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| Status |
Public on Jan 11, 2022 |
| Title |
W44_12wk |
| Sample type |
SRA |
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| Source name |
Mammary epithelial cells
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar-Furth
tissue: Mammary epithelial cells
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| Treatment protocol |
Fresh mammary glands from the abdominal/inguinal regions of 6-week-old and 12-week-old female rats were individually collected, scissor minced and digested for 2 hours at 37°C in 10 mL of GIBCO Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12; ThermoFisher) containing 0.005 g/mL of type 3 collagenase (Worthington-Biochem).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Centrifugation was used to remove fat and collect the cell pellets. Individual cell pellets were washed and resuspended in DMEM/F12 media. Each cell suspension was filtered using 40μm nylon to enrich the mammary ductal fragments and remove stromal cells. The filter was inverted and rinsed to collect the fragments, and the resulting cell pellet containing mammary epithelial cells was diluted in PBS and treated for 10 minutes with 1.5% formaldehyde for DNA/chromatin fixation. After a series of washes, the final cell pellets were collected using centrifugation and stored at -80oC.
A total of 6 samples were sent to Arima Genomic, Inc. (n=3 from each age group) for Arima HiC Service, consisting of complete sample processing for Arima-HiC and library preparation, Illumina Next-Generation sequencing and data upload.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Hi-C reads were processed using HiCPro version 2.7 with the default BowTie2 parameters (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder). Digestion paramters: LIGATION_SITE = GAATAATC,GAATACTC,GAATAGTC,GAATATTC,GAATGATC,GACTAATC,GACTACTC,GACTAGTC,GACTATTC,GACTGATC,GAGTAATC,GAGTACTC,GAGTAGTC,GAGTATTC,GAGTGATC,GATCAATC,GATCACTC,GATCAGTC,GATCATTC,GATCGATC,GATTAATC,GATTACTC,GATTAGTC,GATTATTC,GATTGATC, MIN_FRAG_SIZE = 10, MAX_FRAG_SIZE = 100000, MIN_INSERT_SIZE = 100, MAX_INSERT_SIZE = 1000
Removal of singleton reads, multi-mapped read-pairs and duplicates set to true
10kb contact maps generated with HiCPro 2.7
6wk samples were aggregated (sum), and 12 wk samples were similarly aggregated. ICED normalization was perfomed on both aggregated matrices (default HiCPro).
Genome_build: rn6
Supplementary_files_format_and_content: .matrix
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| Submission date |
Sep 16, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Sushmita Roy |
| E-mail(s) |
sroy@biostat.wisc.edu
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| Organization name |
University of Wisconsin-Madison
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| Department |
Wisconsin Institute For Discovery
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| Street address |
330 N Orchard St
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE184280 |
Deciphering the role of 3D genome organization in breast cancer susceptibility (Hi-C) |
| GSE184285 |
Deciphering the role of 3D genome organization in breast cancer susceptibility |
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| Relations |
| BioSample |
SAMN21461215 |
| SRA |
SRX12204309 |
| 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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