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Sample GSM6594333 Query DataSets for GSM6594333
Status Public on Jan 25, 2024
Title preB #1
Sample type SRA
 
Source name preB cells
Organism Mus musculus
Characteristics tissue: preB cells
cell type: preB
genotype: C57BL/6
treatment: NA
Growth protocol Leukemia cells were cultured in IMDM media supplemented with 10% FBS with IL7 at 37C with 10% CO2.
Extracted molecule total RNA
Extraction protocol preB and leukemia sample RNA was harvested using Qiagen RNA kit (Qiagen) and 500ng-1 ug of total RNA was used for sequencing libraries. ChiP-seq sample lysate were isolated from formaldehyde cross-linked cells and sonicated to release chromatin.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's protocols. ChIP-seq libraries were prepared with KAPA Hyper Prep Kit (Kapa Biosystems)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava 1.8.2 software was used for basecalling.
Sequence reads were mapped to GrCM38/mm10
RNA-seq Read count extraction and normalization were performed using edgeR Bioconductor package version 3.34.15. Peak-calling was performed using MACS2 for ChiP-seq.
Assembly: mm10
Supplementary files format and content: RNA-seq and ChIP-seq: bigwig files created using deepTools version 3.5.0
 
Submission date Sep 20, 2022
Last update date Jan 25, 2024
Contact name Ashley P Ng
E-mail(s) ang@wehi.edu.au
Organization name The Walter and Eliza Hall Institute of Medical Research
Street address 1G Royal Parade, Parkville
City Melbourne
State/province VIC
ZIP/Postal code 3050
Country Australia
 
Platform ID GPL17021
Series (1)
GSE213791 ERG and c-MYC Co-regulate a Critical Gene Network in BCR-ABL1 B-cell Acute Lymphoblastic Leukemia
Relations
BioSample SAMN30935558
SRA SRX17641608

Supplementary file Size Download File type/resource
GSM6594333_1804b_CB2WEANXX_ACTGAT_L002_R1.fastq.gz.subjunc.sorted.bam.bigWig 12.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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