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Sample GSM832714 Query DataSets for GSM832714
Status Public on Sep 08, 2013
Title Thymus Ikaros ZnF4-/- c5
Sample type SRA
Source name Whole Thymus
Organism Mus musculus
Characteristics genotype/variation: Ikaros_ZnF4-/-
tissue: Thymus
age: 4 week
chip antibody: Ikaros-N terminal Ab (IkN)
Growth protocol Single cell suspensions were prepared from whole thymus of 4 week old mice.
Extracted molecule genomic DNA
Extraction protocol Primary thymocytes were fixed in 1% formaldehyde for 10 minutes at room temperature, washed in PBS and snap frozen. Ikaros ChIP was performed with an Ab directed against the Ikaros N-terminal region (Hahm et al., 1994) and tested by PCR for enrichment at published and putative Ikaros binding sites (Primers are given in Table S2). Input DNA was prepared from wt primary thymocytes as negative control. Libraries were prepared for sequencing on the Illumina platform essentially as described (O'Geen et al., 2010). Raw sequences were mapped by Bowtie to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), and significant peaks over background were called using the Sole-Search software (Langmead et al., 2009; Blahnik et al., 2010). Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser ( (Kent et al., 2002).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Bowtie allignment through Galaxy (.bam)
Peaks: Peak detection was performed with Solesearch ( using the input DNA as a control.
Visualization BigWig file created with bedtools (.bigwig or .bedgraph).
Submission date Nov 14, 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)
GSE33679 Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (ChIP-seq: Thymocytes)
GSE33693 Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros
SRA SRX107343
BioSample SAMN00760431
Named Annotation GSM832714_dF4_C5_IkN.bigwig

Supplementary file Size Download File type/resource
GSM832714_dF4_C5_IkN.bam 3.5 Gb (ftp)(http) BAM
GSM832714_dF4_C5_IkN.bigwig 443.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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