|
| Status |
Public on May 09, 2023 |
| Title |
siZFR-2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK-293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK-293 cells
treatment: Transfected with anti-ZFR siRNA (siZFR)
|
| Treatment protocol |
HEK-293 cells were reverse-transfected with 40 nM of the indicated siRNA using Lipofectamine RNAiMAX. Seventy-two hours post-siRNA transfection, cells were harvesed for total RNA.
|
| Growth protocol |
HEK-293 cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml L-glutamine at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Plus Mini RNA isolation kit
2 μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq Stranded RNA Library Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Reads were trimmed using fastp software, with options --detect_adapter_for_pe and --trim_poly_g.
Trimmed reads were aligned with HISAT2, using default parameters and the hg19/grch37 combined genome and transcriptome index provided by the authors.
Gene-level expression quantification was performed with featurecounts, using Ensembl GRCh37.75 transcript annotations.
Differential gene expression was quantified using voom and Topconfects, as implemented by the Degust web server.
Assembly: hg19
Supplementary files format and content: Tab-delimited file contains differential gene expression analysis, read counts, and CPM values for the indicated samples and comparisons.
|
| |
|
| Submission date |
Jun 14, 2022 |
| Last update date |
May 09, 2023 |
| Contact name |
J. Robert Hogg |
| E-mail(s) |
j.hogg@nih.gov
|
| Organization name |
National Heart, Lung, and Blood Institute
|
| Department |
Biochemistry and Biophysics Center
|
| Street address |
50 South Drive, Room 2341
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE206058 |
A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq] |
| GSE206061 |
A network of DZF proteins controls alternative splicing regulation and fidelity. |
|
| Relations |
| BioSample |
SAMN29024426 |
| SRA |
SRX15696409 |
