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| Status |
Public on Jul 17, 2015 |
| Title |
5dd_DOX_plus_H3K36me3_Rep1 |
| Sample type |
SRA |
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| Source name |
reprogramming intermediates of hiF-T cells
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| Organism |
Homo sapiens |
| Characteristics |
antibody epitope, vendor, catalog number, lot: H3K36me3, Active Motif, 61101, #32412003
treatment: DOX days 0-5
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| 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
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
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| Submission date |
Jul 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shannan J Ho Sui |
| E-mail(s) |
shosui@hsph.harvard.edu
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| Organization name |
Harvard T.H. han Scholol of Public Health
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| Department |
Biostatistics
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| Street address |
655 Huntington Ave, Building 2, Rm 437A
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| 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] |
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| Relations |
| BioSample |
SAMN03876631 |
| SRA |
SRX1099970 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1825768_ChIP_absReadFreqW50_Davide_RepS7_K36m3.ChIP.tdf |
76.3 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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