|
Status |
Public on Jun 16, 2020 |
Title |
st38-2_RNA |
Sample type |
SRA |
|
|
Source name |
whole embryo
|
Organism |
Oryzias latipes |
Characteristics |
strain: Hd-rR tissue: embryo developmental stages: stage38
|
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 |
SAMN14891096 |
SRA |
SRX8325516 |