위해 부드럽게 마이크로 튜브를 가볍게. </li><li> 3 초 동안 100 XG에 스핀과 1 ml의 마이크로 피펫으로 가능한 한 PBS로 매우 천천히 제거합니다. 어떤 배아 물질이 피펫 팁에 흡입되어있는 경우 모니터하기 위해 마이크로 튜브를 통해 빛난다 광원을보고하는 동안이 작업을 수행; 이 경우, 천천히 방전 centrifuga를 반복기. </li><li> 신경관 절반 당 RNA 추출을위한 분해 용액 70 μl를 추가하고 내용을 혼합 튜브를 가볍게. 격렬하게 5 분와 소용돌이 실온에서 인큐베이션. 5 분 배양과 와동 두 번 더 반복합니다. -80 ° C에서 보관하십시오. </li><li> 다음 단계에 대한 충분한 수율을 보장하기 위해 샘플 당 최소 8 신경관 반쪽를 수집합니다. 여러 전기 / 해부 세션이 신경 튜브의 충분한 수를 축적해야하는 경우 작은 샘플을 풀. 각 조건에 대한 중복 또는 삼중 충분한 샘플을 보관합니다. </li></ol> 3. Purify는 RNA와 Illumina의 시퀀싱 라이브러리를 준비 <ol><li> -80 ° C 저장에서 샘플을 제거하고 15 ~ 30 분 동안 얼음에 배치합니다. 완료 될 때까지 실온에서 해동을 다시 시작합니다. </li><li> 와동 잘 5 분 동안 실온에서 떠난다. 1 분 15,000 XG에 다시 소용돌이 원심 분리기는 불용성 물질을 펠렛. </li><li> 새로운 튜브에 뜨는을 전송및 총 RNA 분리 키트 설명서 지침에 따라 RNA 추출을 진행합니다. 농도를 증가시키기 위해 최소의 부피로 용출시켰다. NOTE : 청소 후 DNase를 처리 RNA-SEQ 셋 게놈 DNA 서열의 오염 가능성을 피하기 위해 권장된다. </li><li> 내용물을 혼합하고 품질 관리 분석을위한 5 μl를 제거하는 튜브 톡. 라이브러리 준비까지 C ° -80에서 나머지 샘플을 보관; 이들 샘플은 RNA의 분해를 방지하기 위해 단 한번만 해동되어야한다. </li><li> RNA 6000 나노 키트를 사용하여 Bioanalyzer 상품에 정제 된 RNA를 실행; RIN 값은 최소 7 위의 진행을해야합니다. </li><li> 일루미나 호환 RNA-SEQ 라이브러리 준비 키트를 사용하여 라이브러리를 생성하고 하나의 읽기 (100) BP를 생성하기 위해 설정 HiSeq 악기의 한 차선에서 4 라이브러리에 멀티 플렉스. 가능하면, 잠재적 인 기술 유물을 최소화하기 위해 같은 실행의 모든​​ 샘플을 포함한다. 참고 :이 5000 만 R까지 양보해야대부분의 유전자 (13)에 대한 커버리지를 얻을 수있을만큼보다 더 샘플, 당 EADS. </li></ol> 4. 갤럭시 공용 서버 (10)에 RNA-SEQ 데이터 집합을 비교. 참고 : 서버 저장 공간이 제한되며 많은 샘플을 비교 실험 필터링 단계에서 생성 된 중간 파일의 삭제를 요구할 수있다. <ol><li> (갤럭시 공개 서버에 사용자 계정을 만듭니다 <a href="https://usegalaxy.org/">https://usegalaxy.org</a> ) 및 FTP는 fastq 형식으로 Illumina의 데이터 세트를 업로드 할 수 있습니다. </li><li> NGS에서 FastqGroomer (14) 도구를 사용하여 업로드 된 파일 준비 : 품질 관리 및 조작 메뉴를; 품질 평가 점수가 이미 Phred + 33 (생거)으로 인코딩 된 경우, 단순히 각각의 데이터 세트에 대한 속성에서 fastqsanger하는 파일 형식을 변경하여이 단계를 건너 뜁니다. </li><li> QC 및 조작 나를 : 일반 NGS에서 FastQC 도구를 사용하여 각 데이터 세트의 품질 분석뉴. 참고 :이 읽기의 끝을 트리밍에 사용되는 매개 변수에 대한 추정치를 제공하므로 특별한주의가 염기 서열의 품질 별, 염기 서열의 콘텐츠에 대한 결과 그래픽 고려되어야한다. </li><li> 트림 3 &#39;폐기 읽는 도구 NGS에서 FASTQ 품질 트리머 (14) 사용하여 낮은 품질의 데이터로 끝나는 : 품질 관리 및 조작 메뉴를 표시합니다. 만 3 &#39;가 20 아래 품질 평가 점수에 대한 종료 처리하기 위해 도구를 설정합니다. </li><li> 클립 도구 (사용하여 읽기에서 어댑터 시퀀스를 제거 <a href="http://hannonlab.cshl.edu/fastx_toolkit/">http://hannonlab.cshl.edu/fastx_toolkit/</a> QC 및 조작 메뉴 : NGS 아래 참조). 