run_metadata: 55642
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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| 55642 | SRR10586524 | SRX7266915 | SRS5761459 | SRP234691 | PRJNA593445 | A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq] | GSE141427 | Transcriptome Analysis | Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000. | parent bioproject:PRJNA593433 | pubmed:32094115 | 16hpf Hindbrain scRNA seq | GSM4202680 | source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:16hpf|strain:LondonAB|genotype:wt|growth:25°C | 16hpf Hindbrain scRNA seq | 10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts | Dissected hindbrain and surrounding tissues | Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles | tissue:Dissected hindbrain and surrounding tissues|Stage:16hpf|strain:LondonAB|genotype:wt|growth:25°C | GSM4202680 | GSM4202680: 16hpf Hindbrain scRNA seq; Danio rerio; RNA Seq | GSM4202680 | 1 | Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles | GEO Accession:GSM4202680 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP234691 | loader:fastq load.py|options: readTypes=TTB read1PairFiles=TAM677A1 S2 L008 I1 001.fastq.gz read2PairFiles=TAM677A1 S2 L008 R1 001.fastq.gz read3PairFiles=TAM677A1 S2 L008 R2 001.fastq.gz | TAM677A1_S2_L008_R2_001.fastq.gz TAM677A1_S2_L008_R1_001.fastq.gz TAM677A1_S2_L008_I1_001.fastq.gz | fastq fastq fastq | 72155333460.0 | 343596826.0 | GSM4202680 r1 | 0:8 1:101 2:101 | A:16535121466;C:12722320120;G:13646437290;T:29245478028;N:5976556 | 8 | 101 | 101 | 16535121466 | 12722320120 | 13646437290 | 29245478028 | 5976556 | SRX7266915 | SRS5761459 | SRA1006557 | GEO | The Francis Crick Institute | 1 | 0.91053 | 0.09489 | 0.848 | 0.50461 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2019-12-04 | Segmentation | Embryo | Brain | Nervous System |