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Sample GSM2494237 Query DataSets for GSM2494237
Status Public on Jan 02, 2018
Title PKA dKO clone3
Sample type SRA
 
Source name mouse mpkCCD cell line
Organism Mus musculus
Characteristics tissue: Kidney
age: Stable
Treatment protocol After 4 days, cells were incubated in serum- and hormone-free medium with 0.1 nM dDAVP for 3 days. Media was changed daily.
Growth protocol Cells were grown on permeable membrane supports in DMEM/F12 medium containing 2 % serum and other supplements (5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin) for 4 days.
Extracted molecule total RNA
Extraction protocol The mpkCCD cells grown on permeable inserts of 6-well transwell were washed with PBS and lysed with 100 ul Trizol solution. Total RNA was isolated using Direct-zol RNA mini prep plus (ZYMO RESEARCH, R2070) as manufacturer's protocol.
Sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat#RS-122-2201) as manufacturer's instruction. Total RNA (262 ng) of each sample was applied to ribosomal RNA removal beads to deplete ribosomal RNAs. The purified RNA was fragmented and then primed with random hexamers for cDNA synthesis using reverse transcriptase and random primers. First strand cDNA and second strand cDNA were sythesized serially and ligated with indexing adapters. DNA fragments including adapters were amplified by PCR using a PCR primer cocktail. Sample libraries were qualified using Agilent Technologies Bioanalyzer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Sequenced reads were mapped to GENCODE mouse gene set (GRCm38.p5) using STAR v2.5.2a
SAM and BAM files were generated using Samtools
Reads in exons of GENCODE gene set were counted using HOMER (v4.8, analyzeRepeats.pl)
Differential expression analysis was carried out using edgeR
Genome_build: GRCm38.p5 (GENCODE)
Supplementary_files_format_and_content: tab-delimited text files include raw counts/FPKM values for each sample and differential expression of each genes
 
Submission date Feb 16, 2017
Last update date May 15, 2019
Contact name Hyun Jun Jung
E-mail(s) hjung24@jhmi.edu
Organization name Johns Hopkins University School of Medicine
Department Medicine (Nephrology)
Street address 720 Rutland Ave, Ross Research Building 1165B
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL21493
Series (2)
GSE95008 Identification of PKA-dependent signaling network using CRISPR-Cas9 coupled with quantitative transcriptomics, proteomics and phosphoproteomics
GSE95009 Protein kinase A-dependent signaling network revealed by multi-omic analysis
Relations
BioSample SAMN06342940
SRA SRX2568516

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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