왼쪽보다 45 bp의 입력에 사용되는 어댑터의 순서로 읽어 버리고 모두 클리핑 및 비 클리핑 된 시퀀스를 포함하는 출력을 선택할 수있는 도구를 설정합니다. 또한, 가장 낮은 품질의 기지가 이미 마지막 단계에서 제거 된 이후 알 수없는 기지와 시퀀스를 폐기하지 않는 선택. </lI&gt; <li> 도구 트림 시퀀스 (사용 <a href="http://hannonlab.cshl.edu/fastx_toolkit/">http://hannonlab.cshl.edu/fastx_toolkit/</a> NGS 아래)가 FastQC에 의해 검출 된 5 &#39;시퀀스 바이어스 (일반적으로 10)를 제거하기 위해 읽기의 ​​품질 관리 및 조작 메뉴를 첫 번째 기지 트림. 참고 :이 시점에서, 다시 FastQC을 실행하고 데이터 세트의 품질이 향상되었는지 확인하기 위해 이전의 분석과 비교하는 것이 좋습니다. </li><li> 다운로드 일루미나 iGenomes에서 UCSC 게놈 브라우저의 최신 닭 게놈 어셈블리를 풀고 ( <a href="http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn">http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn</a> ) 전체 게놈 FASTA 형식 파일 및 유전자 주석 GTF 형식의 파일을 업로드 데이터 가져 오기 메뉴에서 도구 파일 업로드를 사용하여 갤럭시 역사. </li><li> 지도하에 얼 라이너 (15)를 사용 TopHat2 닭 게놈에 각 샘플에 대해 읽NGS : RNA 분석 메뉴. 역사에서 게놈을 사용하기로 선택한다 (단계 4.7에서 업로드 FASTA 파일을 선택합니다). </li><li> RNA 분석 메뉴 : NGS에서 커프스 16 사용하여 각 샘플에 대한 예측 사체를 구축 할 수 있습니다. 가이드로 참조 주석을 사용한다 (단계 4.7에서 업로드 GTF 파일을 선택)하고 옵션을 켭니다 (역사, 단계 4.7에서 FASTA 파일에서) 바이어스 보정을 수행하고 다 읽어 올바른 사용하도록 선택합니다. </li><li> RNA 분석 메뉴 : NGS에서 Cuffmerge (16)를 사용하여 모든 샘플에 대한 예측 transcriptomes를 병합합니다. (역사, 단계 4.7에서 FASTA 파일) 및 시퀀스 데이터 (단계 4.7에서 GTF 파일) 참조 주석을 사용하여 선택합니다. </li><li> RNA 분석 메뉴 : NGS에서 Cuffdiff 16 사용하여 각 샘플에 대한 TopHat2에 의해 생성 된 BAM 파일을 비교. 필드 성적 증명서에서 나를 선택rged 사체는 Cuffmerge에 의해 생성 옵션 (역사, 단계 4.7에서 FASTA 파일에서) 바이어스 보정을 수행 켜고 다 읽어 올바른 사용합니다. </li><li> 정렬 차동 표현은 필터에서 도구 정렬을 사용하여 숫자 열 (13) (Q 값)의 상승 테이블을 테스트하고 메뉴를 정렬합니다. 참고 : 유전자 / 가장 낮은 Q 값을 제시한다 실험 조건 사이에 상당한 차이 식을 보여주는 성적 증명서. </li><li> 범위 그래프를 시각적으로 결과를 확인하려면 먼저 도구가 BEDTools 메뉴에서 게놈 범위 (17)의 BedGraph를 작성하여 bedGraph 형식으로 BAM 파일을 변환합니다. 보험이없는 지역의보고를 사용하지 않도록 설정, 별개의 간격으로 접합 항목을 처리하고 모든 데이터 세트가 비교되는 염기 서열 깊이를 정규화 계수로 적용 범위를 확장하기 위해 선택합니다. </li><li> 을 사용하여 중요 인물 형식 얻어진 bedGraph 파일 변환도구 가발 / BedGraph - 투 - 중요 인물 ( <a href="http://www.genome.ucsc.edu/">http://www.genome.ucsc.edu/</a> ) 변환 형식 메뉴에서. UCSC 게놈 브라우저 (사용자 지정 트랙으로 중요 인물 파일을 업로드 <a href="http://www.genome.ucsc.edu/">http://www.genome.ucsc.edu/</a> galGal4 어셈블리)와 데이터 세트의 범위를 시각적으로 관심의 유전자를 검색 할 수 있습니다. </li></ol>

