|
| Status |
Public on Aug 23, 2021 |
| Title |
draculin:mCherry+;gata1:GFP- at 52 hpf #1 |
| Sample type |
SRA |
| |
|
| Source name |
hematopoietic cells
|
| Organism |
Danio rerio |
| Characteristics |
developmental_stage: 52 hours post fertilization
transgenic_line: draculin:mCherry;gata1:GFP
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
draculin:mCherry+;gata1:GFP- or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria.
Sorted Cell populations were loaded on a Chromium Single Cell Controller (10X Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3' Reagents Kits v3.1 (10X Genomics). Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). ScRNA-Seq libraries were prepared using Single Cell 3' library Gel Bead Kit v3.1 (10X Genomics) following the manufacture's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina BCL output files were generated to FASTQ files using cellranger mkfastq
Custom reference used for alignment was generated using cellranger mkref (10X genomics) on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences.
cellranger count was used on FASTQ files to perform alignment, filtering, barcode counting, and unique molecular identifier counting.
Filtered outputs from cell ranger (features, barcodes, and matrix) were analyzed using Seurat V4 (Hao et al., 2020) and Monocle 3 (Trapnell et al., 2014; Cao et al., 2019)
Loom files were generated using cellranger output and velocyto pipelines (Gioele La Manno et al., 2018). scVelo (Bergen et al., 2020) was used for downstream loom file analysis.
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: tab-separated value text files were generated using cell ranger and loom files were generate using velocyto (RNA velocities)
|
| |
|
| Submission date |
Aug 16, 2021 |
| Last update date |
Aug 23, 2021 |
| Contact name |
Teresa Bowman |
| E-mail(s) |
teresa.bowman@einsteinmed.org
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Developmental and Molecular Biology
|
| Lab |
Chanin 501
|
| Street address |
1300 Morris Park Avenue
|
| City |
Bronx |
| State/province |
New York |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL21741 |
| Series (1) |
| GSE182213 |
Single-cell RNA sequencing analysis of transgenic zebrafish embryo/larvae |
|
| Relations |
| BioSample |
SAMN20812982 |
| SRA |
SRX11783410 |
