run_metadata: 10399
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10399 | ERR8516971 | ERX8083449 | ERS10521296 | ERP135383 | PRJEB50776 | Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue | E-MTAB-11431 | Other | Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. | ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19 | Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion | Null neurite | SAMEA12922150 | Centre for Developmental Neurobiology, King's College London | ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite | Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue | E MTAB 11431:Null neurite p | Null neurite p | Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue | Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion | Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP135383 | Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue | ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py | 15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz | fastq fastq | E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R | 0:51 1:51 | A:766707527;C:798667604;G:818782599;T:773280942;N:15938306 | 51 | 51 | 766707527 | 798667604 | 818782599 | 773280942 | 15938306 | ERX8083449 | ERS10521296 | ERA8932807 | Centre for Developmental Neurobiology, King | Centre for Developmental Neurobiology, King | 2 | 0.88811 | 0.92834 | 0.21869 | 0.22669 | 0.72878 | 0.72604 | 0.55598 | 0.57831 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | random_priming | ribozero | bulk | bulk | bulk | United Kingdom | 2022-02-19 | Undetermined | Undetermined | Brain | Nervous System |