|
| Status |
Public on May 13, 2020 |
| Title |
lckgfp_s048 |
| Sample type |
SRA |
| |
|
| Source name |
Danio rerio tail
|
| Organism |
Danio rerio |
| Characteristics |
line: Tg(lck:GFP)
tissue: tail
devlopmental stage: 15 dpf
|
| Treatment protocol |
Liberase TL (100 ug/mL) and manual trituration was used to dissociate tail tissue. Cells were FACS sorted (FITC+)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lysis was performed as described in Schaum et al., Nature 2018
A Smart-Seq2 based protocol was used for reverse transcription and cDNA amplification, and a Nextera based protocol was used for library preparation, as described in Schaum et al., Nature 2018
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
none
|
| Data processing |
STAR (2.5)
Htseq (0.8.0) htseq-count -m intersection-nonempty --nonunique all
Genome_build: GRCz10
Supplementary_files_format_and_content: Raw counts of numbers of reads aligned to each feature for each cell, in tab-separated format (lckgfp_counts.txt)
|
| |
|
| Submission date |
Sep 20, 2019 |
| Last update date |
May 13, 2020 |
| Contact name |
Elizabeth Jerison |
| Organization name |
Stanford University
|
| Street address |
Clark Center E300, 318 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE137770 |
Characterization of T cells from the larval zebrafish tail via single-cell RNAseq |
|
| Relations |
| BioSample |
SAMN12795044 |
| SRA |
SRX6877037 |
