run_metadata: 74952

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
74952	SRR24203797	SRX20000418	SRS17345141	SRP433186	PRJNA956844	Gene expression profile at single cell level of sclerotome derived fibroblasts from 52 hpf transgenic zebrafish trunks.	GSE229939	Other	The sclerotome region of the somite labelled by nkx3.1:Gal4 VP16; UAS:NTR mCherry gives rise to numerous fibroblasts populations in the zebrafish trunk. We performed single cell RNA sequencing scRNA seq on sclerotome derived fibroblasts from 52 hpf embryos to determine population heterogeneity and plasticity. Overall design: scRNA seq was performed on mCherry positive cells from trunk regions of 52 hpf Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264 zebrafish isolated by Fluorescence activated cell sorting FACS. The single cell library was prepared using 10X Genomics three prime gene expression profiling droplet based scRNA seq technology v3.1 chemistry according to manufacturer's protocols. Sequencing was performed on the using the Illumina NovaSeq S2 flow cell.		pubmed:37967180		52 hpf mCherry positive	GSM7181573		source name:zebrafish trunks dissected at the beginning of the yolk extension\|cell type:Sclerotome derived cells\|tissue:zebrafish trunks dissected at the beginning of the yolk extension\|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264\|age:52 hpf	52 hpf mCherry positive	A custom zebrafish transcriptome was prepared using V4.3.2 GTFs Lawson et al. 2021 and the GRCz11 Danio rerio reference genome with appended mCherry sequence using standard CellRanger mkgtf and mkref pipelines. FASTQs were then filtered and aligned to the reference using Cellranger count. All pipelines used 10X GEnomics CellRanger v5.0.0 software. Downstream quality control normalization dimension reduction clustering and analysis was performed in R using Seurat v4.0.0. Assembly: GRCz11 Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz features.tsv.gz matrix.mtx.gz	zebrafish trunks dissected at the beginning of the yolk extension		About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco’s phosphate buffered saline ThermoFisher Scientific and strained. Live mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank’s Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics 3’ gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer’s protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles	Zebrafish embryos were raised at 28.5 °C. Embryos older than 24 hours were grown in fish water with added 1 phenyl 2 thiourea PTU to prevent pigmentation.	cell type:Sclerotome derived cells\|tissue:zebrafish trunks dissected at the beginning of the yolk extension\|strain:Tg BACnkx3.1:Gal4 VP16ca101; TgUAS:NTR mCherryca264\|age:52 hpf	GSM7181573	GSM7181573: 52 hpf mCherry positive; Danio rerio; RNA Seq	GSM7181573 r1	GSM7181573	1	About 140 hpf 52 hpf nkx3.1NTR mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped and dissolved tissue was washed with 1% FBS solution in 1x DPBS Dulbecco's phosphate buffered saline ThermoFisher Scientific and strained. Live mCherry+ cells were collected by fluorescence activated cell sorting FACS. Sorted cells were resuspended in 50 μl HBSS Hank's Balanced Salt Solution + 2% BSA Bovine Serum Albumin. 15 000 live mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics three prime gene expression profiling droplet based scRNA seq kit v3.1 chemistry according to manufacturer's protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP433186		loader:fastq load.py	AR_2_S5_L001_I1_001.fastq.gz AR_2_S5_L001_R1_001.fastq.gz AR_2_S5_L001_R2_001.fastq.gz	fastq fastq fastq	11926942872.0	93912936.0	GSM7181573 r2	0:8 1:28 2:91	A:2430702466;C:1919825027;G:2264443130;T:1930929426;N:177127	8	28	91		2430702466	1919825027	2264443130	1930929426	177127	SRX20000418	SRS17345141	SRA1623336	Department of Biochemistry and Molecular Biology, University of Calgary	Department of Biochemistry and Molecular Biology, University of Calgary	1	0.85561		0.24037		0.84678		0.66835		91		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Canada	2023-04-18	Hatching	Embryo	Trunk	Surface Structure