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| Status |
Public on Jun 29, 2017 |
| Title |
d6_wcl_H3K4me1 |
| Sample type |
SRA |
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| Source name |
Commercially available hepatocytes (BioreclamationIVT: lot QSK)
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| Organism |
Homo sapiens |
| Characteristics |
individual: d6
cell type: Primary human hepatocytes
chip antibody: H3K4me1 (Cell Signaling Technologies, catalog# 5326BF, lot# 2)
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| Treatment protocol |
NA
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| Growth protocol |
Cells were thawed and immediately resuspended in CP media (BioreclamationIVT). Cell concentration and viability were assessed prior to use. For ChIP-sequencing, 1×10^6 cells were cross-linked with 1% formaldehyde for 10 min at 37°C prior to freezing in liquid nitrogen.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear lysates were sonicated and histone-DNA complexes were isolated with antibody.
After performing reverse cross linking on sheared chromatin the following steps were performed: end-repair, addition of A base to 3' end of DNA fragments, ligation of adapters to ends of DNA fragments, enrichment by PCR, and gel purification of PCR products.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.0.6 with default parameters
PCR duplicates were removed using samtools version 1.3
Peaks were called using Homer version 4.7 with the following steps: makeTagDirectory was used to preprocess input and histone modification tags. findPeaks was used with options -style histone -auto with whole cell extract tags (input) as a control. pos2bed.pl was used to convert resulting peak files to BED format.
To adjust for potential reference-bias introduced during mapping, alignments were post-processed using WASP (Github commit 467651c)
Samtools pileup version 1.3 was used to obtain reference and alternate allele read counts for each sample at each SNP
A binomial test implemented in the binom_test function of the scipy.stats python library was used to test for allelic bias in read counts for each histone modification. The only relationship to the BED files is that analysis was restricted to regions falling within peaks. Thus only the coordinates of the bed files were used, not any quantitative information about the peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain peaks output by Homer
Supplementary_files_format_and_content: ChIP_allele_skew_SLC16A11_locus.xlsx (The conclusions in the paper are based on this datafile. d1, d3, d6 are the 3 different hepatocyte lots and the 2 numbers in the counts column refer to counts from each allele. Please see README tab.)
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| Submission date |
May 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Suzanne Jacobs |
| Organization name |
The Broad Institute
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| Street address |
75 Ames Street
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| City |
Cambridge |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE99301 |
ChIP-sequencing for histone modifications in primary human hepatocytes from three individuals heterozygous for the T2D risk haplotype at the SLC16A11 locus |
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| Relations |
| BioSample |
SAMN07177545 |
| SRA |
SRX2869677 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2644054_d6_wcl_H3K4me1_peaks.bed.sorted.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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