|
| Status |
Public on Jun 16, 2020 |
| Title |
st15-2_RNA |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Oryzias latipes |
| Characteristics |
strain: Hd-rR
tissue: embryo
developmental stages: stage15
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using both TRIzol and Qiagen RNeasy Micro Kit
Illumina TruSeq stranded mRNA library preparation protocol for RNA-seq samples
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Illumina TruSeq stranded RNA-seq
|
| Data processing |
for TPM.tab file: genome mapping using hisat2(2.1.0), default parameters
for TPM.tab file: gene expression quantification using stringtie(v1.3.3b), default parameters
for fasta file: gene model built from pacbio data and generate transcript sequance
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: Two TPM.tab files are plain text(quantification count matrix by TPM, rows are genes and columns are samples), fasta file is transcript sequence use for quantification.
|
| |
|
| Submission date |
May 11, 2020 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Qiang Tu |
| E-mail(s) |
qtu@genetics.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology
|
| Street address |
No.1 West Beichen Road,Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL25587 |
| Series (1) |
| GSE136018 |
Transcriptome profiling of medaka timecourse embryonic samples and adult tissues samples. |
|
| Relations |
| BioSample |
SAMN14891110 |
| SRA |
SRX8325510 |