<ol>
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The authors have nothing to disclose.

여기에서 우리는 닭 척수의 전기 후 효과 분석을위한 지침을 제공합니다. DNA 벡터의 전기가 더 자주 관심의 유전자를 과발현하는 데 사용되지만, 하나는 또한 유전자 기능 녹다운 조건 19-21를 생성하는 siRNA를 위해 우성 네거티브 quimeric 또는 전구체 단백질을 코딩하는 구조를 이용할 수있다. 실제로, 이득 - 및 기능 상실 분석 모두에 기인 사체 프로파일의 비교는 차별적 따라서 전위가 더 ...

OVO 전기에 DNA 1-5을 구성하여 부분적으로 생체 내에서 배아 구조에 감염 될 수있는 빠르고 저렴한 방법을 나타 내기 때문에 살아있는 유기체에 유전 연구는 자주 모델로 닭 배아를 사용합니다. 이러한 pCIG 6 pMES 7과 같은 목적 유전자와 함께 형광 리포터를 함유 한 증명서를 인코딩 시스 트론 발현 벡터, 하류 분석 배아를 처리하기 전에 실체 현미경을 이용하여 원하는 영역에 형질 전환 품질의 빠른 확인을 허용한다. DNA 시퀀싱 최근 발전으로, 그것은 RNA-SEQ 8,9을 사용하여 RNA 샘플들로부터 디지털 전 사체 발현 프로파일을 획득하는 것이 가능하다. 따라서, 대신 그러한 계내 혼성화, 면역 조직 화학 및 qPCR에,의 cDNA 라이브러리의 제조에서와 같이 병렬로 몇 유전자 산물의 분석을 가능하게 시간이 걸리는 방법높은 처리량 시퀀싱 전 사체의 정보를 제공 할 수있다. 모든 단일 유전자의 발현 수준에 대한 효과 실험 관찰 차례로 사용 구조체에 의해 변경 경로에 강력한 통찰력을 제공 할 수있다. 이 사용 유기체의 게놈 어셈블리를 사용할 수있는 경우 특히 쉽고, 따라서 병아리 배아는 다시 적당한 모델이다. 사용자가 신뢰할 수있는 게놈 시퀀싱 센터에 액세스하는 경우, 주요 문제는 고품질의 RNA 샘플을 획득한다. 본 연구는 생성 된 데이터 세트의 실리코 분석을 위해 RNA-SEQ 적합한 형질 신경 튜브뿐만 아니라 하류 단계로부터 RNA 샘플을 얻는 방법을 설명한다. 48 시간 배양 한 다음 HH12-13에 전기 한 후, 형질 전환 된 트렁크 척수 절반은, 리보 뉴 클레아가없는 상태에서 해부 즉시 용해 및 추가 RNA 정화 및 라이브러리는 준비 될 때까지 매우 낮은 동결에 의해 분해로부터 보호했다이온. 갤럭시 공공 서버 (10)는 높은 처리량 시퀀싱 데이터 분석을위한 무료 자원에 대한 액세스를 제공합니다. 등록 된 사용자를 위해 제공되는 공간의 크기는 국부적 계산 된 기반 구조에 대한 필요성을 제거, 소형 실험에 충분하다. RNA-SEQ 데이터 분석 필터링, 정렬 및 유전자 발현의 정량 / 비교를 포함한다. RNA-SEQ 데이터 분석에 대한 일반적인 가이드 라인이 있지만, 필터링 파라미터 시퀀싱의 품질에 크게 의존 할 것으로 예상되며, 원 데이터의 품질 관리 분석을 통해 결정되어야한다. 이 프로토콜은 획득 및 생체 내에서 형질 전환 닭의 배아 척수에서 RNA-SEQ 프로파일을 비교하는 단계에 대해 설명합니다. 대표적인 결과, 빈 벡터로 형질 개의 독립 제어 샘플들로부터 얻어진 데이터 세트의 비교 방법은 재현성 및 차등 EXPRES의 식별을 허용한다는 것을 보여 주었다실험 샘플에 나오지도 성적 증명서. 따라서, 이러한 방법의 응용이 크게 하나의 실험 후에 발견의 수를 증가하고, 따라서 후속 조사를 위해 큰 데이터 세트를 제공하는 잠재력을 가지고있다.

