|
| Status |
Public on Oct 13, 2021 |
| Title |
Intestine3 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish intestine
|
| Organism |
Danio rerio |
| Characteristics |
genotype: wild-type
tissue: intestine
strain: TLAB
|
| Growth protocol |
Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14/10 hour light/dark cycle)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol. To obtain polyA+ RNA, the poly(A) selection kit from LEXOGEN was used.
Strand-specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode
BAM files containing sequencing reads were converted to fastq files using samtools (v1.9)
Barcoded libraries were demultiplexed using fastx-toolkit (v0.0.14)
Sequencing adapters were trimmed with cutadapt (v1.18) and only reads longer than 25 bases were kept
Reads were aligned to GRCz11 with Hisat2 v2.1.0, using the Ensembl transcriptome release 102. The following parameters were used: hisat2 -q --dta --rna-strandness R -k 12 --no-unal
Quantification at the gene level (to obtain transcript per million (TPM)) was perfomed using Kallisto (v0.43.0)
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab delimited files containing TPM
|
| |
|
| Submission date |
Apr 12, 2021 |
| Last update date |
Oct 13, 2021 |
| Contact name |
Luis Enrique Cabrera Quio |
| E-mail(s) |
luis.cabrera.quio@imp.ac.at
|
| Organization name |
Research Institute of Molecular Pathology
|
| Lab |
Pauli lab
|
| Street address |
Campus Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE171906 |
RNA-Seq from zebrafish adult tissues |
|
| Relations |
| BioSample |
SAMN18715704 |
| SRA |
SRX10579904 |
