|
| Status |
Public on Nov 18, 2021 |
| Title |
MDA-PCa-2b_acute_IL-1a_1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-PCa-2b
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate cancer
cell line: MDA-PCa-2b
treated: 25 ng/ml IL-1a for 3 days
|
| Treatment protocol |
MDA-PCa-2b cells were chronically cultured in 0.5 ng/ml IL-1 alpha or IL-1 beta (in HPC1 + 20% FBS) for 4 months. IL-1 is cytotoxic/static, so the viable, proliferating colonies that emerged after 4 months in IL-1 alpha or IL-1 beta were expanded to generate the IL-1a subline (MDA-αs1) and the IL-1b subline (MDA-βs1). MDA-PCa-2b parental cells were cultured in vehicle (0.1% BSA in 1xPBS) in HPC1 + 20% FBS. For RNA sequencing, MDA-PCa-2b parental, MDA-αs1 and MDA-βs1 cells were plated and cultured in HPC1 + 20% FBS for 3 days and the MDA-PCa-2b parental cells were also treated with 25 ng/ml IL-1a or IL-1b for 3 days. Total RNA was isolated from 3 biological replicates for RNA sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells treated with cytokines using GeneJET RNA Purification kit (Thermo Fisher Scientific, Waltham, MA; K0732) as per manufacturer’s instructions. Genomic DNA contamination was removed by treating 1 ug of RNA with 1 U of DNase-I (Thermo scientific, Waltham, MA; EN0521) following manufacturer’s instructions.
RNA-seq was performed by the Genome Center at tThe University of Texas at Dallas (Richardson, TX). Total RNA library was prepared using Illumina Truseq Stranded Total RNA prep Gold kit (Illumina). The prepared libraries were sequenced on an Illumina NextSeq 500 platform (San Diego, CA) with 75bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
parental cell line treated with 25 ng/ml IL-1a for 3 days
|
| Data processing |
Raw data were de-multiplexed and converted to fastq files using bcl2fastq (v2.17)
The fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Sequencing reads were mapped to hg19 reference genome (from igenomes) using STAR (v2.5.3a), counted using featureCounts (subread/v1.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with raw read counts calculated using igenomes gtf file
|
| |
|
| Submission date |
Jul 30, 2021 |
| Last update date |
Nov 18, 2021 |
| Contact name |
Nikki Delk |
| E-mail(s) |
[email protected]
|
| Phone |
9728832581
|
| Organization name |
University of Texas at Dallas
|
| Department |
Biological Sciences
|
| Street address |
800 West Campbell Road
|
| City |
Richardson |
| ZIP/Postal code |
75080 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE181229 |
Chronic IL-1 Exposed AR+ PCa Cell Lines Show Conserved Loss of IL-1 Sensitivity and Evolve Both Conserved and Unique Differential Gene Expression Profiles |
|
| Relations |
| BioSample |
SAMN20506592 |
| SRA |
SRX11613068 |
