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Sample GSM797708 Query DataSets for GSM797708
Status Public on Sep 08, 2013
Title Ikaros ZnF4-/- Thymus rep2
Sample type SRA
Source name Whole Thymus
Organism Mus musculus
Characteristics strain: Ikaros_ZnF4-/-
tissue: Thymus
age: 4_week
Growth protocol Single cell suspensions were prepared from whole thymus of 4 week old mice.
Extracted molecule polyA RNA
Extraction protocol Cell suspensions were prepared from 4 week old whole thymus and filtered through 70 m nylon cell strainer (BD Biosciences). RNA was prepared by the use of TRI Reagent (Molecular Research Center, Inc.) followed by purification using RNeasy kit (Qiagen) with on-column RNase-free DNase I treatment. For RNA-Seq analysis, cDNA library was prepared for the Illumina Sequencing platform using the fragmented double-stranded cDNA protocol (Nagalakshmi et al., 2010), and sequenced on an Illumina GAIIx machine with 76 bp single-end reads (replicate 1) or on an Illumina HiSeq machine with 50 bp single-end reads at the Broad Stem Cell Research Center High Throughput Sequencing Core at UCLA.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Raw data was uploaded to the Galaxy website ( and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Blankenberg et al., 2010; Goecks et al., 2010). Genome coverage visualization files were created in Galaxy (replicate 1) or with BEDtools (replicate 2) and uploaded to the UCSC genome browser ( (Kent et al., 2002). Tophat alignment through Galaxy resulted in .sam and .bedgraph files.
Submission date Sep 16, 2011
Last update date May 15, 2019
Contact name Hilde Schjerven
Organization name UCSF
Department Laboratory Medicine
Street address 513 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
Platform ID GPL13112
Series (2)
GSE32190 Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: Thymocytes)
GSE33693 Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros
Reanalyzed by GSE80797
SRA SRX097651
BioSample SAMN00722029
Named Annotation GSM797708_dZnF4_2_Thym.bigwig

Supplementary file Size Download File type/resource
GSM797708_dZnF4_2_Thym.bigwig 220.1 Mb (ftp)(http) BIGWIG
GSM797708_dZnF4_2_Tophat_accepted_hits.bam 3.0 Gb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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