|
| Status |
Public on Jun 14, 2018 |
| Title |
Fishmeal-based control sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
head kidney
|
| Organism |
Salmo salar |
| Characteristics |
tissue: head kidney
diet: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Head kidney was dissected from each individual, and stored in RNAlater (Ambion) at -80ºC till RNA extraction. Total RNA was isolated from homogenized samples (TissueRuptor, Qiagen) using the miRNeasy mini kit according to the manufacturer’s instructions (Qiagen), and analyzed with an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent). A transcriptome library for each sample was prepared from 2 microgram total RNA, using the TruSeq™ RNA Sample Prep Kit v2 following the manufacturer’s instructions (Illumina Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 2
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw1_versus_control.xlsx
DiffExpr_diet_sw2_versus_control.xlsx
|
| Data processing |
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
Reads were aligned to Salmo salar cDNA sequences downloaded from NCBI (strategy 1) or to a de novo assembled Salmo salar head kidney cDNA contig reference (strategy 2) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9) (Anders and Huber, 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Salmo_salar_head_kidney_cDNA.fa (strategy 2)
Supplementary_files_format_and_content: (Strategy 1) DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx and DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx: Microsoft Office Excel file (.xlsx) with the following columns: Gene; Sample x; Sample x; Sample x; Sample x; Sample x; Sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj
Supplementary_files_format_and_content: (Strategy 2) DiffExpr_diet_sw1_versus_control.xlsx and DiffExpr_diet_sw2_versus_control.xlsx: Microsoft Office Excel file (.xlsx) with the following columns: Contig ID; Description; Sample x; Sample x; Sample x; Sample x; Sample x; Sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj
|
| |
|
| Submission date |
Jul 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ron P Dirks |
| E-mail(s) |
dirks@futuregenomics.tech
|
| Phone |
+31-71-2074610
|
| Organization name |
Future Genomics Technologies BV
|
| Street address |
Sylviusweg 74
|
| City |
Leiden |
| ZIP/Postal code |
2333 BE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL23792 |
| Series (1) |
| GSE101545 |
Immunomodulatory effects of dietary seaweeds in LPS challenged Atlantic salmon Salmo salar as determined by deep RNA sequencing of the head kidney transcriptome |
|
| Relations |
| BioSample |
SAMN07358664 |
| SRA |
SRX3010513 |
