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| Status |
Public on Aug 14, 2018 |
| Title |
ctrl_2_HiC |
| Sample type |
SRA |
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| Source name |
Myeloid leukaemia
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HL60/S4
differentiation: neutrophil-like (4 days all-trans retinoic acid)
passages: 8
migration pore size: none
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| Growth protocol |
A seed-lot store was generated of cells at 4 passages. Cells were grown in suspension in RPMI 1640 (ThermoFisher, 11875119) with 10% FBS (medi’Ray, MG-FBS0820-500ML-GEN), 1% pen/strep (ThermoFisher, 15140122), and 1% GlutaMAXTM (ThermoFisher, 35050061). Cells were differentiated into a granulocytic phenotype with 1µm all trans retinoic acid (ATRA)(Sigma Aldrich, R2625-50MG) for four days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C protocol as described in Rao et al 2014 with MboI restriction enzyme
Illumina Truseq Nano kit (Truseq Nano DNA LT Sample Preparation Kit, FC-121-4001) was used, following kit instructions
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
first principle component of pooled libraries (*PC1only.bed)
TAD binsignal of pooled libraries
Called domains, boundaries, and gaps of pooled libraries (*domains.txt)
Total significant contacts (*significant_ints.csv)
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| Data processing |
Read quality was confirmed with FastQC v0.11.4
Libraries were pooled and downsampled so that the three conditions (control, 5µm pores, 14µm pores) had the same number of valid reads (144,382,298)
HiCUP output was converted to HOMER input using the hicuptohomer script provided by HiCUP
The first principle component of the correlation matrix of each chromosome was found in HOMER v4.9.1 at 300kb resolution, 500kb super-resolution on a matrix normalised with the HOMER default
Significant and differential contacts were identified in HOMER at 40kb resolution, 100kb super-resolution with default normalisation, minimum distance 100kb, maximum distance 5Mb
HOMER was used to generate chromosomal matrices at 50kb resolution for topologically associated domain (TAD) analysis in TopDom v0.0.2 using a window size of 5
Genome_build: hg38
Supplementary_files_format_and_content: bedfile of the frst principle component of each condition. Total significant contacts in each condition (csv). Contacts with significantly increased and decreased frequency in 5mig and 14mig compared to control (csv). Binsignal output from TopDom in each condition (tsv)
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| Submission date |
Jun 11, 2018 |
| Last update date |
Aug 14, 2018 |
| Contact name |
Justin M. O'Sullivan |
| E-mail(s) |
[email protected]
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| Organization name |
University of Auckland
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| Department |
Liggins Institute
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| Street address |
85 Park Road, Grafton
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| City |
Auckland |
| ZIP/Postal code |
1023 |
| Country |
New Zealand |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE115633 |
Migration through a small pore disrupts inactive chromatin organisation in neutrophil-like cells [Hi-C] |
| GSE115634 |
RNA-seq and Hi-C sequencing of neutrophil-like cells migrated through large or small pores |
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| Relations |
| BioSample |
SAMN09395180 |
| SRA |
SRX4194157 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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