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Sample GSM3995429 Query DataSets for GSM3995429
Status Public on Jun 01, 2020
Title Crohn's Disease rep 1
Sample type SRA
 
Source name macrophage
Organism Homo sapiens
Characteristics disease: Crohn's Disease
Treatment protocol SM buffer or viral-like particle (VLP) preparation from non-IBD or IBD tissue or ileostomy was pre-treated for 30 minutes with polymixin B to ensure endotoxin-free conditions. Media was removed from the cells and SM buffer (for mock condition) or VLP preparation was added drop-wise onto the cells at a volume sufficient to cover the well surface. Treatment was left on cells for 1 hour at 37C with occasional rocking. After 1 hour, treatments were removed entirely, cells were gently washed with PBS, and media was replaced. Cells were collected 24 hours after the end of treatment.
Growth protocol Peripheral blood mononuclear cells were isolated from the blood of healthy human donors using a Ficoll-based density gradient. Following isolation, adherent cells were cultured on tissue culture-treated plated plates in X-VIVO media containing 100ng/mL rhM-CSF and allowed to differentiate into mature macrophages for 7 days. At this point, cells were counted and replated overnight in fresh media for treatment.
Extracted molecule total RNA
Extraction protocol Cells were lysed in 350µL buffer RLT and RNA was isolated using the Qiagen RNeasy Mini Kit with on-column DNase digest (all according to manufacturer's instruction).
100ng of total RNA from each sample was used for library preparation. First, poly(A)-tailed RNA was enriched for using the NEBnext Poly(A) mRNA magnetic isolation module (E7490; according to manufacturer's instructions). This poly(A)-enriched RNA was then used to construct libraries using the NEBnext Ultra II RNA Library Prep Kit for Illumina (E7770; according to manufacturer's instructions). To allow for multiplexed reads, libraries were dual indexed using indices from NEBnext Multiplex Oligos for Illumina (E6440). Sequencing was done on a NovaSeq S4 flow cell.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Transcriptome mapping was performed with STAR version 2.5.4a by using the NCBI37 assembly gene annotations
Read counts for individual genes were produced using the unstranded count feature in HTSeq 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each sample
 
Submission date Aug 01, 2019
Last update date Jun 02, 2020
Contact name Kate L Jeffrey
Organization name Massachusetts General Hospital
Department Medicine
Street address 50 Blossom Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL24676
Series (1)
GSE135223 Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections
Relations
BioSample SAMN12421238
SRA SRX6631850

Supplementary file Size Download File type/resource
GSM3995429_CD_CCAGTTGA_GACGTCAT.txt.gz 228.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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