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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 24, 2010 |
| Title |
IgG-ChIP-Seq, Nrl ko, 1 |
| Sample type |
SRA |
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| Source name |
Retina, Nrl ko, IgG ChIP
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Nrl-/-
age: 8 weeks
tissue: retina
chip antibody: IgG
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| Growth protocol |
Retinas were isolated from adult C57BL/6 and Nrl-/- mice, and Crx-ChIP-Seq and IgG-ChIP-Seq were performed.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crx-DNA complexes were isolated from retinal lysates with anti-Crx-antibody. Anti-IgG-antibody was used as a control. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin IP against IgG.
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| Data processing |
Mapping: 36 bp tags were mapped to the mouse genome (NCBI Build 37, mm9) using the Genomatix mapping algorithm allowing one mismatch.
Clustering: Peak (Cluster) detection was performed with the Genomatix NGS Analyzer.
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| Submission date |
Jan 22, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Langmann |
| E-mail(s) |
thomas.langmann@klinik.uni-regensburg.de
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| Phone |
+49-941-944-5423
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| Fax |
+49-941-944-5402
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| Organization name |
Institute of Human Genetics
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| Department |
University of Regensburg
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| Street address |
Franz-Josef-Strauss-Allee 11
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| City |
Regensburg |
| ZIP/Postal code |
93042 |
| Country |
Germany |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE20012 |
Deciphering the cis-regulatory architecture of mammalian photoreceptors |
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| Relations |
| SRA |
SRX018603 |
| BioSample |
SAMN00010729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM499740_IgG_Nrl_ko_1.bed.gz |
187.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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