run_metadata: 74417

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
74417	SRR23929941	SRX19740079	SRS17106153	SRP428435	PRJNA941866	Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish	GSE226841	Transcriptome Analysis	The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage		pubmed:37595046		10X 22 022 2 dy post double ablation	GSM7085296		source name:krt4 lineage traced cells in adult zebrafish pancreas\|genotype:WT\|tissue:pancreas\|cell type:krt4 lineage traced cells\|treatment:ablation\|time:2 dy post double ablation	10X 22 022 2 dy post double ablation	The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files	krt4 lineage traced cells in adult zebrafish pancreas	We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.	Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.		genotype:WT\|tissue:pancreas\|cell type:krt4 lineage traced cells\|treatment:ablation\|time:2 dy post double ablation	GSM7085296	GSM7085296: 10X 22 022 2 dy post double ablation; Danio rerio; RNA Seq	GSM7085296 r1	GSM7085296	1	Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP428435		loader:fastq load.py	P25452_5001_S1_L002_R1_001.fastq.gz P25452_5001_S1_L002_R2_001.fastq.gz	fastq fastq	44183541338.0	374436791.0	GSM7085296 r1	0:28 1:90	A:12516849477;C:9732461815;G:10343631784;T:11577097367;N:13500895	28	90			12516849477	9732461815	10343631784	11577097367	13500895	SRX19740079	SRS17106153	SRA1608504	Karolinska Institute	Karolinska Institute	2	0.00804	0.91216	0.00229	0.10832	0.9906	0.79539	0.33148	0.51054	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	10x		Sweden	2023-03-07	Adult	Adult	Pancreas	Endocrine System