|
| Status |
Public on Dec 05, 2013 |
| Title |
E36_Eed_+/+_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
E36 ES cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
cell type: E36 ES cells
chip antibody: H3K4me3 (Active Motif, catNo:39159, Lot: 01609004)
|
| 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 HiSeq 2000 |
| |
|
| Description |
Chromatin precipitatin using a specific antibody against H3K4me3
|
| 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.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: mm9
Supplementary_files_format_and_content: Alignment file generated by Bowtie is converted to SAM file format which is compressed to generate BAM file using SAMTools. Wig files generated by MACS were normalized to sequencing depth and converted to bigWig format using UCSC wigToBigwig tool.
|
| |
|
| Submission date |
Jul 19, 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 |
GPL13112 |
| Series (2) |
| GSE39496 |
Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E36 with H3K27ac, H3K27me1, and H3K4me1/3) |
| GSE40118 |
Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells |
|
| Relations |
| SRA |
SRX160820 |
| BioSample |
SAMN01091692 |
| Named Annotation |
GSM970227_E36_Eed_+_+_H3K4me3.bigWig |
