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Sample GSM1019770 Query DataSets for GSM1019770
Status Public on Oct 16, 2012
Title H3K36me2_ChIPSeq
Sample type SRA
Source name H3K36me2_ChIPSeq
Organism Mus musculus
Characteristics cell line: E14Tg2A
cell type: embryonic stem cells
genotype/variation: wild type
antibody: H3K36me2 - Abcam, #9049
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 Genome Analyzer IIx
Description Chromatin IP against H3K36me2 (peaks not provided; raw data was used to perform average profiles of H3K36me-reads around TSS or around the center of Phf19-binding sites)
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: peaks not provided; raw data was used to perform average profiles of H3K36me-reads around TSS or around the center of Phf19-binding sites
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 GPL11002
Series (1)
GSE41589 Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity [ChIP-Seq]
SRA SRX195316
BioSample SAMN01765650

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

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