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Status |
Public on Dec 08, 2015 |
Title |
R-Ctrl-Flag ChIP-rep1 |
Sample type |
SRA |
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Source name |
R-Ctrl-Flag ChIP
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Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 genotype/variation: Foxd3 conditional knockout cell type: embryonic stem cells (ESCs; R cells) cell line of origin: Foxd3 conditional knockout C57BL/6 ESCs treatment: Lif 2i chip antibody: M2 anti-Flag chip antibody vendor: Sigma chip antibody cat. #: F1804 chip antibody lot #: SLBG5673V
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Treatment protocol |
Tamoxifen was added at 1uM for 36 hours to induce Foxd3 KO
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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).
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Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted using a standard ChIP protocol Library was constructed using a standard Illumina protocol
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Jun 11, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Raga Krishnakumar |
E-mail(s) |
raga.krishnakumar@gmail.com
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Organization name |
UCSF
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Lab |
Blelloch
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Street address |
912E RMB, 35 Medical Center Way
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City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94143 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN02850863 |
SRA |
SRX590292 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data not provided for this record |
Processed data are available on Series record |
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