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| Status |
Public on Aug 24, 2020 |
| Title |
MGH3535-K36me3_ChIP-seq |
| Sample type |
SRA |
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| Source name |
Colon tumor
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| Organism |
Homo sapiens |
| Characteristics |
sample type: Colon tumor
biological sample: MGH3535-K36me3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed as described previously (Liau et al., 2016). In brief, crosslinked cells were lysed and DNA was sheared to between 400 and 2,000 base pair fragments. Antibodies were as follows: CTCF (Cell signaling #3418), H3K27ac (Active Motif #39133), H3K9me3 (Abcam #8898), H3K27me3 (Cell Signaling #97335). ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3′ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters. Barcoded fragments were amplified via PCR. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.
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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 |
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Methylation data processing. BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
HiC Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
HiChip Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Supplementary_files_format_and_content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary_files_format_and_content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.
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| Submission date |
May 04, 2020 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Alejandro Reyes |
| Organization name |
Novartis Institutes For BioMedical Research
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| Department |
Data Sciences
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| Street address |
Fabrikstrasse 22
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| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE133928 |
A topological atlas reveals layers of genome reorganization in colorectal cancer |
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| Relations |
| BioSample |
SAMN14829408 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4513993_MGH3535-K36me3.bw |
118.5 Mb |
(ftp)(http) |
BW |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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