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Sample GSM3722644 Query DataSets for GSM3722644
Status Public on Sep 25, 2020
Title 2D_1 ATAC-seq
Sample type SRA
Source name MDCKII cells
Organism Canis lupus familiaris
Characteristics cell line: MDCKII
culturing time: day 4
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.
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.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
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
Submission date Apr 15, 2019
Last update date Sep 25, 2020
Contact name Shaying Zhao
Organization name University of Georgia
Lab Shaying Zhao
Street address B304B Life Sciences, 120 Green Street
State/province GA
ZIP/Postal code 30602
Country USA
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
BioSample SAMN11418828
SRA SRX5685999

Supplementary file Size Download File type/resource 344.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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