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Sample GSM480679 Query DataSets for GSM480679
Status Public on Jan 27, 2010
Title shJarid2_Jarid2_ChIPseq
Sample type SRA
 
Source name Embyonic stem cells
Organism Mus musculus
Characteristics strain: 129/Ola
cell type: Embyonic stem cells
genome/variation: Infected with Jarid2 shRNA expression lentivirus
antibody: Jarid2
Growth protocol ES cells were infected with lentivirus expressing a Neomycin resistant construct expressing either control (SCR) and Jarid2 specific shRNA, cells were selected with 0.5mg/ml of G418 and cultured for two weeks under selection prior collection of samples for ChIPseq analyses.
Extracted molecule genomic DNA
Extraction protocol ChIP analyses were performed as described in Pasini et al. (2008). Genes Dev 22, 1345-1355. DNA from 3 independent ChIP experiments was pooled and prepared for sequencing with the Illumina ChIPSeq Sample Prep kit (IP-102-1001). DNA libraries were quantified using a fluorometer (Fluoroscan, Ascent) and diluted to 5-10 pM. Diluted libraries were used directly for cluster generation and sequencing analysis using the Genome Analyzer II (Illumina) following the protocol of the manufacturer. Basecalling and mapping of the 36 bp sequences were done using Illumina's analysis Pipeline v1.4 allowing up to two mismatches in the first 32 bases of a read against mouse genomes July 2007 release (mm9).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Chromatin IP against Jarid2
Data processing Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Illumina Genome Analyzer Pipeline version 1.4 alowing up to 2 mismatches in the first 32 bases of the read. Only reads that align uniquely are reported.
Peaks: Peak detection was performed with CisGenome software (http://www.biostat.jhsph.edu/~hji/cisgenome/) as described in Hongkai et al. (2008) Nature Biotechnology, 26: 1293-1300.
 
Submission date Dec 07, 2009
Last update date May 15, 2019
Contact name Diego Pasini
E-mail(s) diego.pasini@ieo.it
Organization name European Institute of Oncology
Department Experimental Oncology
Street address Via Adamello, 16
City Milano
ZIP/Postal code 20139
Country Italy
 
Platform ID GPL9250
Series (1)
GSE19365 Genome wide mapping of Jarid2 and Suz12 binding sites in mouse ES cells before and after Jarid2 depletion
Relations
SRA SRX016253
BioSample SAMN00008317

Supplementary file Size Download File type/resource
GSM480679_shJarid2_Jarid2.aligned.txt.gz 74.4 Mb (ftp)(http) TXT
GSM480679_shJarid2_Jarid2.peaks.txt.gz 275 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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