|
| Status |
Public on Dec 08, 2015 |
| Title |
dY-Foxd3CKO-Tam-H3K27me3 ChIP-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
dY-Foxd3CKO-Tam-H3K27me3 ChIP
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Foxd3 conditional knockout
cell type: EpiLC (dY cells); epiblast-like cells
cell line of origin: Foxd3 conditional knockout C57BL/6 ESCs
treatment: -Lif -2i day 3
chip antibody: H3K4me3
chip antibody vendor: Millipore
chip antibody cat. #: 07-449
chip antibody lot #: 2275589
|
| Treatment protocol |
Tamoxifen was added at 1uM for 36 hours to induce Foxd3 KO
|
| Growth protocol |
All cells were grown in Knockout DMEM with 15%FBS (excpet EpiSCs, that were grown in a 50:50 mix of DMEM:glutamax and Neurobasal with N2 and B27 supplements), Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using a standard ChIP protocol
Library was constructed using a standard Illumina protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: dYT-K27me3.bw
|
| Data processing |
Fastq files were mapped to the genome using Bowtie2 with the following setting: -p 4 -q -D 15 -R 10 -L 22 -i S,1,1.15
ChromHMM was run on a subset of the data for identifying 6 chromatin states
MACS2 was used for peak finding using the following settings:
Dip-finding for nucleosome-free regions was performed as per: Wamstad, J. A., Alexander, J. M., Truty, R. M., Shrikumar, A., Li, F., Eilertson, K. E., et al. (2012). Cell, 151(1), 206–220. doi:10.1016/j.cell.2012.07.035
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format for all ChIP-seq files; duplicates for Foxd3 conditional knockout data have been consolidated into one bigwig file
|
| |
|
| Submission date |
Jun 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Raga Krishnakumar |
| E-mail(s) |
raga.krishnakumar@gmail.com
|
| Organization name |
UCSF
|
| Lab |
Blelloch
|
| Street address |
912E RMB, 35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE58407 |
Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [ChIP-seq] |
| GSE58408 |
Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation |
|
| Relations |
| BioSample |
SAMN02850800 |
| SRA |
SRX590340 |
