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| Status |
Public on May 04, 2021 |
| Title |
Sample 1 |
| Sample type |
SRA |
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| Source name |
Total embryo
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| Organism |
Oryzias latipes |
| Characteristics |
Stage: Embryo
strain: Cab
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| Treatment protocol |
Blastomeres from zebrafish were transplanted into isochronic medaka blastulae.
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| Growth protocol |
Zebrafish embryos were raised in E3 medium at 28C, medaka and zebraka embryos were raised in ERM at 28C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to the Trizol manufacture’s instructions.
poly A selection for the RNA from the NEBnext Poly A module
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Each sample was mapped against the index genome built from both oryLat2 and danRer10 assembly using Hisat2 (Kim et al., 2015)
The aligned read SAM files were assembled into transcripts and their abundance was estimated by Cufflinks v2.2.1(Trapnell et al., 2012)
Genome_build: danRer10
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Cufflinks output)
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| Submission date |
May 07, 2020 |
| Last update date |
May 05, 2021 |
| Contact name |
Lorena Buono |
| Organization name |
CABD
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| Street address |
Carretera de Utrera km 1
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| City |
Sevilla |
| State/province |
Sevilla |
| ZIP/Postal code |
41013 |
| Country |
Spain |
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| Platform ID |
GPL23039 |
| Series (1) |
| GSE150009 |
Transcriptome analysis of zebrafish, medaka and zebraka chimeras |
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| Relations |
| BioSample |
SAMN14847395 |
| SRA |
SRX8284501 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4520644_sample1medaka_genes.fpkm_tracking.txt.gz |
647.9 Kb |
(ftp)(http) |
TXT |
| GSM4520644_sample1zebra_genes.fpkm_tracking.txt.gz |
683.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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