|
| Status |
Public on Oct 24, 2016 |
| Title |
Miller201511_HYMBO_st26a |
| Sample type |
SRA |
| |
|
| Source name |
NF stage 26 replicate #1
|
| Organism |
Hymenochirus boettgeri |
| Characteristics |
strain: wild-type
developmental stage: NF stage 26
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole tissue was minced before mRNA extraction; mRNA was extracted with TRIzol protocol; the column purification was performed after extraction.
Standard strand-specific RNA-seq protocol for Illumina HiSeq, with poly-A capturing method
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Mapped reads to de novo assembled transcripts using Kallisto (0.42.4), to calculate TPM
Genome_build: HYMBO_TrinityV1_cdna (de novo assembled transcripts)
Supplementary_files_format_and_content: FASTA file containing de novo assembled transcripts, and their TPM values among samples calculated by Kallisto
|
| |
|
| Submission date |
Dec 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Taejoon Kwon |
| E-mail(s) |
tkwon@unist.ac.kr
|
| Organization name |
Ulsan National Institute of Science and Technology
|
| Department |
Department of Biomedical Engineering
|
| Street address |
50 Unist-gil
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21252 |
| Series (1) |
| GSE76089 |
Developmental gene expression of Hymenochirus boettgeri |
|
| Relations |
| BioSample |
SAMN04347399 |
| SRA |
SRX1487344 |
