|
| Status |
Public on Dec 21, 2022 |
| Title |
HUPEC_13_G1G2_UD3 |
| Sample type |
SRA |
| |
|
| Source name |
podocyte-like epithelial cells (HUPEC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUPEC_13
differentiation status: Undifferentiated
genotype: APOL1 G1/G2
|
| Treatment protocol |
Podocytes were differentiated by culturing in the same medium formulation at 37°C for 14 days, exchanging medium every 2-3 days.
|
| Growth protocol |
Undifferentiated podocytes were cultured in RPMI 1640 medium (Gibco, ThermoFisher Scientific, Gaithersburg, MD), supplemented with 10% fetal bovine serum and insulin/transferrin/selenium (Gibco, Thermo Fisher Scientific, Gaithersburg, MD) at 33 °C, 95% air and 5% CO2) for expansion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were resuspended with QIAzol (QIAGEN, Hilden, Germany) and RNA was extracted (Zymo Direct-zol RNA miniprep kit).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded Total RNA library protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
9_12_13_G1G2_UD3
|
| Data processing |
Illumina RTA v3.4.4 software was used for base calling. Bcl2fastq v2.17 was used for sample demultiplexing.
Adapters from the samples were trimmed using Cutadapt 1.18 software.
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome hg38 and HIV-1 (NC_001802.1) and GENCODE v30 for human genome.
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1.
Genome_build: hg38 and HIV-1: NC_001802.1
Supplementary_files_format_and_content: RawCountFile_rsemgenes.xlsx
|
| |
|
| Submission date |
Jan 25, 2022 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Teruhiko Yoshida |
| E-mail(s) |
teruhiko.yoshida@nih.gov
|
| Phone |
301-496-2988
|
| Organization name |
National Institutes of Health
|
| Department |
NIDDK - KDB
|
| Street address |
10 Center Drive, 9N208
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE194330 |
Transcriptomic analysis of human podocytes [total RNA] |
| GSE194337 |
Transcriptomic analysis of human podocytes |
|
| Relations |
| BioSample |
SAMN25242349 |
| SRA |
SRX13897132 |
