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Sample GSM3722655 Query DataSets for GSM3722655
Status Public on Sep 25, 2020
Title MDCKII 3D-D3-1 RNA-seq
Sample type SRA
Source name MDCKII cells
Organism Canis lupus familiaris
Characteristics cell line: MDCKII
genotype: wildtype
culturing time: day 3
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 2D cultures, cells were seeded on transwell inserts grown until over-confluence. The cells for seeding were regarded as day0 samples.
Extracted molecule total RNA
Extraction protocol Cysts grown for 24h, 3, 5, 8, 14 days, cells for seeding (day 0) and over-confluent cells were collected and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-seq libraries were constructed using KAPA Stranded mRNA-Seq Kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Read pairs were aligned to the dog reference genome canFam3 with HISAT v2.1.0.
Cufflinks v2.2.1 was used to quantify gene expression in FPKM, guided by canine gene annotation CanFam3.1.84 downloaded from UCSC genome browser
Genome_build: canFam3
Supplementary_files_format_and_content: Tab-delimited files with expression values in FPKM 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 GPL20988
Series (2)
GSE129823 RNA-seq for MDCKII 3D and 2D epithelial morphogenesis.
GSE129824 ATAC-seq and RNA-seq for MDCKII 3D and 2D epithelial morphogenesis
BioSample SAMN11418758
SRA SRX5685917

Supplementary file Size Download File type/resource
GSM3722655_3D-D3-1-FPKM.txt.gz 198.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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