|
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 |