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Sample GSM1387573 Query DataSets for GSM1387573
Status Public on Aug 04, 2014
Title 2 - macrophage + fibroblast
Sample type SRA
Source name primary macrophages
Organism Homo sapiens
Characteristics cell type: primary macrophages
treatment: co-culture with fibroblast
barcode: CAGATC
Treatment protocol Mono- or co-cultures were then treated with or without TNFa (20ng/mL) for 2 days.
Growth protocol Human CD14+ cells isolated from PBMCs were differentiated into macrophages for 1 day with MCSF (10ng/mL) in RPMI/10% FBS. Transwell chambers with or without synovial fibroblasts were then placed above the macrophages. (Human synovial fibroblast cell lines were generated from synovial tissue extracted during knee arthroplasty, minced and collagenase digested. Adherent cells at passage 4 or beyond were used for macrophage-fibroblast co-cultures.)
Extracted molecule polyA RNA
Extraction protocol Macrophage RNA was isolated with RNAeasy mini kit (Qiagen) and polyA mRNA purified with the Truseq kit (Illumina).
Libraries were generated with the Truseq kit (Illumina).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description M (Fib) -
Data processing The TopHat program was used to align the reads to the UCSC Hg19 human reference genome.
The Cufflinks program was used to calculate measurements of transcript abundance (represented by Fragments Per Kilobase of exon model per Million mapped reads (FPKM)).
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM
Submission date May 16, 2014
Last update date May 15, 2019
Contact name Laura Donlin
Phone 212-774-2743
Organization name Hospital for Special Surgery
Department Arthritis and Tissue Degeneration Program
Street address 535 E. 70th St.
City New York
State/province NY
ZIP/Postal code 10021
Country USA
Platform ID GPL16791
Series (1)
GSE57723 Modulation of the TNF-induced macrophage response by synovial fibroblasts
BioSample SAMN02781628
SRA SRX544934

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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