|
| Status |
Public on Sep 27, 2019 |
| Title |
317E5 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Danio rerio |
| Characteristics |
transgenic line: Tg(fabp10a-pt-beta-catenin)
age: 6 months post fertilization
treatment at larval stage: No treatment
diagnosis: HCC
|
| Treatment protocol |
Larvae were treated with either 0.1% ethanol or 10micromolar 4-hydroxytamoxifen from 3 to 6 days post fertilization.
|
| Growth protocol |
Fish were raised following IACUC-approved protocols in insititutional zebrafish facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis (HCC or no HCC). The other half of each dissected liver was flash-frozen on dry ice and stored in -80C prior to RNA extraction. RNA was isolated using TriReagent (Cat# R2050-1-50, Zymo Research) and Direct-Zol RNA Mini prep kit (Cat# R2050, Zymo Research) including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase-/DNase-free water.
Sample quality control, library preparation, sequencing and alignments were performed by the Huntsman Cancer Institute (HCI) High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired-read, 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell.
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
15743R_counts.txt
15743X6
|
| Data processing |
The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab-delimited matrix where each column denotes a sample and each row corresponds to a gene.
|
| |
|
| Submission date |
Sep 20, 2019 |
| Last update date |
Sep 27, 2019 |
| Contact name |
Kimberley Jane Evason |
| Organization name |
University of California, San Francisco
|
| Department |
Pathology
|
| Street address |
513 Parnassus Ave, Room M545
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL24995 |
| Series (2) |
| GSE137787 |
Bulk transcriptomic analysis of two models of zebrafish beta-catenin-driven HCC |
| GSE137788 |
Transcriptomic analysis of two models of zebrafish beta-catenin-driven HCC |
|
| Relations |
| BioSample |
SAMN12797858 |
| SRA |
SRX6879056 |
