|
Status |
Public on May 13, 2020 |
Title |
lckgfp_s031 |
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 |
SAMN12795022 |
SRA |
SRX6877020 |