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Sample GSM5503524 Query DataSets for GSM5503524
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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