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| Status |
Public on Apr 21, 2020 |
| Title |
met2set25_Hi-C |
| Sample type |
SRA |
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| Source name |
mixed stage embryos
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: GW0638
genotype: met-2(n4256) set-25(n5021) III
tissue: mixed stage embryos
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| Treatment protocol |
We isolated nuclei, digested with DpnII restriction enzyme, filled in the restriction overhangs with biotinylated nucleotides, and ligated as in Brejc et al 2017.
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| Growth protocol |
Worms were grown on NGM plates with concentrated HB101 bacteria until gravid. Adults were collected and bleached to release mixed-stage embryos.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We purfied, sheared, and size-selected DNA and pulled down biotinylated fragments as in Brejc et al 2017.
We performed end repair, A-tailing, ligation of NEXTflex DNA Barcodes, and amplification as in Brejc at al 2017.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Library strategy: Hi-C
Libraries were sequenced with Illumina's HiSeq 4000 Platform using 100 bp paired end reads. Reads were mapped to the ce11 reference genome, binned at 50 kb, and iteratively corrected using scripts derived from those available at https://bitbucket.org/mirnylab/hiclib as in Brejc et al 2017. For each genotype, interaction frequencies after iterative correction from the replicates were combined.
To correct for experimental variation in the decay of chromatin contacts with genomic distance, we calculated Hi-C Z scores using a LOESS method (Imakaev et al 2012) with scripts available at https://github.com/dekkerlab/cworld-dekker
Compartments were quantified using principal component analysis with scripts available at https://github.com/dekkerlab/cworld-dekker
To quantify TAD boundaries, we calculated insulation scores from the Hi-C interaction data as in Crane et al 2015 using the following parameters: insulation square 500000, insulation delta span 200000, insulation mode mean, and noise threshold 0.1.
Genome_build: ce11
Supplementary_files_format_and_content: .matrix files are tab-delimited tables of genome-wide interaction frequencies iteratively corrected and normalized for read depth as in Crane et al 2015.
Supplementary_files_format_and_content: .zScore.matrix files are tab-delimited tables of Z scores.
Supplementary_files_format_and_content: .compartment files give the eigenvector values and eigenvalues for the first three principal components
Supplementary_files_format_and_content: .insulation files give the insulation score and delta vector for each 50 kb bin in the genome, as defined in Crane et al 2015
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| Submission date |
Jan 25, 2020 |
| Last update date |
Apr 22, 2020 |
| Contact name |
Barbara J. Meyer |
| E-mail(s) |
bjmeyer@berkeley.edu
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| Phone |
510 643 5583
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| Organization name |
HHMI/UCB
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| Department |
MCB
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| Lab |
Meyer
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| Street address |
16 Barker Hall #3204
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL22765 |
| Series (2) |
| GSE144252 |
Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring (Hi-C) |
| GSE144253 |
Histone H3K9 methylation promotes formation of genome compartments in C. elegans via chromosome compaction and perinuclear anchoring |
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| Relations |
| BioSample |
SAMN13921539 |
| SRA |
SRX7630550 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4284461_met2set25_50kb.compartments.txt.gz |
83.8 Kb |
(ftp)(http) |
TXT |
| GSM4284461_met2set25_50kb.insulation.txt.gz |
68.9 Kb |
(ftp)(http) |
TXT |
| GSM4284461_met2set25_50kb.matrix.txt.gz |
10.5 Mb |
(ftp)(http) |
TXT |
| GSM4284461_met2set25_50kb.zScore.matrix.txt.gz |
15.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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