|
| Status |
Public on Jan 02, 2018 |
| Title |
Control clone1 |
| 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 |
SAMN06342945 |
| SRA |
SRX2568511 |