<table border="0" cellpadding="0" cellspacing="0" width="1031">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:425px;">Name of Material/ Equipment</td>
			<td style="width:175px;">Company</td>
			<td style="width:164px;">Catalog Number</td>
			<td style="width:267px;">Comments/Description</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Indian &#236;nk</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">18G x 1 1/2 needle</td>
			<td>BD</td>
			<td>305196</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">3 ml syringe</td>
			<td>BD</td>
			<td>309657</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Tris</td>
			<td>MP Biomedicals</td>
			<td>819620</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">F D &#38; C Blue 1</td>
			<td>Spectra Colors Corporation</td>
			<td>5.FC.0010P0</td>
			<td>Food Dye used to visualize DNA injection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ringer&#39;s solution (1 L)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#160;&#160;&#160;&#160; - 7.2 g NaCl</td>
			<td>Sigma-Aldrich</td>
			<td>S-9888</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#160;&#160;&#160;&#160; - 0.37 g KCl</td>
			<td>Sigma-Aldrich</td>
			<td>P-4504</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - 0.225 g CaCl2.2H2O</td>
			<td>Fisher Scientific</td>
			<td>10043-52-4</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - 0.217 g Na2HPO4.7H2O</td>
			<td>Sigma-Aldrich</td>
			<td>S-9390</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - 0.02 g KH2PO4</td>
			<td>Sigma-Aldrich</td>
			<td>P-5379</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - ddH2O to 800 ml and adjust pH to 7.4</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - ddH2O to 1 L</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#160;&#160;&#160;&#160; - Filter and autoclave</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">PBS (Phosphate Buffered Solution) (1 L)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#160;&#160;&#160;&#160; - 8 g NaCl</td>
			<td>Sigma-Aldrich</td>
			<td>S-9888</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#160;&#160;&#160;&#160; - 0.2 g KCl</td>
			<td>Sigma-Aldrich</td>
			<td>P-4504</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - 1.15 g Na2HPO4.7H2O</td>
			<td>Sigma-Aldrich</td>
			<td>S-9390</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - 0.2 g KH2PO4</td>
			<td>Sigma-Aldrich</td>
			<td>P-5379</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - ddH2O to 800 ml and adjust pH to 7.2</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">&#160;&#160;&#160;&#160; - ddH2O to 1 L and filter</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#160;&#160;&#160;&#160; - 1 ml DEPC (Diethylpyrocarbonate)</td>
			<td>Sigma-Aldrich</td>
			<td>D-5758</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#160;&#160;&#160;&#160; - Shake vigorously and let stand overnight at room temperature</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#160;&#160;&#160;&#160; - Autoclave</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Sieved spoon</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Sterile 60 x 15 mm polystirene Petri dishes</td>
			<td>Corning Life Sciences</td>
			<td>351007</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">RNaseZap RNase decontamination solution</td>
			<td>Life Technologies</td>
			<td>AM9780</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Fine point surgical scissors</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Straight fine point tweezers</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Pulled glass needle made from 1.1 x 75 mm glass capillary tubes</td>
			<td>Kimble Chase</td>
			<td>40A502</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">9&#39;&#39; glass Pasteur pipette</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Manual pipette pump</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Clear 1.5 ml microcentrifuge polypropilene tubes</td>
			<td>Corning Life Sciences</td>
			<td>MCT-150-C</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Microcentrifuge</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">RNAlater solution for RNA stabilization</td>
			<td>Life Technologies</td>
			<td>AM7020</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">RNAqueous total RNA isolation kit</td>
			<td>Life Technologies</td>
			<td>AM1912</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Molecular Biology Grade Ethanol</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">RNA 6000 Nano Kit</td>
			<td>Agilent Technologies</td>
			<td>5067-1511</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">2100 Electrophoresis Bioanalyzer Instrument</td>
			<td>Agilent Technologies</td>
			<td>G2939AA</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Truseq RNA Sample Preparation Kit v2</td>
			<td>Illumina</td>
			<td>RS-122-2001/RS-122-2002</td>
			<td></td>
		</tr>
	</tbody>
</table>

rna-seq analysis of differential gene expression in electroporated chick embryonic spinal cord

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome wide analysis of differentially expressed transcripts after such an experimental manipulation has the potential to uncover an almost complete picture of the downstream effects caused by the transfected construct. This work describes a simple method for comparing transcriptomes from samples of transfected embryonic spinal cords comprising all steps between electroporation and identification of differentially expressed transcripts. The first stage consists of guidelines for electroporation and instructions for dissection of transfected spinal cord halves from HH23 embryos in ribonuclease-free environment and extraction of high-quality RNA samples suitable for transcriptome sequencing. The next stage is that of bioinformatic analysis with general guidelines for filtering and comparison of RNA-Seq datasets in the Galaxy public server, which eliminates the need of a local computational structure for small to medium scale experiments. The representative results show that the dissection methods generate high quality RNA samples and that the transcriptomes obtained from two control samples are essentially the same, an important requirement for detection of differential expression genes in experimental samples. Furthermore, one example is provided where experimental overexpression of a DNA construct can be visually verified after comparison with control samples. The application of this method may be a powerful tool to facilitate new discoveries on the function of neural factors involved in spinal cord early development.

