|
| 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 (http://genome.ucsc.edu) (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 (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi) 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 |
|
| Relations |
| SRA |
SRX107343 |
| BioSample |
SAMN00760431 |
| Named Annotation |
GSM832714_dF4_C5_IkN.bigwig |
