|
| Status |
Public on Dec 11, 2012 |
| Title |
LFB_HOXA1KD_hiseq_repC |
| Sample type |
SRA |
| |
|
| Source name |
LFB_HOXA1KD_hiseq_repC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung fibroblasts
transfection: HOXA1 knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturers’ instructions. RNA quality was assessed using an Aglient Bioanalyzer. RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions. Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.
TruSeq RNA-Seq kit v1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
All reads aligned with TopHat version 1.4.0 using the following options: "-a 5" against hg19 and annotated UCSC coding transcripts.
Aligments were processed with Cuffdiff version 2.0.0 using default options.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff expression tracking
|
| |
|
| Submission date |
May 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Cole Trapnell |
| E-mail(s) |
cole@broadinstitute.org
|
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology
|
| Lab |
John Rinn
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE37703 |
Differential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq [Illumina] |
| GSE37704 |
Differential analysis of gene regulation at transcript resolution by RNA-Seq |
|
| Relations |
| SRA |
SRX145667 |
| BioSample |
SAMN00990709 |
