|
| Status |
Public on Mar 31, 2019 |
| Title |
Untreated Set 2 |
| Sample type |
SRA |
| |
|
| Source name |
Control/Untreated
|
| Organism |
Homo sapiens |
| Characteristics |
differentiation status: Differentiated
cell type: Podocytes (Glomerulus cells)
differentiation duration: 14 day differentiation
|
| Treatment protocol |
Podocytes were incubated 4hours in the serum free RPMI medium and injury was given using PAN (100μg/ml) and Adriamycin (0.25μg/ml) for 48 hours.
|
| Growth protocol |
RPMI 1640-based medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 2 g/liter of sodium bicarbonate (NaHCO3), insulin-transferrin-selenium (ITS) supplement (Sigma-Aldrich), and 200 units/ml penicillin and streptomycin (Roche Applied Science)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the qiagen RNeasy Mini Kit (Cat. No # 74104) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Immortalized Human Podocytes Cell Lines
|
| Data processing |
Downstream bioinformatics analyses was performed by using a combination of programs including Bowtie2, Tophat2, HTseq and Cufflink .
Reference genome and gene model annotation files were acquired from NCBI/UCSC/Ensemble genome browser.
Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Gene expression level quantification was done using HTSeq v0.6.1 and for each gene read numbers counts were mapped, whereas, Reads Per Kilobase of exon model (RPKM) of each gene was calculated based on the length of the gene and expression levels were analyzed
DESeq2 R package (2_1.6.3) database was used for the differential expression (DE) analyses. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach and adjusted P-value <0.05 found by DESeq2 were assigned as DE. Analyses of DE of two conditions was performed using the DEGSeq R package (1.12.0). The P-values were also adjusted using Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as threshold for significantly differential expression.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Jan 03, 2019 |
| Last update date |
Mar 31, 2019 |
| Contact name |
Deepak Nihalani |
| E-mail(s) |
nihalani@musc.edu
|
| Organization name |
Medical University of South Carolina
|
| Department |
Medicine/Nephrology
|
| Lab |
DDB520
|
| Street address |
70 President St.
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29424 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE124622 |
Next Generation Sequencing of control (Untreated), PAN injured and Adriamycin injured human podocytes |
|
| Relations |
| BioSample |
SAMN10689641 |
| SRA |
SRX5202528 |
