{"database": "metadata", "table": "run_metadata", "rows": [[29200, "SRR27321693", "SRX22998810", "SRS19963380", "SRP479569", "PRJNA1055522", "Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin", "GSE251828", "Transcriptome Analysis", "This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal  bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition  the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings  together with the identification of novel fin regenerate markers  advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration  we harvested single cells and FACS enriched for siam+  shha+  osterix+  RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.", null, "pubmed:38318374", null, "1st round of regeneration", "GSM7988806", null, "source name:Fin|tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing", "1st round of regeneration", "A reference based on GRCz10  Ensembl annotation e98 was created  by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format.", "Fin", "Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa  cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS  Roche #10269638001 for 10 min at 28\u00b0C. The sample was pipetted slowly up and down with an elongated  flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 \u00b5m cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2  Gibco #12082739. post centrifugation 15 minutes  1800 rpm  4\u00b0C  the supernatant was discarded and the remaining cell pellet resuspended in 500 \u00b5l 2% BSA in PBS. Calcein violet 1\u00b5l 10mM  Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet  GFP and mCherry+ cells were collected in 50 \u00b5l 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system  10X library preparation according to the manufacturer's instructions.", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3\u2019 RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer\u2019s guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "tissue:Fin|cell type:siam+  shha+  osterix+  RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation", "GSM7988806", "GSM7988806: 1st round of regeneration; Danio rerio; RNA Seq", "GSM7988806 r1", "GSM7988806", "1", "For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 \u00b5l of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short  the droplets were directly subjected to reverse transcription  the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles  it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent  30 ng cDNA were used to prepare sc RNA seq libraries   involving fragmentation  dA Tailing  adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification  both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively  thus generating 60 90 mio. fragments for the transcriptome library on average.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP479569", null, null, "L32023_osteoblasts_reg1_R1.fastq.gz L32023_osteoblasts_reg1_R2.fastq.gz", "fastq fastq", 15070528207.0, 181572629.0, "GSM7988806 r1", "0:26 1:57", "A:4238593010;C:3314457079;G:3500292725;T:4013398538;N:3786855", 26, 57, null, null, 4238593010, 3314457079, 3500292725, 4013398538, 3786855, "SRX22998810", "SRS19963380", "SRA1774238", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", "Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden", 2, 0.01031, 0.92947, 0.00392, 0.17331, 0.98526, 0.81815, 0.4321, 0.54688, 26, 57, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-12-21", "Undetermined", "Undetermined", "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": ["29200"], "units": {}, "query_ms": 11.463574002846144}