|
| Status |
Public on Mar 23, 2022 |
| Title |
MPI MT 1 |
| Sample type |
SRA |
| |
|
| Source name |
Adult zebrafish liver dissection
|
| Organism |
Danio rerio |
| Characteristics |
genotype: mpi+/- (mss7)
tissue: Liver
|
| Growth protocol |
Adult fish were maintained on a 14:10 light/dark cycle at 28°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were dissected from 18-month-old adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols, and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads.
Library construction was performed as per 10X Genomics v3 chemistry kit.
10X chromium
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger
Genome_build: danRer11
|
| |
|
| Submission date |
Aug 12, 2021 |
| Last update date |
Mar 23, 2022 |
| Contact name |
Jaime Chu |
| E-mail(s) |
jaime.chu@mssm.edu
|
| Phone |
2122410227
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Pediatrics
|
| Lab |
Jaime Chu Lab
|
| Street address |
1 Gustave L. Levy Place, Annenberg 14-12
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE181987 |
Single-cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver |
|
| Relations |
| BioSample |
SAMN20745938 |
| SRA |
SRX11729085 |
