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SRX15391589: GSM5172865: LIB046510_TRA00182851_S5_quant; Homo sapiens; RNA-Seq
4 ILLUMINA (NextSeq 500) runs: 29.9M spots, 2.2G bases, 885.7Mb downloads

External Id: GSM5172865_r1
Submitted by: Harvard medical school (DMBI)
Study: Liver Stromal Cells Restrict Macrophage Maturation and Stromal IL-6 Limits the Differentiation of Cirrhosis-linked Macrophages
show Abstracthide Abstract
Liver disease is the cause of approximately two million deaths globally per year, yet effective therapies are lacking. Iterative tissue injury leads to prolonged inflammation, extensive fibrosis, and the possible progression to deadly chronic-end stage disease, such as cirrhosis and hepatocellular carcinoma (HCC). In this study we investigated the ability of liver stromal cells to effect macrophage maturation and differentiation by using an in vitro human stromal-myeloid coculture systems and single cell RNA sequencing. Overall design: Human liver tissue were disaggregated and profiled using the Chromium Single Cell 3' Library and Gel Bead Kit v2 (10X Genomics) . In vitro human stromal-myeloid coculture systems Please note that the records have been updated with raw data on May 11 and May 20, 2022.
Sample: LIB046510_TRA00182851_S5_quant
SAMN18314887 • SRS13119046 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM5172865
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Prior to plating, the freshly isolated CD14+ cells were pelleted and lysed, and RNA isolation was performed using the Qiagen RNEasy Mini Kit. Likewise, RNA was isolated from liver stromal cell lines, previously plated at 10,000 cells per well 24hrs prior. This was performed following two rinses by gently- pipetted 200 uL volumes of sterile, room temperature PBS (Life Technologies). CD14+ cells were then plated alone, with stromal cell coculture, or in the presence of 500 pg/mL recombinant human IL6 (R&D Systems). Following 72 hours in culture, monocytes from each condition were harvested by pipetting and pelleted by centrifugation at 1000 RPM for 10 minutes. Stromal cell cultures adherent in the plate were rinsed twice with 200 uL volumes of sterile, room temperature PBS (Life Technologies). CD14+ Monocytes were re-purified using the CD14 MACS positive isolation kit (Milteyni) to minimize stromal cell contamination. RNA was prepared using the Qiagen RNEasy Mini Kit, according to manufacturer's instructions. Conditioned supernatant was pooled for each condition and frozen in sterile eppendorf tubes at -20°C prior to CBA analysis. Aliquots of RNA preparations were analyzed for quality and concentration at the Biopolymers facility at Harvard Medical School using the Agilent Bioanalyzer.
Runs: 4 runs, 29.9M spots, 2.2G bases, 885.7Mb
Run# of Spots# of BasesSizePublished
SRR193319307,489,641561.7M221.9Mb2022-05-20
SRR193319317,401,568555.1M217.7Mb2022-05-20
SRR193319327,566,642567.5M225.3Mb2022-05-20
SRR193319337,464,894559.9M220.9Mb2022-05-20

ID:
21931353

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