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| Status |
Public on May 29, 2019 |
| Title |
Central A - Library1 |
| Sample type |
SRA |
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| Source name |
Gill filaments
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| Organism |
Oryzias latipes |
| Characteristics |
developmental stage: Adult
strain: Cab
tissue: Gill - Branchial Arch
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| Extracted molecule |
total RNA |
| Extraction protocol |
Manual dissection of apical and central domain of gill. Trizol was used to extract Total RNA.
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 oryLat2 assembly using Hisat2 (Kim et al., 2015)
The aligned read SAM files were assembled into transcripts, their abundance was estimated and tested for differential expression by Cufflinks v2.2.1(Trapnell et al., 2012)
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Cufflinks output) and DEGs analysis (Cuffdiff output)
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| Submission date |
May 09, 2019 |
| Last update date |
May 30, 2019 |
| 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) |
| GSE130939 |
Transcriptome analysts of a growth domain and a differentiated domain of the medaka gill. |
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| Relations |
| BioSample |
SAMN11607869 |
| SRA |
SRX5809557 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3756543_new6_cufflinks.txt.gz |
657.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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