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Sample GSM3722674 Query DataSets for GSM3722674
Status Public on Sep 25, 2020
Title MDCKII DENND5A-KD1 2D-D7 RNA-seq
Sample type SRA
 
Source name MDCKII cells
Organism Canis lupus familiaris
Characteristics cell line: MDCKII
genotype: DENND5A-KD
culturing time: day 7
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 NextSeq 500
 
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
E-mail(s) szhao@uga.edu
Organization name University of Georgia
Lab Shaying Zhao
Street address B304B Life Sciences, 120 Green Street
City ATHENS
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL21400
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
Relations
BioSample SAMN11418776
SRA SRX5685936

Supplementary file Size Download File type/resource
GSM3722674_2-1-D7-FPKM.txt.gz 200.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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