GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1019777 Query DataSets for GSM1019777
Status Public on Oct 16, 2012
Title IgG_ChIPSeq(Hi)
Sample type SRA
Source name IgG_ChIPSeq
Organism Mus musculus
Characteristics cell line: E14Tg2A
cell type: embryonic stem cells
genotype/variation: wild type
antibody: IgG; Abcam, #46540
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). Immunoprecipitated DNA was eluted, reverse crosslinked and purified using Qiagen columns.
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 HiSeq 2000
Description Chromatin IP against IgG (control sample for Phf19 experiment; peaks not provided)
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 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: control sample for Phf19 experiment; peaks not provided
Submission date Oct 15, 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 GPL13112
Series (1)
GSE41589 Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity [ChIP-Seq]
SRA SRX195323
BioSample SAMN01765657

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap