run_metadata: 31680

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
31680	SRR28490925	SRX24093151	SRS20882447	SRP498465	PRJNA1093008	Distinct features of the regenerating heart uncovered through comparative single cell profiling	GSE262689	Other	Adult humans respond to heart injury by forming a permanent scar yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features we compared cardiac injury responses in zebrafish and medaka two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single cell transcriptional profiling to create a time resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach we identified several key features that distinguish cardiac injury response in the non regenerating medaka heart. By comparing immune responses to injury we found altered cell recruitment and a distinct pro inflammatory gene program in medaka leukocytes and an absence of the injury induced interferon response seen in zebrafish. In addition we found a lack of pro regenerative signals including nrg1 and retinoic acid from medaka endothelial and epicardial cells. Finally we identified alterations in the myocardial structure in medaka where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates. Overall design: scRNA seq of dissected ventricles from zebrafish and medaka fish before injury 3 days and 14 xxx post injury				zebrafish 3dpi rep3	GSM8173837		source name:Heart Ventricle\|tissue:Heart Ventricle\|treatment:3 xxx post injury\|geo loc name:missing\|collection date:missing	zebrafish 3dpi rep3	Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments and ASM223467v1 for Medaka. Assembly: GRCz11 ASM223467v1 Supplementary files format and content: Tab separated values files and matrix files	Heart Ventricle	Cryoinjuries were performed on the ventricle apex of both medaka and zebrafish as described previously González Rosa et al. 2011. Briefly 0.02% and 0.04% Tricaine MS 222 was used to anesthetize zebrafish and medaka respectively. Fish were mounted on a moist sponge. The ventricle apex was exposed by making a small thoracic incision using forceps and dissecting scissors. A cryoprobe was constructed as described previously using a 0.5 mm diameter copper wireGonzález Rosa and Mercader 2012. post submersion in liquid nitrogen for at least 2 minutes the probe was placed in contact with the ventricle apex for exactly 23 seconds. post injury fish were placed back into freshwater tanks to recover then transferred back into the fish facility for monitoring.	To prepare cells for scRNA seq adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer’s specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish and CAB medaka aged 6 month 18 month unless otherwise stated were used for all experiments. All zebrafish and medaka work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Heart Ventricle\|treatment:3 xxx post injury	GSM8173837	GSM8173837: zebrafish 3dpi rep3; Danio rerio; RNA Seq	GSM8173837 r1	GSM8173837	1	To prepare cells for scRNA seq adult fish were euthanized by immersion in ice cold water. post dissection and removal of hearts the remaining atrium and bulbus arteriosus tissue were cut away with scissors to isolate the ventricle. Ventricles were placed in PBS solution and gently squeezed with forceps to remove residual blood prior to digestion. Whole ventricles were placed Biology Open • Accepted manuscript in 200 µl dissociation solution containing 1mg/mL liberase DH Millipore Sigma cat# 5401089001 in 1X HBSS. Ventricles were digested at 37°C for 30 min on a benchtop shaker at 250RPM with additional pipetting every 5 min to break apart the tissue. post complete digestion the reaction was quenched with ice cold PBS/50% Fetal Bovine Serum and passed through a 40 µM strainer. The cells were then centrifuged at 250 RCF for 10 minutes at 4°C and resuspended in ice cold PBS with 0.04% Bovine Serum Albumin. Cells were then assessed for viability and dissociation quality using acridine orange and propidium iodide staining with a Nexcelom Cellometer automated cell imager. Each sample viability was assessed to be >85%. Cells were loaded onto a 10X Genomics Chromium controller and processed according to the manufacturer's specifications. cDNA libraries were prepared for sequencing on the Illumina Novaseq platform at a depth of approximately 400M reads/sample. Libraries wer constructed according to the manufacturer's protocol 10X chromium controller		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP498465		loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 I1 001.fastq.gz read2PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 I2 001.fastq.gz read3PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 R1 001.fastq.gz read4PairFiles=19630X6 220407 A00421 0430 AHL27JDSX3 S6 L004 R2 001.fastq.gz	19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_I1_001.fastq.gz 19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_I2_001.fastq.gz 19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_R1_001.fastq.gz 19630X6_220407_A00421_0430_AHL27JDSX3_S6_L004_R2_001.fastq.gz	fastq fastq fastq fastq	127733838606.0	645120397.0	GSM8173837 r1	0:10 1:10 2:28 3:150	A:33907907612;C:25406584124;G:25352400361;T:30160949616;N:3588953	10	10	28	150	33907907612	25406584124	25352400361	30160949616	3588953	SRX24093151	SRS20882447	SRA1835934	Gagnon, Biology, University of Utah	Gagnon, Biology, University of Utah												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2024-03-28	Adult	Adult	Heart	Cardiovascular System