run_metadata: 60004
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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| 60004 | SRR12083656 | SRX8610750 | SRS6900395 | SRP268708 | PRJNA641707 | Transcriptional profiling of pax2a Low and pax2a High thyroid follicular cells in zebrafish | GSE153197 | Transcriptome Analysis | Thyroid follicular cells TFCs are responsible for generation storage and release of thyroid hormone. Single cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population Gillotay et al. bioRxiv 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single cell RNA Seq.: GSE133466. Particularly TFC displayed transcriptional heterogeneity in the expression of pax2a a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity we generated a pax2a knock in line in which mKO2 expression is driven by endogenous pax2a locus. Using Tgtg:nls EGFP; pax2a:mKO2 Knock in we sorted for TFCs GFP+ and separated the pax2a Low mKO2 Low and pax2a High mKO2 High populations for NGS. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile pax2a high and pax2a low TFCs from 5 mpf animals. Cells were sorted directly into lysis buffer provided in ReliaPrep™ RNA Miniprep Systems Promega Z6011 and mRNA isolated according to the manufactor's protocol. cDNA was generated using Ribozome depletion protocol followed by adapter ligation. Sequencing was performed on llumina NextSeq500. Reads were splice aligned to the zebrafish genome GRCz11 using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene. | pubmed:33140917 | Pax2a Low TFC 2 | GSM4635493 | tissue:Thyroid Follicular Cells TFCs|age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | Pax2a Low TFC 2 | Mapping using HISAT2 against GRCz11with default parameters Counts per gene generated using FeatureCounts with default parameters Genome build: Zebrafish GRCz11 Supplementary files format and content: read counts as tsv file | Thyroid Follicular Cells TFCs | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | age:5 mpf|genotype/variation:Tgtg:nls EGFP pax2a:mKO2 Knock in|population:pax2a Low mKO2 Low | GSM4635493 | GSM4635493: Pax2a Low TFC 2; Danio rerio; RNA Seq | GSM4635493 | 1 | Enzymatic Dissociation Ribozyme depletion adapter ligation followed by llumina NextSeq500 | GEO Accession:GSM4635493 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP268708 | Pax2a-lowset2_S11_R2_001.fastq.gz Pax2a-lowset2_S11_R1_001.fastq | fastq fastq | 14562196360.0 | 85940573.0 | GSM4635493 r1 | 0:100.38 1:100.53 | A:3643644077;C:3784618122;G:3352785620;T:3780129729;N:1018812 | 100 | 100 | 3643644077 | 3784618122 | 3352785620 | 3780129729 | 1018812 | SRX8610750 | SRS6900395 | SRA1090834 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.16299 | 0.15776 | 0.06375 | 0.06201 | 0.93162 | 0.93117 | 0.63175 | 0.62162 | 101 | 101 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | Belgium | 2020-06-24 | Adult | Adult | Multi-tissue | Multi-system |