|
Status |
Public on Oct 05, 2021 |
Title |
Untransduced_stim_B |
Sample type |
SRA |
|
|
Source name |
SV40-transformed skin fibroblasts
|
Organism |
Homo sapiens |
Characteristics |
cell type: SV40-transformed skin fibroblasts unstim or stim: Stimulated replicate number: 2
|
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 |
Untransduced_stim_B_S15
|
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 |
SAMN20585348 |
SRA |
SRX11651201 |