run_metadata: 74147
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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| 74147 | SRR23570565 | SRX19457378 | SRS16850065 | SRP423736 | PRJNA937226 | Single cell transcriptomics on zebrafish gliovascular niche | GSE225721 | Transcriptome Analysis | To investigate the cell types involved in the gliovascular niche of the zebrafish brain we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions. Overall design: Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide as descibed Bhatatrai et al. 2016 and cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom GRChZ 11 and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit and Sequencing done by Illumina. | pubmed:38260431;pubmed:38598053;pubmed:38902234 | vascular AB42 | GSM7054715 | source name:telencephalon|tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:AB42|geo loc name:missing|collection date:missing | vascular AB42 | The demultiplexing barcoded processing gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger | telencephalon | Tgher4.1:dRED and Tgfli1a:GFP lines were injected with Amyloid beta 42 peptide and PBS as control as descibed Bhatatrai et al. 2016. | Cells from zebrafish telencephalon were dissociated cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics | Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle pH 7.5 at 28 °C ±1 °C in groups of 20 animals per 2.8 L. | tissue:telencephalon|genotype:Tgher4.1:dRED|treatment:AB42 | GSM7054715 | GSM7054715: vascular AB42; Danio rerio; RNA Seq | GSM7054715 r1 | GSM7054715 | 1 | Cells from zebrafish telencephalon were dissociated cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP423736 | loader:fastq load.py|options: readTypes=TTBB read1PairFiles=CP016 S1 L004 I1 001.fastq.gz read2PairFiles=CP016 S1 L004 I2 001.fastq.gz read3PairFiles=CP016 S1 L004 R1 001.fastq.gz read4PairFiles=CP016 S1 L004 R2 001.fastq.gz | CP016_S1_L004_I1_001.fastq.gz CP016_S1_L004_I2_001.fastq.gz CP016_S1_L004_R1_001.fastq.gz CP016_S1_L004_R2_001.fastq.gz | fastq fastq fastq fastq | 45689271216.0 | 205807528.0 | GSM7054715 r2 | 0:10 1:10 2:101 3:101 | A:11389510151;C:7463425109;G:7607679289;T:15111473568;N:1032539 | 10 | 10 | 101 | 101 | 11389510151 | 7463425109 | 7607679289 | 15111473568 | 1032539 | SRX19457378 | SRS16850065 | SRA1593841 | Columbia University Irving Medical Center | Columbia University Irving Medical Center | 2 | 0.00031 | 0.89955 | 0.0001 | 0.28522 | 0.99991 | 0.74205 | 1.0 | 0.53119 | 101 | 101 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-02-21 | Undetermined | Undetermined | Brain | Nervous System |