 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 08, 2017 |
| Title |
control zebrafish endothelial cells rep2 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
genotype/variation: normal
cell type: endothelial cells
age: 28hpf
tissue: trunk
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, RNA was isolated from endothelial cells of control, mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 101 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to the zv9 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Genome_build: zv9
Supplementary_files_format_and_content: reads_count_HTSeq.xls: Reads count for each gene of all samples
|
| |
|
| Submission date |
Nov 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bao-Fa Sun |
| E-mail(s) |
[email protected]
|
| Organization name |
Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)
|
| Street address |
Da-Tun Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE89655 |
Transcriptomics analysis of gene expressions, m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos |
|
| Relations |
| BioSample |
SAMN06005693 |
| SRA |
SRX2336791 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
