|
| Status |
Public on Oct 05, 2021 |
| Title |
RK_transduced_stim_A |
| Sample type |
SRA |
| |
|
| Source name |
SV40-transformed skin fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SV40-transformed skin fibroblasts
genotype/variation: infected with HOIL1-R/K lentiviral particles
unstim or stim: Stimulated
replicate number: 1
|
| Treatment protocol |
Stimulated with 10ng/mL IL-1b for 4h
|
| Growth protocol |
Patient-derived skin fibroblasts were immortalized by transfection with a plasmid expresing SV40 large T antigen. Cells were then infected with HOIL1-WT or HOIL1-R/K lentiviral particles and subsequently propagated in complete DMEM.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with a RNeasy Mini Plus Kit (Qiagen)
RNA samples were prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England BioLabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RK_transduced_stim_A_S20
|
| Data processing |
RNA was sequenced on the Illumina NextSeq 500 with Paired End 42bp x 42bp reads
Read sequences were aligned to the Homo sapiens reference sequence (UCSC hg19) using STAR aligner (version STAR_2.5.0b)
Assembly of transcripts and measurement of abundance was done using Cufflinks (Version 2.2.1)
TMM analysis using EdgeR was used for raw count normalization
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Raw counts and normalized counts are presented as .csv matrix files
|
| |
|
| Submission date |
Aug 04, 2021 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Stuart E Turvey |
| E-mail(s) |
sturvey@cw.bc.ca
|
| Phone |
6048753131
|
| Organization name |
The University of British Columbia
|
| Department |
Pediatrics
|
| Street address |
A5-122 950 W 28th Avenue
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V5Z 4H4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE181493 |
MALT1-dependent cleavage of HOIL1 modulates canonical NF-kB signaling and inflammatory responsiveness |
|
| Relations |
| BioSample |
SAMN20585356 |
| SRA |
SRX11651212 |
