{"database": "metadata", "table": "run_metadata", "rows": [[25133, "SRR25634296", "SRX21361065", "SRS18605555", "SRP454944", "PRJNA1005241", "Nkx2.7 is a Conserved Regulator of Craniofacial Development", "GSE240780", "Transcriptome Analysis", "Pharyngeal arch cells are comprised of endoderm  mesoderm  and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 /  samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 /  embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR  which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 /  samples were pooled for submission.", null, "pubmed:40268889", null, "KC002  scRNAseq", "GSM7709162", null, "source name:Pharyngeal arches|genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing", "KC002  scRNAseq", "The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files", "Pharyngeal arches", null, "From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28\u00b0C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4\u00b0C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 \uf06dm cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 \u03bcm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 \uf06dm  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf", "GSM7709162", "GSM7709162: KC002  scRNAseq; Danio rerio; RNA Seq", "GSM7709162 r1", "GSM7709162", "1", "From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28\u00b0C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4\u00b0C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 \uf06dm cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 \u03bcm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 \uf06dm  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP454944", null, "loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=KC002 S1 L004 I1 001.fastq.gz   read2PairFiles=KC002 S1 L004 I2 001.fastq.gz   read3PairFiles=KC002 S1 L004 R1 001.fastq.gz   read4PairFiles=KC002 S1 L004 R2 001.fastq.gz", "KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 65825988564.0, 296513462.0, "GSM7709162 r1", "0:10 1:10 2:101 3:101", "A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035", 10, 10, 101, 101, 14990994149, 11485312838, 11921291570, 21497933732, 187035, "SRX21361065", "SRS18605555", "SRA1692494", "SangesLab Computational Genomics, NEUROSCIENCE, SISSA", "SangesLab Computational Genomics, NEUROSCIENCE, SISSA", 2, 0.00059, 0.93473, 2e-05, 0.14487, 0.99949, 0.78364, 0.5, 0.52799, 101, 101, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Italy", "2023-08-14", "Pharyngula", "Embryo", "Pharyngeal Arch", "Multi-system"]], "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": ["25133"], "units": {}, "query_ms": 11.9688820122974}