|
| Status |
Public on Jan 01, 2013 |
| Title |
IgG_ChIPSeq_2 |
| 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)
originally submitted as: GSM1019774
|
| 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 1.3.7.1 (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 |
| E-mail(s) |
luciano.dicroce@crg.eu
|
| 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 |
|
| Relations |
| Reanalysis of |
GSM1019774 |
| SRA |
SRX206423 |
| BioSample |
SAMN01818986 |
