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| Status |
Public on Sep 29, 2024 |
| Title |
MB3662-hic |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
Sex: M
disease: medulloblastoma
disease subgroup: SHH
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| Treatment protocol |
None
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| Growth protocol |
The majority of samples were uncultured, primary patient tissue. The brain tissue culture was grown as described previously (Michealraj et al. Cell. 2020; PMID: 32445698).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 2.5M cells were used for In-situ Hi-C library approach (Rao et al. Cell. 2014; PMID: 25497547) with library preparation performed as described previously (Johnston et al. Genome Research. PMID: 31249064). Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).
In-situ Hi-C
Kapa RNA HyperPrep kit prepared and sequenced at Ontario Institute for Cancer Research (OICR)
Paired-end, stranded RNA-Seq
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Fastqs were processed to hic files using Juicer v1.6.
Contact domains were annotated from hic files using Arrowhead from Juicer Tools v1.19.02 with parameters ‘--ignore-sparsity -k SCALE’ for the following data resolutions (kb): 10, 25, 50, 100.
Loops were annotated from hic files using HiCCUPS from Juicer Tools v1.19.02 with parameters ‘--cpu -m 4096 --ignore-sparsity -k SCALE’ for resolutions (kb): 10, 25.
Compartments were annotated from hic files using the leading eigenvectors of the Juicer Tools Pearsons with parameters ‘SCALE BP 50000 -p’
Boundary scores were annotated from 50-kb contact matrices using Robustad v1.0
RNA-seq alignment: reads aligned to hg38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) using HISAT2 (v2.1.0) with parameters ‘--rna-strandness RF --downstream-transcriptome-assembly’
RNA-Seq quantification: SAM output was sorted, converted to BAM, and indexed using samtools (v1.9). A counts table was prepared using the count function of HTSeq (v0.13).
RNA-Seq differential expression testing: Limma with Voom transformation (v3.44)
RNA-Seq coverage: BigWig tracks were generated using DeepTools bamCoverage with parameters --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --binSize 1. Separate files for positive and negative strand were generated with parameters --filterRNAstrand "forward" or --filterRNAstrand "reverse"
Assembly: hg38, GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set
Supplementary files format and content: TSV; BoundaryScores.max.50kb.tsv: Summary table of RobusTAD scores for all samples
Supplementary files format and content: BDG; BoundaryScores.max.50kb.bedgraph: BEDGRAPH format values from RobusTAD boundary quantification
Supplementary files format and content: WIG; BoundaryScores.max.50kb.wig: WIGGLE format values from RobusTAD boundary quantification
Supplementary files format and content: TSV; TADBoundaryCalls.50kb.tsv: Summary table of RobusTAD boundaries for all samples
Supplementary files format and content: WIG; eigenvalue_allChr_50kb.wig: Eigenvalues of leading PC indicating genome compartmentalization
Supplementary files format and content: TSV; compartment_eigenvalues.tsv: Summary table of eigenvalues for all samples
Supplementary files format and content: HIC; inter_30.hic: Hi-C contact maps generated by Juicer
Supplementary files format and content: BigWig; pos.bw: RNA-seq coverage corresponding to the positive strand
Supplementary files format and content: BigWig; neg.bw: RNA-seq coverage corresponding to the negative strand
Supplementary files format and content: TSV; limma.*.wrt.*.tsv: Differential expression calls between tumor subgroups generated using limma
Supplementary files format and content: TSV; union_arrowhead_scores.tsv: Summary table of Arrowhead contact domain scores for all samples
Supplementary files format and content: BEDPE; merged_loops.bedpe: Loop calls generated using HiCCUPS
Supplementary files format and content: TSV; union_hiccups_scores.tsv: Summary table of HiCCUPS loop scores for each sample
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| Submission date |
Oct 24, 2023 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Marco Gallo |
| E-mail(s) |
marco.gallo@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Pediatrics
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| Street address |
1102 Bates Avenue
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE246125 |
3D genome topology distinguishes molecular subgroups of medulloblastoma |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7856786_MB3662.BoundaryScores.max.50kb.bedgraph.gz |
631.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM7856786_MB3662.BoundaryScores.max.50kb.wig.gz |
284.5 Kb |
(ftp)(http) |
WIG |
| GSM7856786_MB3662.merged_loops.bedpe.gz |
362.8 Kb |
(ftp)(http) |
BEDPE |
| GSM7856786_MB3662_eigenvalue_allChr_50kb.wig.gz |
249.3 Kb |
(ftp)(http) |
WIG |
| GSM7856786_MB3662_inter_30.hic |
5.5 Gb |
(ftp)(http) |
HIC |
| Raw data not provided for this record |
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