|
| Status |
Public on Mar 23, 2017 |
| Title |
J1IP1 |
| Sample type |
SRA |
| |
|
| Source name |
mESCs_KAP1_ChIP-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 12910la
cell line: J1
cell type: mouse embryonic stem cells (mESCs)
transduced with: none
chip antibody: KAP1 (custom rabbit polyclonal)
|
| Treatment protocol |
Cells were transduced 5 days before fixation
|
| Growth protocol |
mESCs were cultured in 2i medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was prepared from 10 million cells as previously described (Rowe et al., 2013b).
Libraries were ligated with Illumina adaptors
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Alignement for ChIP-seqs were done with bowtie2: bowtie2 -p 8 -t --sensitive-local -x $index -U $reads
Peak calling for ChIP-seqs were done using SICER for histone marks (SICER.sh . chip.bed ti.bed . mm9 1 200 150 0.74 400 100) and MACS for Trim28 (macs14 -t $chipbam -c $tibam -g $org -n $name)
Genome_build: mm9
Supplementary_files_format_and_content: A bed file containing the output of the peak called by SICER or MACS is provided
|
| |
|
| Submission date |
Jan 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Evarist Planet |
| E-mail(s) |
evarist.planet@epfl.ch
|
| Organization name |
EPFL
|
| Lab |
LVG
|
| Street address |
Route Cantonale
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE94323 |
A family of double-homeodomain transcription factors promotes zygotic genome activation in placental mammals [ChIP-seq_d2] |
| GSE94325 |
A family of double-homeodomain transcription factors promotes zygotic genome activation in placental mammals. |
|
| Relations |
| BioSample |
SAMN06284973 |
| SRA |
SRX2529733 |
