|
| Status |
Public on Apr 18, 2017 |
| Title |
Adult wildtype zebrafish muLECs 1 |
| Sample type |
SRA |
| |
|
| Source name |
purified muLECs
|
| Organism |
Danio rerio |
| Characteristics |
sample type: Lyve1 Dsred
genotype: wildtype
cell type: muLEC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Adult zebrafish brains were dissociated using Liberase and lyve1 Dsred postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate, with 6 brains used per samples.
libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
adaptor trimming done by bcl2fastq2
Individual fastq files were aligned to the reference genome with Rsubread 1.20.6 with default settings in R version 3.2.2. Counts were then combined across all lanes associated with each biological sample to generate data reflecting the true biological samples.
Yugene-normalised values were calculated using a protocol from Lê Cao et al, 2014, Genomics. This a simple transform (applied to each individual sample) that assigns a modified cumulative proportion value to each measurement, without losing essential underlying information on data distributions or experimental correlates.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text files include yugene-normalised data for each sample
|
| |
|
| Submission date |
Apr 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Othmar Korn |
| Organization name |
Australian Institute for Bioengineering and Nanotechnology
|
| Street address |
University of Queensland
|
| City |
St. Lucia |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE97650 |
Mural lymphatic endothelial cells regulate meningeal angiogenesis in the zebrafish |
|
| Relations |
| BioSample |
SAMN06710122 |
| SRA |
SRX2733021 |