설명 된 방법을 검증하기 위해, 두 개의 제어 샘플은 빈 벡터 pMES 7 삽입 닭 SCRT2 (18)의 아연 손가락 도메인을 인코딩 SCRT2-ZNF를, 구성이 포함 된 동일한 벡터로 형질 전환 된 배아에서 하나의 샘플에 electroporation하여 배아에서 발생했다. 각 11-22 μg의 총 RNA를 산출 샘플은 8 ~ 12 배아의 풀에서 얻었다. 모든 3 개의 시료 고품질 RNA이 프로토콜로 얻을 수있는 것을 보여주는 Bioanalyzer 기기 ...

Watch this Scientific Journal Video about RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord at JoVE.com

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

This video shows the basic steps for performing whole transcriptome analysis on dissected chick embryonic spinal cord samples after transfection with in ovo electroporation.

electroporation하여 병아리 배아 척수에서 차동 유전자 발현의 RNA-SEQ 분석

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome ...

rna-seq-analysis-differential-gene-expression-electroporated-chick

Research

JoVE Journal

Neuroscience

14.4K 조회수.  Universidade de São Paulo. This video shows the basic steps for performing whole transcriptome analysis on dissected chick embryonic spinal cord samples after transfection with in ovo electroporation.

비디오: RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

Dissection and Culture of Commissural Neurons from Embryonic Spinal Cord

Commissural neurons have been widely used to investigate the mechanisms underlying axon guidance during embryonic spinal cord development. The cell bodies of these neurons are located in the dorsal spinal cord and their axons follow stereotyped trajectories during embryonic development. Commissural axons initially project ventrally towards the floorplate. After crossing the midline, these axons turn anteriorly and project towards the brain. Each of these steps is regulated by the action of several guidance cues. Cultures highly enriched in commissural neurons are ideally suited for many experiments addressing the mechanisms of axon pathfinding, including turning assays, immunochemistry and biochemistry. Here, we describe a method to dissect and culture commissural neurons from E13 rat dorsal spinal cord. First, the spinal cord is isolated and dorsal strips are dissected out. The dorsal tissue is then dissociated into a cell suspension by trypsinization and mechanical disruption. Neurons are plated onto poly-L-lysine-coated glass coverslips or tissue-culture dishes. After 30 hours in vitro, most neurons have extended an axon. The purity of the culture (Yam et al. 2009), typically over 90%, can be assessed by immunolabeling with the commissural neuron markers DCC, LH2 and TAG1 (Helms and Johnson, 1998). This neuronal preparation is a useful tool for in vitro studies of the cellular and molecular mechanisms of commissural axon growth and guidance during spinal cord development.

This video demonstrates a method to dissect and culture commissural neurons from E13 rat dorsal spinal cord. Dissociated commissural neurons are useful to study the cellular and molecular mechanisms of axon growth and guidance.

배아 척수에서 뉴런의 Commissural 해부와 문화

Commissural neurons have been widely used to investigate the mechanisms underlying axon guidance during embryonic spinal cord development. The cell bodies ...

연구

신경과학

Spinal Cord Electrophysiology II: Extracellular Suction Electrode Fabrication

Development of neural circuitries and locomotion can be studied using neonatal rodent spinal cord central pattern generator (CPG) behavior. We demonstrate a method to fabricate suction electrodes that are used to examine CPG activity, or fictive locomotion, in dissected rodent spinal cords. The rodent spinal cords are placed in artificial cerebrospinal fluid and the ventral roots are drawn into the suction electrode. The electrode is constructed by modifying a commercially available suction electrode. A heavier silver wire is used instead of the standard wire given by the commercially available electrode. The glass tip on the commercial electrode is replaced with a plastic tip for increased durability. We prepare hand drawn electrodes and electrodes made from specific sizes of tubing, allowing consistency and reproducibility. Data is collected using an amplifier and neurogram acquisition software. Recordings are performed on an air table within a Faraday cage to prevent mechanical and electrical interference, respectively.

A demonstration of the fabrication and use of an extracellular suction electrode used to measure electrophysiological recordings of neonatal rodent spinal cords in vitro

척수 전기 생리학 II : 세포 흡입 전극 제작

Development of neural circuitries and locomotion can be studied using neonatal rodent spinal cord central pattern generator (CPG) behavior. We demonstrate ...

Dissection and Culture of Chick Statoacoustic Ganglion and Spinal Cord Explants in Collagen Gels for Neurite Outgrowth Assays

