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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
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.   pubmed:38318374   1st round of regeneration GSM7988806   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°C. 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 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 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 µl 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’ 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.   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 µl 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     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     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   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure