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Sample GSM1582731 Query DataSets for GSM1582731
Status Public on Feb 01, 2015
Title ALL65 untreated
Sample type SRA
 
Source name ALL65 T-ALL cells
Organism Mus musculus
Characteristics immunophenotype: GFPhigh
treatment: untreated
cell source: splenocytes of leukemic recipient mice
cell type: T-ALL cells
Treatment protocol Leukemic mice were untreated or treated with Dox for 3 days, resulting in shutdown of GFP-linked shRNA expression and restoration of endogenous Ikaros expression
Growth protocol Spleen cells were isolated from leukemic mice and T-ALL cells were isolated using FACS
Extracted molecule total RNA
Extraction protocol FACS sorted cell pellets were lysed and RNA prepared using QIAGEN RNeasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina CASAVA pipeline version 1.8.2 used for basecalling
Reads were aligned to the mouse genome by Rsubread version 1.12.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI exon annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene
 
Submission date Jan 12, 2015
Last update date May 15, 2019
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL13112
Series (2)
GSE64893 Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL65) cells following Ikaros restoration
GSE64928 Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia) cells following Ikaros restoration
Relations
BioSample SAMN03283195
SRA SRX840149

Supplementary file Size Download File type/resource
GSM1582731_65Ch-D0.txt.gz 167.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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