The sensory organs of the chicken inner ear are innervated by the peripheral processes of statoacoustic ganglion (SAG) neurons. Sensory organ innervation depends on a combination of axon guidance cues1 and survival factors2 located along the trajectory of growing axons and/or within their sensory organ targets. For example, functional interference with a classic axon guidance signaling pathway, semaphorin-neuropilin, generated misrouting of otic axons3. Also, several growth factors expressed in the sensory targets of the inner ear, including Neurotrophin-3 (NT-3) and Brain Derived Neurotrophic Factor (BDNF), have been manipulated in transgenic animals, again leading to misrouting of SAG axons4. These same molecules promote both survival and neurite outgrowth of chick SAG neurons in vitro5,6.
Here, we describe and demonstrate the in vitro method we are currently using to test the responsiveness of chick SAG neurites to soluble proteins, including known morphogens such as the Wnts, as well as growth factors that are important for promoting SAG neurite outgrowth and neuron survival. Using this model system, we hope to draw conclusions about the effects that secreted ligands can exert on SAG neuron survival and neurite outgrowth. 
SAG explants are dissected on embryonic day 4 (E4) and cultured in three-dimensional collagen gels under serum-free conditions for 24 hours. First, neurite responsiveness is tested by culturing explants with protein-supplemented medium. Then, to ask whether point sources of secreted ligands can have directional effects on neurite outgrowth, explants are co-cultured with protein-coated beads and assayed for the ability of the bead to locally promote or inhibit outgrowth. We also include a demonstration of the dissection (modified protocol7) and culture of E6 spinal cord explants. We routinely use spinal cord explants to confirm bioactivity of the proteins and protein-soaked beads, and to verify species cross-reactivity with chick tissue, under the same culture conditions as SAG explants. These in vitro assays are convenient for quickly screening for molecules that exert trophic (survival) or tropic (directional) effects on SAG neurons, especially before performing studies in vivo. Moreover, this method permits the testing of individual molecules under serum-free conditions, with high neuron survival8.

We demonstrate how to dissect and culture chick E4 statoacoustic ganglion and E6 spinal cord explants. Explants are cultured under serum-free conditions in 3D collagen gels for 24 hours. Neurite responsiveness is tested with growth factor-supplemented medium and with protein-coated beads.

Neurite 가지의 Assays에 대한 해부와 칙 Statoacoustic 신경절과 콜라겐 젤에서 척수의 Explants의 문화

The sensory organs of the chicken inner ear are innervated by the peripheral processes of statoacoustic ganglion (SAG) neurons. Sensory organ innervation ...

DiI-Labeling of DRG Neurons to Study Axonal Branching in a Whole Mount Preparation of Mouse Embryonic Spinal Cord

Here we present a technique to label the trajectories of small groups of DRG neurons into the embryonic spinal cord by diffusive staining using the lipophilic tracer 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI)1. The comparison of axonal pathways of wild-type with those of mouse lines in which genes are mutated allows testing for a functional role of candidate proteins in the control of axonal branching which is an essential mechanism in the wiring of the nervous system. Axonal branching enables an individual neuron to connect with multiple targets, thereby providing the physical basis for the parallel processing of information. Ramifications at intermediate target regions of axonal growth may be distinguished from terminal arborization. Furthermore, different modes of axonal branch formation may be classified depending on whether branching results from the activities of the growth cone (splitting or delayed branching) or from the budding of collaterals from the axon shaft in a process called interstitial branching2 (Fig. 1).
The central projections of neurons from the DRG offer a useful experimental system to study both types of axonal branching: when their afferent axons reach the dorsal root entry zone (DREZ) of the spinal cord between embryonic days 10 to 13 (E10 - E13) they display a stereotyped pattern of T- or Y-shaped bifurcation. The two resulting daughter axons then proceed in rostral or caudal directions, respectively, at the dorsolateral margin of the cord and only after a waiting period collaterals sprout from these stem axons to penetrate the gray matter (interstitial branching) and project to relay neurons in specific laminae of the spinal cord where they further arborize (terminal branching)3. DiI tracings have revealed growth cones at the dorsal root entry zone of the spinal cord that appeared to be in the process of splitting suggesting that bifurcation is caused by splitting of the growth cone itself4 (Fig. 2), however, other options have been discussed as well5.
This video demonstrates first how to dissect the spinal cord of E12.5 mice leaving the DRG attached. Following fixation of the specimen tiny amounts of DiI are applied to DRG using glass needles pulled from capillary tubes. After an incubation step, the labeled spinal cord is mounted as an inverted open-book preparation to analyze individual axons using fluorescence microscopy.

The stereotyped projections of sensory afferents into the rodent spinal cord offer an easily accessible experimental system to study axonal branching through the tracing of single axons.

마우스 배아 척수의 전체 마운트 준비 분기 Axonal 공부 DRG 뉴런의 DiI - 라벨링

Here we  present a technique to label the trajectories of small groups of DRG neurons  into the embryonic spinal cord by diffusive staining using the ...

In ovo Expression of MicroRNA in Ventral Chick Midbrain

Non-coding RNAs are additional players in regulating gene expression. Targeted in ovo electroporation of specific areas provides a unique tool for spatial and temporal control of ectopic microRNA expression. However, ventral brain structures like ventral midbrain are rather difficult to reach for any manipulations. Here, we demonstrate an efficient way to electroporate miRNA into ventral midbrain using thin platinum electrodes. This method offers a reliable way to transfect specific areas of the midbrain and a useful tool for in vivo studies.

