|
| Status |
Public on Aug 22, 2017 |
| Title |
Endo_6dpf_E1 |
| Sample type |
SRA |
| |
|
| Source name |
Endothelial cell
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 6dpf
tissue: Endothelial
stain: GFP
|
| Growth protocol |
Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee (# 2015-11473).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Transgenic fish were treated with Liberase to disociate the cells. After FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zv9 whole genome using STAR v2.3.0
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using Cufflink software ( Annotation gtf for Zv9)
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefania Nicoli |
| E-mail(s) |
stefania.nicoli@yale.edu
|
| Phone |
203 654 6801
|
| Organization name |
Yale University
|
| Department |
Internal Medicine
|
| Street address |
300 George street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL10164 |
| Series (2) |
| GSE81340 |
microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues |
| GSE81341 |
mRNA and miRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues |
|
| Relations |
| BioSample |
SAMN04990181 |
| SRA |
SRX1756832 |
