|
| 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
|
| 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 |
