|
Status |
Public on Apr 14, 2020 |
Title |
WIZ del Rep 2 (RNA-Seq) |
Sample type |
SRA |
|
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Source name |
Mouse embryonic stem cells v6.5
|
Organism |
Mus musculus |
Characteristics |
genotype: WIZ deletion cell line: mESC v6.5
|
Growth protocol |
V6.5 murine embryonic stem cells (mESCs) (male) were grown on irradiated murine embryonic fibroblasts under standard conditions, as previously described (Dowen et al, 2014)
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Cells were resuspended in 1ml Trizol (Invitrogen, 15596018). Chloroform (Sigma Aldrich, C2432) was added for phase separation. RNA was purified using the Zymo RNA Clean and Concentrator Kit (Zymo, R1013) Libraries were prepared using a TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) with indexes AR001-AR009. Library cleanup was performed using Agencourt AMPure XP beads (Beckman Coulter A63881).
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Alignment: reads were aligned to the mm10 genome with bowtie v 1.2.2 with parameters -v 2 -p 24 -S -m 1 --best --strata PCR Duplicate Removal: duplicates removed with samtools v 1.9 fixmate -m followed by markdup -r -s Coverage File Generation: bigwig files were generated deeptools (v 3.0.1) genomecov with parameters -p 24 -bs 10 --normalizeUsing RPKM -ignore chrX Reads Per Gene: Reads per gene were analyzed using STAR --runThreadN 24 -c SortedByCoordinate Genome_build: mm10 Supplementary_files_format_and_content: For each replicate, a bigwig file is provided for viewing in UCSC genome browser.
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|
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Submission date |
Sep 11, 2019 |
Last update date |
Apr 15, 2020 |
Contact name |
Jill Dowen |
E-mail(s) |
jilldowen@unc.edu
|
Organization name |
UNC Chapel Hill
|
Street address |
250 Bell Tower Drive, CB 7100 3360 Genome Sciences Building
|
City |
Chapel Hill |
State/province |
NC |
ZIP/Postal code |
27599 |
Country |
USA |
|
|
Platform ID |
GPL21103 |
Series (2) |
GSE137271 |
A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [RNA-Seq] |
GSE137285 |
A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity |
|
Relations |
BioSample |
SAMN12730461 |
SRA |
SRX6831831 |