{"database": "metadata", "table": "run_metadata", "rows": [[67811, "SRR17312072", "SRX13488771", "SRS11384713", "SRP352163", "PRJNA791663", "Single cell resolution of MET  and EMT like programs in osteoblasts during zebrafish fin regeneration", "GSE192498", "Transcriptome Analysis", "We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse  mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components  or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump  and in differentiating osteoblastic cells in the regenerate  the latter of which are enriched in EMT signatures. We also show that esrp1  a regulator of alternative splicing in epithelial cells that is associated with MET  is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration  and supports the contribution of MET  and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3", null, "pubmed:35169687", null, "5 dpa", "GSM5747967", null, "source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA", "5 dpa", "Base calls were converted to fastq format using Illumina's bcl2fastq v2.20  tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information  while the R2 reads contain the transcriptome sequence. In the demultiplexing process  the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted  and duplicates were removed using the UMI sequence  reverse transcription RT index  and read 2 end coordinate  tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices  the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes  gene annotations  and a gene count sparse matrix for each Sample", "adult caudal fin", null, "Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.", null, "strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA", "GSM5747967", "GSM5747967: 5 dpa; Danio rerio; RNA Seq", "GSM5747967 r1", "GSM5747967", "1", "Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP352163", null, "loader:fastq load.py|options:  appendBCtoName", "RK6.fq.gz", "fastq", 10033219500.0, 100332195.0, "GSM5747967 r1", "0:100", "A:3474987443;C:1873037986;G:1979251566;T:2705812216;N:130289", 100, null, null, null, 3474987443, 1873037986, 1979251566, 2705812216, 130289, "SRX13488771", "SRS11384713", "SRA1347953", "Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington", "Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington", 1, 0.71399, null, 0.43822, null, 0.84161, null, 0.72626, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2021-12-22", "Adult", "Adult", "Fin", "Surface Structure"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["67811"], "units": {}, "query_ms": 10.037398998974822}