|
| Status |
Public on Nov 21, 2016 |
| Title |
RNA-seq_MEF_Smarcb1II |
| Sample type |
SRA |
| |
|
| Source name |
MEF_Smarcb1
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6/129
genotype/variation: Smarcb1-KO
cell type: mouse embryonic fibroblast
|
| Treatment protocol |
Cells were infected with retrovisur expressing Cre, and selected with puromycine. 72 hours post selection, cells were harvested and used.
|
| Growth protocol |
MEFs were cultured in DMEM with 10% FBS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen) and further purified using RNeasy MinElute Cleanup Kit (Qiagen).
2 μg of total RNA was used to make the RNA-Seq library using TruSeq Total RNA Sample Prep Kit (Illumina) and sequenced with the Hi-Seq Illumina genome analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The sequenced reads from each sample were aligned to the mouse genome+transcriptome assembly NCBIM37.67 using TopHat v2.0.8 with default parameters except turning off novel junction search ( -G <gtf> --no-novel-juncs).
Genomic coverage was calculated in R using BioConductor packages Rsamtools and Granges
Genome_build: mm9
Supplementary_files_format_and_content: wig file showing unnormalized RNA-seq coverage
|
| |
|
| Submission date |
Jul 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE71508 |
The SWI/SNF chromatin remodeling complex is required for lineage specific enhancer activity [MEF_RNA-seq] |
| GSE71509 |
The SWI/SNF chromatin remodeling complex is required for lineage specific enhancer activity |
|
| Relations |
| BioSample |
SAMN03943851 |
| SRA |
SRX1123956 |
