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Sample GSM1825749 Query DataSets for GSM1825749
Status Public on Jul 17, 2015
Title hiF-T_P15_H3K4me2_Rep2
Sample type SRA
 
Source name immortalized human inducible fibroblasts-like cells (hiF-T)
Organism Homo sapiens
Characteristics passage (pre-reprogramming): 15
antibody epitope, vendor, catalog number, lot: H3K4me2, Active Motif, 39141,#01008001
Growth protocol Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript. http://www.cell.com/cell/abstract/S0092-8674%2815%2900700-X
Extracted molecule genomic DNA
Extraction protocol Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
ChIP-seq Illumina libraries were prepared and analyzed as previously described (Mikkelsen et al., 2010) starting from one million cells crosslinked in 1% PFA. ChIP-Seq libraries were sequenced with approximately 20 million 50-bp single end reads each.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description FinalIDR_HIFT_Fib_H3K4me2_macs2.regionPeak
Data processing ChIP-Seq data was aligned to the hg19 reference genome using bwa version 0.5.7 with default parameter settings. Subsequently, reads were filtered for duplicates and extended by 200bp. Visualization of read count data was performed by converting raw bam files to .tdf files using IGV tools (Thorvaldsdóttir et al., 2013) and normalizing to 1 million reads.
For H3K4me2 and H3K27ac histone marks, the Irreproducible Discovery Rate (IDR) framework with a cutoff of 0.05 in combination with the MACS2 peak caller version 2.1 was used to identify peaks taking advantage of both replicates (if available) for each condition. For MACS2 peak calling, we used an initial p-value cutoff of 0.01 and the corresponding whole cell extract (WCE) control library as background.
Genome_build: hg19
Supplementary_files_format_and_content: All coordinates are based on hg19. ENCODE narrowPeak Format: chromosome,chromstart,chromend,peak name,macs2 integer score, strand, fold change over background,-log10pvalue,-log10qvalue,relative summit position to peak star. For the K4me1 and K36me3: .tdf files can be displayed in the IGV.
 
Submission date Jul 17, 2015
Last update date May 15, 2019
Contact name Shannan J Ho Sui
E-mail(s) shosui@hsph.harvard.edu
Organization name Harvard T.H. han Scholol of Public Health
Department Biostatistics
Street address 655 Huntington Ave, Building 2, Rm 437A
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL16791
Series (2)
GSE62777 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
GSE71033 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [ChIP-Seq]
Relations
BioSample SAMN03876612
SRA SRX1099951

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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