run_metadata: 61429
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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| 61429 | SRR12749699 | SRX9221655 | SRS7455356 | SRP285950 | PRJNA666695 | Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae | GSE158851 | Transcriptome Analysis | Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets previously described by our group to govern zebrafish fin regeneration and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP. | pubmed:34732706;pubmed:35664055 | Uncut caudal fin scRNA | GSM4812244 | source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation | Uncut caudal fin scRNA | Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'. | caudal fin | Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. | tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation | GSM4812244 | GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq | GSM4812244 | 1 | Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222 Sigma in zebrafish water. Approximately 150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument. | GEO Accession:GSM4812244 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP285950 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=Uncut S8 L001 R1 001.fastq.gz read2PairFiles=Uncut S8 L001 R2 001.fastq.gz read3PairFiles=Uncut S8 L001 I1 001.fastq.gz | Uncut_S8_L001_I1_001.fastq.gz Uncut_S8_L001_R1_001.fastq.gz Uncut_S8_L001_R2_001.fastq.gz | fastq fastq fastq | 18909629967.0 | 153736829.0 | GSM4812244 r1 | 0:28 1:87 2:8 | A:5220924848;C:4279280050;G:4788532540;T:4619612909;N:1279620 | 28 | 87 | 8 | 5220924848 | 4279280050 | 4788532540 | 4619612909 | 1279620 | SRX9221655 | SRS7455356 | SRA1136463 | GEO | Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm | 1 | 0.63376 | 0.11724 | 0.8393 | 0.55679 | 87 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | France | 2020-09-30 | Larval | Larval | Fin | Surface Structure |