run_metadata: 39683
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 39683 | SRR2039718 | SRX1038070 | SRS945234 | SRP058706 | PRJNA284916 | Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2 | GSE69219 | Other | The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2 resulting in red shifted spectral sensitivity of the visual system. We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone so we profiled the RPE from TH and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE conducted in triplicate | pubmed:26549260 | zebrafish RPE T3 | GSM1695524 | source name:retinal pigment epithelium RPE|treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium | zebrafish RPE T3 | bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One 2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset curated zebrafish transcriptome with cyp27 family transcripts added PLoS One 2013. 87: p. e67801 included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data | retinal pigment epithelium RPE | Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. | Zebrafish were treated for three weeks with TH or a vehicle control. | treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium | GSM1695524 | GSM1695524: zebrafish RPE T3; Danio rerio; RNA Seq | GSM1695524 | 1 | Zebrafish RPE was isolated by dissection and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. | GEO Accession:GSM1695524 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP058706 | zebrafish_RPE_T3.fq.gz | fastq | 1384311250.0 | 27686225.0 | GSM1695524 r1 | 0:50 | A:365623713;C:318733172;G:322931194;T:376515371;N:507800 | 50 | 365623713 | 318733172 | 322931194 | 376515371 | 507800 | SRX1038070 | SRS945234 | SRA269915 | GEO | Washington University School of Medicine | 1 | 0.86222 | 0.24783 | 0.76124 | 0.64632 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | ribozero | bulk | unknown | unknown | United States | 2015-05-26 | Undetermined | Undetermined | Eye | Sensory System |