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Sample GSM1041376 Query DataSets for GSM1041376
Status Public on Jan 01, 2013
Title IgG_old_ChIPSeq
Sample type SRA
Source name Embryonic stem cells (E14)
Organism Mus musculus
Characteristics strain: 129/Ola
antibody: Rabbit IgG- ab37415
cell type: Embryonic stem cells (E14)
Growth protocol Wild-type (E14Tg2A) ES cells were cultured feeder-free in plates coated with 0.1% of gelatin in Glasgow minimum essential medium (Sigma) supplemented with β-mercaptoethanol, sodium pyruvate, essential amino acids, GlutaMAX, 20% fetal bovine serum (Hyclone), and leukemia inhibitory factor (LIF).
Extracted molecule genomic DNA
Extraction protocol ESCs were trypsinized and crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 0.125 M glycine for 5 min. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 14 min in a Bioruptor. ChIP-Seq experiments were performed as previously described (Morey et al, Cell Stem Cell. 2012, 10: 47-62)
It was performed using the NEBNext DNA Sample Prep Reagents Set 1
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against IgG
Data processing Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version (for Suz12 and Ring1B and and IgG_old as control) 40 bp and 1.4.1 (for Cbx7, RYBP and IgG as control)
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing peak coordinates
Submission date Nov 26, 2012
Last update date May 15, 2019
Contact name Luciano Di Croce
Phone +34933160132
Organization name Centre for Genomic Regulation
Street address Dr. Aiguader, 88
City Barcelona
ZIP/Postal code 08003
Country Spain
Platform ID GPL11002
Series (1)
GSE42466 RYBP and Cbx7 define specific biological functions of PRC1 complexes in mouse embryonic stem cells
SRA SRX206422
BioSample SAMN01818985

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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