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Sample GSM4074278 Query DataSets for GSM4074278
Status Public on Apr 14, 2020
Title WIZ del Rep 3 (RNA-Seq)
Sample type SRA
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).
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.
Submission date Sep 11, 2019
Last update date Apr 15, 2020
Contact name Jill Dowen
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
BioSample SAMN12730460
SRA SRX6831832

Supplementary file Size Download File type/resource 49.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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