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Sample GSM1572689 Query DataSets for GSM1572689
Status Public on Dec 08, 2015
Title dY-Tam-HDAC1-rep2
Sample type SRA
 
Source name dY-Tam-HDAC1
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Foxd3 conditional knockout
cell type: EpiC (dY cells)
cell line of origin: epiblast cells: EpiC (dY cells)
treatment: -Lif -2i day 3
chip antibody: HDAC1
chip antibody vendor: Abcam
chip antibody cat. #: ab7028
chip antibody lot #: GR123373-9
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: dY-Tam-HDAC.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 Dec 23, 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 SAMN03272985
SRA SRX823834

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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