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| Status |
Public on Jul 31, 2020 |
| Title |
Fetal_Rep3_H3K4me3 (chip-seq) |
| Sample type |
SRA |
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| Source name |
Fetal anterior temporal cortex
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| Organism |
Homo sapiens |
| Characteristics |
developmental stage: Fetal
tissue: brain (anterior temporal cortex)
chip antibody: H3K4me3 (Abcam, ab8580, lot# GR224426-1)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit. Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.
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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 were mapped to human reference genome hg19 using Bowtie. The first 36 bases of each read were used for mapping. We only use non-redundant reads to eliminate possible duplicates from biased PCR amplification.
The paired-end easy Hi-C reads were mapped to hg19 using BOWTIE. Because nearly all the mappable reads start with HindIII sequence AGCTT, we trimmed the first 5 bases from every read, took the next 36 bases, and added the 6-base sequence AAGCTT to the 5’ of every read before mapping using the whole 42 bases.
For eHi-C library, the only type of invalid cis- pairs are self-circles with two ends within the same HindIII fragment facing each other. We excluded those pairs from further analysis.
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
Genome_build: hg19
Supplementary_files_format_and_content: For each Chip-Seq replicate, processed results are provided in the bed file.
Supplementary_files_format_and_content: For eHi-C, processed results are provided in the frag_loop.txt files. Each has 4 columns: frag1_location, frag1_strand, frag2_location, and frag2_strand
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| Submission date |
Jul 09, 2018 |
| Last update date |
Jul 31, 2020 |
| Contact name |
Xiaoxiao Liu |
| E-mail(s) |
xxl244@case.edu
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| Phone |
(216) 368-5293
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| Organization name |
Case Western Reserve University
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| Department |
Genetics and Genomes Sciences
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| Lab |
Fulai Jin
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| Street address |
10900 Euclid Ave
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| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44120 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE116825 |
Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases |
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| Relations |
| BioSample |
SAMN09633684 |
| SRA |
SRX4370437 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3262295_ME47_H3K4me3.monoclonal.bed.gz |
74.1 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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