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Sample GSM826708 Query DataSets for GSM826708
Status Public on Jun 15, 2017
Title CME182
Sample type SRA
Source name Sox6 ChIP-seq
Organism Mus musculus
Characteristics Stage: E13.5 embryos
strain: CD1 wildtype
tissue: Limbs and tails
chip antibody: anti-Sox6
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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
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 (, and the called peaks are lifted over from mm8 to mm9 using UCSC liftover tools ( .
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 (
Submission date Nov 02, 2011
Last update date May 15, 2019
Contact name Thomas Lufkin
Organization name Clarkson University
Department Biology
Lab Stem Cells & Regenerative Medicine
Street address 8 Clarkson Avenue
City Potsdam
State/province NY
ZIP/Postal code 13699
Country USA
Platform ID GPL11002
Series (1)
GSE33419 In vivo genome-wide chromatin immunoprecipitation for the chondrogenic transcription factors, Sox9, Sox5 and Sox6
SRA SRX104236
BioSample SAMN00750046

Supplementary file Size Download File type/resource
GSM826708_CME182_macs_peaks.txt.gz 6.8 Kb (ftp)(http) TXT
GSM826708_CME182_mm9.bed.gz 288.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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