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Sample GSM5979712 Query DataSets for GSM5979712
Status Public on Oct 02, 2023
Title HIVE scRNA-seq CYR61 rep3
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics strain: C57Bl/6J
gender: male
age: 10 weeks
agent: CYR61
Treatment protocol bone marrow was isolated from hind limbs of mice and cultured for 3 days with M-CSF. Cells were then treated for 24 hours with or without 4ug/mL Cyr61.
Extracted molecule total RNA
Extraction protocol Cells were removed from culture plate with accutase and processed using HIVE platform (https://download.honeycomb.bio/)
RNA libraries were prepared for sequencing using standard HIVE scRNA-seq protocols (https://honeycomb.bio/)
HIVE single-cell RNA-Seq ( https://honeycomb.bio/)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description HIVE scRNA-seq CYR61 rep3
Data processing Data was processed by tool beenet analyze function (version 1.1): $BEENET analyze --sample-name=$sample --ref=$refDir --num-barcodes=5000 --out=$outPath $data1 $data2 (https://download.honeycomb.bio/)
Assembly: mm10 (beenet reference: 20210714-mm10.104)
Supplementary files format and content: Transcript Count Matrix generated by beenet (version 1.1)
 
Submission date Mar 28, 2022
Last update date Oct 02, 2023
Contact name Shuchang Liu
E-mail(s) shl96@pitt.edu
Organization name University of Pittsburgh
Department Pathology
Street address 203 Lothrop Street
City Pittsburgh
State/province PA
ZIP/Postal code 15261
Country USA
 
Platform ID GPL24247
Series (2)
GSE199639 CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages [HIVE single-cell RNA-seq]
GSE199640 CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages
Relations
BioSample SAMN27028686
SRA SRX14643210

Supplementary file Size Download File type/resource
GSM5979712_Cyr1_2_20211129142640_TCM.tsv.gz 3.3 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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