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| Status |
Public on Sep 25, 2020 |
| Title |
2D_2 ATAC-seq |
| Sample type |
SRA |
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| Source name |
MDCKII cells
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| Organism |
Canis lupus familiaris |
| Characteristics |
cell line: MDCKII
culturing time: day 4
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| Growth protocol |
MDCKII cells were maintained in Eagle’s minimal essential medium with 5% fetal bovine serum, 10 mM HEPES, 2 mM glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin; For 3D cultures, cells were grown on top of matrigel for 19 days. For 2D cultures, cells were seeded on transwell inserts grown until over-confluence (day4). The cells for seeding were regarded as day0 samples.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Day 0 and 2D cells were collected using cell scraper, and 3D cysts were isolated from m3atrigel with cell recovery solution (Corning). After washing with cold PBS, the cells were dissociated in lysis buffer (1% NP40, 10mM Tris pH7.5, 10mM NaCl, 3mM MgCl2, 1mM EDTA) using syringe. The samples were filtered with miracloth. Crude nuclei were sorted by flow cytometer (Beckman Coulter MoFlo XDP) with DAPI. The nuclei were pelleted and resuspended in the transposase reaction mix (25 μl 2xTagmentation buffer, 2.5 μL transposase and 22.5 μL nuclease-free water), and incubated at 37°C for 30 min.
Immediately following transposition, transposed DNA was purified with Qiagen minElute Reaction Cleanup Kit, and amplified using Phusion DNA polymerase (NEB) for 10-13 cycles.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequencing reads were mapped to the Canfam3 genome using BWA v0.7.10.
Mitochondrial reads were removed.
ATAC-seq peaks were identified using MACS v2.1.1 (FDR 0.05).
Genome_build: canFam3
Supplementary_files_format_and_content: Bigwig files for each sample
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| Submission date |
Apr 15, 2019 |
| Last update date |
Sep 25, 2020 |
| Contact name |
Shaying Zhao |
| E-mail(s) |
szhao@uga.edu
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| Organization name |
University of Georgia
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| Lab |
Shaying Zhao
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| Street address |
B304B Life Sciences, 120 Green Street
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| City |
ATHENS |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL21400 |
| Series (2) |
| GSE129822 |
ATAC-seq for MDCKII 3D and 2D epithelial morphogenesis |
| GSE129824 |
ATAC-seq and RNA-seq for MDCKII 3D and 2D epithelial morphogenesis |
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| Relations |
| BioSample |
SAMN11418827 |
| SRA |
SRX5686000 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3722645_2D_2_pileup.bw |
243.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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