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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 15, 2017 |
| Title |
CME179 |
| Sample type |
SRA |
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| Source name |
Sox5 ChIP-seq negative control
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| Organism |
Mus musculus |
| Characteristics |
Stage: E13.5 embryos
strain: CD1 wildtype
tissue: Limbs and tails
chip antibody: rabbit IgG
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates was obtained from sonicated nuclei and protein-DNA complexes were immunoprecipitated with respective antibodies. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 (32 to 52 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 15 cycles and library fragments of ~200 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 IIx |
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| Data processing |
BED_Alignment: Sequence reads were obtained and mapped to the Mouse genomes (CME018,CME019 mapped to mm8, CME179,CME180,CME181,CME182 mapped to mm9) using the Illumina Genome Analyzer Pipeline (Eland). All uniquely mapped reads that are with two or fewer mismatches were retained.
LIFTOVER_TXT_Peaks: (Treatment: CME018; Control: CME019) Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS ver. 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), and the called peaks are lifted over from mm8 to mm9 using UCSC liftover tools (http://genome.ucsc.edu/) .
TXT_Peaks: (Treatment: CME180; Control: CME179), (Treatment: CME182; Control: CME181) Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS ver. 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/).
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| Submission date |
Nov 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Lufkin |
| E-mail(s) |
tlufkin@clarkson.edu
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| Organization name |
Clarkson University
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| Department |
Biology
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| Lab |
Stem Cells & Regenerative Medicine
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| Street address |
8 Clarkson Avenue
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| City |
Potsdam |
| State/province |
NY |
| ZIP/Postal code |
13699 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE33419 |
In vivo genome-wide chromatin immunoprecipitation for the chondrogenic transcription factors, Sox9, Sox5 and Sox6 |
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| Relations |
| SRA |
SRX104233 |
| BioSample |
SAMN00750043 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM826705_CME179_mm9.bed.gz |
239.1 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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