|
| Status |
Public on Jun 30, 2023 |
| Title |
HAP1_IFNG_4h_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HAP-1 cells treated with 10ng/mL IFNG for 4 hours, biological replicate-#2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HAP-1
treatment: 0.1% DMSO for 1 hour, then 10ng/mL IFN-gamma for 4 hours
|
| Treatment protocol |
Cells were pre-treated with vehicle control (0.1% DMSO) or 1 μM Senexin B for 1 hour, and then treated with or without 10ng/mL IFN-gamma for 4 hours.
|
| Growth protocol |
HAP-1 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well. 24 hours post seeding, cells were treated as indicated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent).
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Pre-treated with 0.1% DMSO for 1 hour and then treated with 10ng/mL IFN-gamma for 4 hours.
S8
|
| Data processing |
Indexed sequences were checked quality by Fastqc.
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5.
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10.
Assembly: GRCh38.98
Supplementary files format and content: HAP1_IFNG_SnxB_geneCounts.txt: Tab-delimited text file includes gene counts for each sample.
|
| |
|
| Submission date |
Apr 13, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
HAO JI |
| E-mail(s) |
[email protected]
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE200735 |
Effects of CDK8/19 mediator kinase inhibition by Senexin B in HAP-1 cells treated with or without interferon-gamma |
| GSE200754 |
Transcriptomic and Proteomic Effects of CDK8 and CDK19 Mediator Kinases |
|
| Relations |
| BioSample |
SAMN27565390 |
| SRA |
SRX14842813 |
