|
| Status |
Public on Jan 10, 2024 |
| Title |
MF317_A1_GEX_zebrafish_multiseq |
| Sample type |
SRA |
| |
|
| Source name |
Kidney marrow
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Kidney marrow
cell type: Neutrophils
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Each kidney marrow was split into four portions, labelled with lipid anchor plus individual barcode solution (2 μM) for 5’ on ice and then incubated with lipid co-anchor (2 μM) for 5’ on ice. Each cell portion was individually FACS-sorted to obtain one population (mmp9 NO, INT, HI or WKM). All cells were gated on live gate, for WKM debris was excluded in a FSC/SSC gate, and mmp9 NO, INT, HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine-CAAX expression.
Single cell suspensions were immediately subjected to scRNA-seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics, Pleasanton, CA), according to the manufacturer’s protocols (10x Genomics) and sequenced by protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
We used the CellRanger v3.1.0 software (10x Genomics) for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2.
Assembly: GRCz11-3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes (Citrine and CFPNTR, sequences from snapgene.com).
Supplementary files format and content: compressed matrix files of CellRanger outputs
Supplementary files format and content: rds file containting Seurat object
Supplementary files format and content: hd5a file containting Seurat object
|
| |
|
| Submission date |
Jan 09, 2024 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Florian Halbritter |
| Organization name |
St. Anna Children's Cancer Research Institute (CCRI)
|
| Lab |
Developmental Cancer Genomics
|
| Street address |
Zimmermannplatz 10
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE252788 |
Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation |
|
| Relations |
| BioSample |
SAMN39308705 |
| SRA |
SRX23138318 |