In ovo Expression of MicroRNA in Ventral Chick Midbrain

Ectopic expression is one technique to elucidate the microRNAs role in brain development. However, targeting specific areas using in ovo electroporation is challenging. Here, we show an efficient way to selectively electroporate ventral and dorsal midbrain regions.

복부 병아리 중뇌에있는 마이크로 RNA의 오보, 식

Non-coding RNAs are additional players in regulating gene expression. Targeted in ovo electroporation of specific areas provides a unique tool for spatial ...

Stereotaxic Injection of a Viral Vector for Conditional Gene Manipulation in the Mouse Spinal Cord

Intraparenchymal injection of a viral vector enables conditional gene manipulation in distinct populations of neurons or particular regions of the central nervous system. We demonstrate a stereotaxic injection technique that allows targeted gene expression or silencing in the dorsal horn of the mouse spinal cord. The surgical procedure is brief. It requires laminectomy of a single vertebra, providing for quick recovery of the animal and unimpaired motility of the spine. Controlled injection of a small vector suspension volume at low speed and use of a microsyringe with beveled glass cannula minimize the tissue lesion. The local immune response to the vector depends on the intrinsic properties of the virus employed; in our experience, it is minor and short-lived when a recombinant adeno-associated virus is used. A reporter gene such as enhanced green fluorescent protein facilitates monitoring spatial distribution of the vector, and the efficacy and cellular specificity of the transfection.

Viral vectors allow for targeted gene manipulation. We demonstrate a method for conditional gene expression or ablation in the mouse spinal cord, using stereotaxic injection of a viral vector into the dorsal horn, a prominent site of synaptic contact between primary somatosensory afferents and neurons of the central nervous system.

마우스 척추 조건부 유전자 조작을위한 바이러스 성 벡터의 Stereotaxic 주입

Intraparenchymal injection of a viral vector enables conditional gene manipulation in distinct populations of neurons or particular regions of the central ...

Dissection and Lateral Mounting of Zebrafish Embryos: Analysis of Spinal Cord Development

The zebrafish spinal cord is an effective investigative model for nervous system research for several reasons. First, genetic, transgenic and gene knockdown approaches can be utilized to examine the molecular mechanisms underlying nervous system development. Second, large clutches of developmentally synchronized embryos provide large experimental sample sizes. Third, the optical clarity of the zebrafish embryo permits researchers to visualize progenitor, glial, and neuronal populations. Although zebrafish embryos are transparent, specimen thickness can impede effective microscopic visualization. One reason for this is the tandem development of the spinal cord and overlying somite tissue. Another reason is the large yolk ball, which is still present during periods of early neurogenesis. In this article, we demonstrate microdissection and removal of the yolk in fixed embryos, which allows microscopic visualization while preserving surrounding somite tissue. We also demonstrate semipermanent mounting of zebrafish embryos. This permits observation of neurodevelopment in the dorso-ventral and anterior-posterior axes, as it preserves the three-dimensionality of the tissue.

Developmental processes such as proliferation, patterning, differentiation, and axon guidance can be readily modeled in the zebrafish spinal cord. In this article, we describe a mounting procedure for zebrafish embryos, which optimizes visualization of these events.

해부 및 제브라 피쉬 배아의 측면 장착 : 척수 개발의 분석

The zebrafish spinal cord is an effective investigative model for nervous system research for several reasons. First, genetic, transgenic and gene ...

Spinal Cord Transection in the Larval Zebrafish

Mammals fail in sensory and motor recovery following spinal cord injury due to lack of axonal regrowth below the level of injury as well as an inability to reinitiate spinal neurogenesis. However, some anamniotes including the zebrafish Danio rerio exhibit both sensory and functional recovery even after complete transection of the spinal cord. The adult zebrafish is an established model organism for studying regeneration following spinal cord injury, with sensory and motor recovery by 6&#160;weeks post-injury. To take advantage of in vivo analysis of the regenerative process available in the transparent larval zebrafish as well as genetic tools not accessible in the adult, we use the larval zebrafish to study regeneration after spinal cord transection. Here we demonstrate a method for reproducibly and verifiably transecting the larval spinal cord. After transection, our data shows sensory recovery beginning at 2&#160;days post-injury (dpi), with the C-bend movement detectable by 3 dpi and resumption of free swimming by 5 dpi. Thus we propose the larval zebrafish as a companion tool to the adult zebrafish for the study of recovery after spinal cord injury.

After spinal transection, adult zebrafish have functional recovery by six weeks post-injury. To take advantage of larval transparency and faster recovery, we present a method for transecting the larval spinal cord. After transection, we observe sensory recovery beginning at 2&#160;days post-injury, and C-bend movement by 3 days post-injury.

애벌레 Zebrafish의 척수 절개

Mammals fail in sensory and motor recovery following spinal cord injury due to lack of axonal regrowth below the level of injury as well as an inability ...

