run_metadata: 32553
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 32553 | SRR30792563 | SRX26194054 | SRS22736395 | SRP512205 | PRJNA1120771 | Transcriptomic neuron types vary topographically in function and morphology | GSE269232 | Transcriptome Analysis | We transcriptionally profiled the neuronal types of the zebrafish larvae optic tectum and matched them with their functional and morphological properties. Overall design: Wild type larvae were raised until 6 or 7 dpf. The optic tectum and torus longitudinalis of 6 dpf and 7 dpf larvae were then carefully dissected under a stereoscope followed by cell dissociation and sequencing. Please note that batches 5 6 and 8 the raw data with technical replica i.e. replica 1 replica 2 were processed together and the resulting processed data is linked to the corresponding replica 1 sample records. | pubmed:39939759 | optic tectum batch 12 scRNAseq additional sequencing | GSM8536814 | source name:optic tectum|tissue:optic tectum|age:7 dpf type:all cells|genotype:wild type|treatment:no treatment|geo loc name:missing|collection date:missing | optic tectum batch 12 scRNAseq additional sequencing | Demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v7.1.0 Assembly: GRCz11 genome assembly Ensembl release 98 Supplementary files format and content: Tab separated values files and matrix files | optic tectum | The optic tectum and torus longitudinalis of 6 dpf and 7 dpf larvae were carefully dissected under a stereoscope. Cell dissociation was performed using the Papain Dissociation System Worthington Biochemical Corporation. libraries according to the manufacturer’s instructions Chromium Single Cell 3′ Reagent Kit v3 10x Genomics. single cell 3′ barcoded cDNA | tissue:optic tectum|age:7 dpf type:all cells|genotype:wild type|treatment:no treatment | GSM8536814 | GSM8536814: optic tectum batch 12 scRNAseq additional sequencing; Danio rerio; RNA Seq | GSM8536814 r1 | GSM8536814 | 1 | The optic tectum and torus longitudinalis of 6 dpf and 7 dpf larvae were carefully dissected under a stereoscope. Cell dissociation was performed using the Papain Dissociation System Worthington Biochemical Corporation. libraries according to the manufacturer's instructions Chromium Single Cell 3′ Reagent Kit v3 10x Genomics. single cell 3′ barcoded cDNA | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP512205 | loader:fastq load.py | dr_7_dpf_tectum12_S1_b_L001_I1_001.fastq.gz dr_7_dpf_tectum12_S1_b_L001_I2_001.fastq.gz dr_7_dpf_tectum12_S1_b_L001_R1_001.fastq.gz dr_7_dpf_tectum12_S1_b_L001_R2_001.fastq.gz | fastq fastq fastq fastq | 8950711602.0 | 64860229.0 | GSM8536814 r1 | 0:10 1:10 2:28 3:90 | A:1849918393;C:1118618358;G:1252858411;T:1615952915;N:72533 | 10 | 10 | 28 | 90 | 1849918393 | 1118618358 | 1252858411 | 1615952915 | 72533 | SRX26194054 | SRS22736395 | SRA1978976 | Max Planck Institute for Biological Intelligence | Max Planck Institute for Biological Intelligence | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2024-09-25 | Larval | Larval | Brain | Nervous System |