|
| Status |
Public on Jun 27, 2019 |
| Title |
Chr13.1-cl KO B6 ES cells #14 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
strain: B6
genotype/variation: Chr13.1-cl KO/KO
media: 20% FCS
|
| Growth protocol |
ES cells were grown in DMEM supplemented with 20% FCS and LIF or in 2i media as indicated in the sample information.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from ES cells was purified and depleted from genomic DNA using the RNeasy Plus minikit (Qiagen). Tissues were lysed using TRIzol reagent and RNA was purified after Isopropanol precipitation with RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina) or the SureSelect mRNA sequencing kit (Agilent) and polyA enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Reads were aligned to the mouse reference genome using Tophat (--I 200000 --g 1)
Mapped reads were converted to bigwig files with DeepTools (--normalizeUsing RPKM --ignoreDuplicates).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files
|
| |
|
| Submission date |
Jun 04, 2018 |
| Last update date |
Jun 27, 2019 |
| Contact name |
Gernot Wolf |
| Organization name |
NIH
|
| Department |
NICHD
|
| Lab |
Macfarlan lab
|
| Street address |
6 Center Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE115288 |
Genome-wide analysis of differential transcription in KRAB-ZFP cluster knock-out ES cells and mouse tissues |
| GSE115291 |
Retrotransposon reactivation and mobilization upon deletions of megabase-scale KRAB zinc finger gene clusters in mice |
|
| Relations |
| BioSample |
SAMN09322246 |
| SRA |
SRX4159375 |