An Ex Vivo Laser-induced Spinal Cord Injury Model to Assess Mechanisms of Axonal Degeneration in Real-time

Injured CNS axons fail to regenerate and often retract away from the injury site. Axons spared from the initial injury may later undergo secondary axonal degeneration. Lack of growth cone formation, regeneration, and loss of additional myelinated axonal projections within the spinal cord greatly limits neurological recovery following injury. To assess how central myelinated axons of the spinal cord respond to injury, we developed an ex vivo living spinal cord model utilizing transgenic mice that express yellow fluorescent protein in axons and a focal and highly reproducible laser-induced spinal cord injury to document the fate of axons and myelin (lipophilic fluorescent dye Nile Red) over time using two-photon excitation time-lapse microscopy. Dynamic processes such as acute axonal injury, axonal retraction, and myelin degeneration are best studied in real-time. However, the non-focal nature of contusion-based injuries and movement artifacts encountered during in vivo spinal cord imaging make differentiating primary and secondary axonal injury responses using high resolution microscopy challenging. The ex vivo spinal cord model described here mimics several aspects of clinically relevant contusion/compression-induced axonal pathologies including axonal swelling, spheroid formation, axonal transection, and peri-axonal swelling providing a useful model to study these dynamic processes in real-time. Major advantages of this model are excellent spatiotemporal resolution that allows differentiation between the primary insult that directly injures axons and secondary injury mechanisms; controlled infusion of reagents directly to the perfusate bathing the cord; precise alterations of the environmental milieu (e.g., calcium, sodium ions, known contributors to axonal injury, but near impossible to manipulate in vivo); and murine models also offer an advantage as they provide an opportunity to visualize and manipulate genetically identified cell populations and subcellular structures. Here, we describe how to isolate and image the living spinal cord from mice to capture dynamics of acute axonal injury.

An Ex Vivo Laser-induced Spinal Cord Injury Model to Assess Mechanisms of Axonal Degeneration in Real-time

We present a protocol utilizing two-photon excitation time-lapse microscopy to simultaneously visualize the dynamics of axon and myelin injuries in real time. This proposed protocol permits studies of both intrinsic and extrinsic factors which can influence central myelinated axon fate after injury and contribute to permanent clinical disability.

<em&gt; 전의 VIVO</em&gt; 레이저에 의한 척수 손상 모델은 실시간으로 축삭 변성의 메커니즘을 평가하기 위해

Injured CNS axons fail to regenerate and often retract away from the injury site. Axons spared from the initial injury may later undergo secondary axonal ...

Adeno-associated Virus-mediated Transgene Expression in Genetically Defined Neurons of the Spinal Cord

Selective manipulation of spinal neuronal subpopulations has mainly been achieved by two different methods: 1) Intersectional genetics, whereby double or triple transgenic mice are generated in order to achieve selective expression of a reporter or effector gene (e.g., from the Rosa26 locus) in the desired spinal population. 2) Intraspinal injection of Cre-dependent recombinant adeno-associated virus (rAAV); here Cre-dependent AAV vectors coding for the reporter or effector gene of choice are injected into the spinal cord of mice expressing Cre recombinase in the desired neuronal subpopulation. This protocol describes how to generate Cre-dependent rAAV vectors and how to transduce neurons in the dorsal horn of the lumbar spinal cord segments L3-L5 with rAAVs. As the lumbar spinal segments L3-L5 are innervated by those peripheral sensory neurons that transmit sensory information from the hindlimbs, spontaneous behavior and responses to sensory tests applied to the hindlimb ipsilateral to the injection side can be analyzed in order to interrogate the function of the manipulated neurons in sensory processing. We provide examples of how this technique can be used to analyze genetically defined subsets of spinal neurons. The main advantages of virus-mediated transgene expression in Cre transgenic mice compared to classical reporter mouse-induced transgene expression are the following: 1) Different Cre-dependent rAAVs encoding various reporter or effector proteins can be injected into a single Cre transgenic line, thus overcoming the need to create several multiple transgenic mouse lines. 2) Intraspinal injection limits manipulation of Cre-expressing cells to the injection site and to the time after injection. The main disadvantages are: 1) Reporter gene expression from rAAVs is more variable. 2) Surgery is required to transduce the spinal neurons of interest. Which of the two methods is more appropriate depends on the neuron population and research question to be addressed.

Intraspinal injection of recombinase dependent recombinant adeno-associated virus (rAAV) can be used to manipulate any genetically labelled cell type in the spinal cord. Here we describe how to transduce neurons in the dorsal horn of the lumbar spinal cord. This technique enables functional interrogation of the manipulated neuron subtype.

척수의 유전으로 정의 된 신경에 있는 Adeno 관련 바이러스 중재 Transgene 식

Selective manipulation of spinal neuronal subpopulations has mainly been achieved by two different methods: 1) Intersectional genetics, whereby double or ...