run_metadata: 68098
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 68098 | SRR17604949 | SRX13773734 | SRS11653735 | SRP354901 | PRJNA796794 | Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation | GSE193591 | Transcriptome Analysis | We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types | pubmed:35250998 | Krt Ctrl rep1 | GSM5814808 | tissue:epithelial|age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | Krt Ctrl rep1 | Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file | epithelial | Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively. | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols. | age:3dpf|batch:1|genotype:wild type|cell type:keratinocyte|cell type id:CL:0000312 | GSM5814808 | GSM5814808: Krt Ctrl rep1; Danio rerio; RNA Seq | GSM5814808 r1 | GSM5814808 | 1 | Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP354901 | B9_ACCTCA_L004_R1_001.fastq.gz | fastq | 1094625173.0 | 10837873.0 | GSM5814808 r2 | 0:101 1:0 | A:230674174;C:270764802;G:381635055;T:211445587;N:105555 | 101 | 0 | 230674174 | 270764802 | 381635055 | 211445587 | 105555 | SRX13773734 | SRS11653735 | SRA1356563 | University of Wisconsin-Madison | University of Wisconsin-Madison | 1 | 0.93399 | 0.22867 | 0.93774 | 0.75465 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2022-01-13 | Larval | Larval | Multi-tissue | Multi-system |