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| Status |
Public on Mar 06, 2019 |
| Title |
Mix_1μM_3 |
| Sample type |
SRA |
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| Source name |
Precision cut liver slices
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| Organism |
Gadus morhua |
| Characteristics |
agent: BaP_1000nM+EE2_1000nM
tissue: Liver
Sex: Female
body weight (g): 425
liver weight (g): 19
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen slices using mirVana™ miRNA Isolation Kit (Cat# AM1560, Ambion, Austin, TX, USA). The RNA was treated using TURBO DNase (TURBO DNA-free kit, Ambion) and further purified using RNA Clean & Concentrator-5 (Zymo Research Corp, Irvine, CA, USA) and eluted with RNase-free water. The concentration of total RNA was measured using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA quality was assessed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA samples (0.4 μg total RNA per sample) were sequenced according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide on Illumina HiSeq 4000 (Illumina, Inc., San Diego, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
The quality of the sequenced RNA samples was verified using FastQC v0.11.5
Paired reads were aligned to the published CDS of Atlantic cod using HISAT v2.1.0
Counts were generated from the alignments using idxstats from SAMtools v1.4.1
Genome_build: ftp://ftp.ensembl.org/pub/release-90/fasta/gadus_morhua/cds/Gadus_morhua.gad
Supplementary_files_format_and_content: TAB-delimited text files with each line consisting of reference sequence name, sequence length, # mapped reads and # unmapped reads
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| Submission date |
Nov 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Fekadu Yadetie |
| E-mail(s) |
fekadu.yadetie@mbi.uib.no
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| Organization name |
University of Bergen
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| Department |
Biology
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| Lab |
Environmental Toxicology
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| Street address |
Thormøhlensgt. 53A/B
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| City |
Bergen |
| ZIP/Postal code |
5008 Bergen |
| Country |
Norway |
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| Platform ID |
GPL24273 |
| Series (1) |
| GSE106968 |
Transcriptome (RNA-Seq) analysis of Atlantic cod (Gadus morhua) precision cut liver slices (PCLS) exposed to benzo[a]pyrene (BaP) and ethynylestradiol (EE2) |
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| Relations |
| BioSample |
SAMN08031663 |
| SRA |
SRX3397830 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2858458_17.count.txt.gz |
180.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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