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Sample GSM4159958 Query DataSets for GSM4159958
Status Public on Feb 25, 2021
Title WT-Inhibitor_RNA_1
Sample type SRA
 
Source name murine BM
Organism Mus musculus
Characteristics genotype: WT
tissue: bone marrow
treatment: DOT1L inhibitor (EPZ-5676)
Treatment protocol During passaing, cells were treated with 100uM DOT1L inhibitor (EPZ-5676) or vehicle (DMSO).
Growth protocol Bone marrow was isolated from Smc3+/f or WT mice that were treated with pIpC to induced excision of one Smc3 allele. Cells were collected after one week in passage.
Extracted molecule total RNA
Extraction protocol RNA was isolated using Trizol.
RNA libraries were created following the NEBNext Ultra RNA Library Prep Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Reads were aligned to mm10 using STAR, with default parameters on basepairtech.com
Cufflinks was used to estimate the transcript abundances
DESeq was used to identify differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: gtf files (output from cufflinks)
 
Submission date Nov 13, 2019
Last update date Feb 25, 2021
Contact name Katelyn Elizabeth Heimbruch
Organization name Medical College of Wisconsin
Street address 8727 Watertown Plank Road
City Miwaukee
State/province Wisconsin
ZIP/Postal code 53213
Country USA
 
Platform ID GPL19057
Series (2)
GSE140359 DOT1L inhibitors block abnormal self-renewal induced by cohesin loss [RNA-seq]
GSE140361 DOT1L inhibitors block abnormal self-renewal induced by cohesin loss
Relations
BioSample SAMN13280814
SRA SRX7135953

Supplementary file Size Download File type/resource
GSM4159958_WTI1.mm10.transcripts.gtf.gz 4.8 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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