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Sample GSM1410330 Query DataSets for GSM1410330
Status Public on Dec 08, 2015
Title R-H3K4me1 ChIP
Sample type SRA
 
Source name R-H3K4me1 ChIP
Organism Mus musculus
Characteristics cell type: embryonic stem cells (ESCs; R cells)
cell line of origin: dual miRNA reporter V6.5 ESCs
treatment: Lif 2i
chip antibody: H3K4me1
chip antibody vendor: Abcam
chip antibody cat. #: ab8895
chip antibody lot #: GR149140-1
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
 
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 SAMN02850841
SRA SRX590262

Supplementary file Size Download File type/resource
GSM1410330_R-K4me1.bw 123.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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