RNA-seq of brain for 4 different strains: Neurotranscriptome profiles of four zebrafish strains
Survey
10.1016/j.gdata.2015.06.004
GSE61108
Behavioral displays or physiological responses are often influenced by intrinsic and extrinsic mechanisms in the context of the organism's evolutionary history. Understanding differences in transcriptome profiles can give insight into adaptive or pathological responses. We utilize high throughput sequencing (RNA-sequencing) to characterize the neurotranscriptome profiles in both males and females across four strains of zebrafish (Danio rerio). Strains varied by previously documented differences in stress and anxiety-like behavioral responses, and generations removed from wild-caught individuals. Here we describe detailed methodologies and quality controls in generating the raw RNA-sequencing reads that are publically available in NCBI's Gene Expression Omnibus database (GSE61108).
True
mickael.dong
Jan. 12, 2018, 3:45 a.m.
Oct. 23, 2018, 1:58 a.m.
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007070BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | AB | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002092AA | DCD013683BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002476SQ | DCD002488TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002093AA | DCD013684BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002477SQ | DCD002489TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007071BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | AB | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002094AA | DCD013685BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002478SQ | DCD002490TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002095AA | DCD013686BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002479SQ | DCD002491TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007072BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | SH | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002096AA | DCD013687BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002480SQ | DCD002492TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002097AA | DCD013688BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002481SQ | DCD002493TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007073BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | SH | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002098AA | DCD013689BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002482SQ | DCD002494TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002099AA | DCD013690BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002483SQ | DCD002495TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007074BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | LSB | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002100AA | DCD013691BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002484SQ | DCD002496TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002101AA | DCD013692BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002485SQ | DCD002497TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007075BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | LSB | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002102AA | DCD013693BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002486SQ | DCD002498TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002103AA | DCD013694BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002487SQ | DCD002499TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007076BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | HSB | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002104AA | DCD013695BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002488SQ | DCD002500TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002105AA | DCD013696BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002489SQ | DCD002501TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Controlled By | anatomical_term | Treatment | Hours Post Fertilization | Mutation Description |
|---|---|---|---|---|---|---|---|---|---|---|
| DCD007077BS | DCD000392SR | tissue | Wong lab, University of Nebraska Omaha | HSB | 90 Days-2 Years | brain | — | adult | — |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002106AA | DCD013697BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD002490SQ | DCD002502TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | unstranded | 09/04/2014 |
| Applied Assay ID | Biosample Replicate | Assay | Controlled By |
|---|---|---|---|
| DCD002107AA | DCD013698BR | RNA-seq_Wong_lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|---|
| DCD002491SQ | DCD002503TR | Wong lab, University of Nebraska Omaha | Illumina | GAIIx | TruSeq RNA Sample Prep V2 | ✘ | unstranded | — | 09/04/2014 |