|
| Status |
Public on Dec 11, 2013 |
| Title |
E14_H3K27me1 |
| Sample type |
SRA |
| |
|
| Source name |
E14 ES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
strain: 129/Ola
chip antibody: H3K27me1
antibody vendor/catalog/lot: Cell Signaling/No 07-448/Lot 24439
|
| Treatment protocol |
Exponentially growing ES cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using proteinA coupled beads and recovered DNA was used for highthrouput sequencing.
|
| Growth protocol |
ES cell lines were grown on 0.1% gelatinized tissue culture dishes in GMEM supplemented with 15% fetal calf serum, 2 mM glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin, 0.1 mM non-essential aminoacids, 1 mM Na-Pyruvate, 50 μM β-mercaptoethanol-phosphate-buffered saline and Leukemia Inhibitory Factor.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the Illumina ChIPSeq Sample Prep kit (IP-102-1001) and multiplexing oligonucleotide kit (PE-400-1001).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin precipitatin using a specific antibody against H3K27me1
|
| Data processing |
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie. The alignments were performed allowing zero to two mismatches and keeping only the reads that align to unique positions in the genome.
Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: mm9
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sri Ganesh Jammula |
| E-mail(s) |
sriganesh.jammula@ieo.eu
|
| Organization name |
IFOM-IEO
|
| Street address |
Via Adamello 16
|
| City |
Milan |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE40109 |
Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E14 and E36 with H3K27me1/2 and H3) |
| GSE40118 |
Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells |
|
| Relations |
| SRA |
SRX176650 |
| BioSample |
SAMN01113286 |
| Named Annotation |
GSM985054_E14_H3K27me1.bigWig |
