run_metadata: 25134

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
25134	SRR25634297	SRX21361064	SRS18605556	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.		pubmed:40268889		KC001 scRNAseq	GSM7709161		source name:Pharyngeal arches\|genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf\|geo loc name:missing\|collection date:missing	KC001 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		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°C 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°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m 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 μm 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 m 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 3’ 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.		genotype:wild type\|tissue:Pharyngeal arches\|strain:AB\|developmental stage:26 hpf	GSM7709161	GSM7709161: KC001 scRNAseq; Danio rerio; RNA Seq	GSM7709161 r1	GSM7709161	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°C 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°C. The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m 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 μm 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 m 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP454944		loader:fastq load.py\|options: readTypes=TTBB read1PairFiles=KC001 S1 L004 I1 001.fastq.gz read2PairFiles=KC001 S1 L004 I2 001.fastq.gz read3PairFiles=KC001 S1 L004 R1 001.fastq.gz read4PairFiles=KC001 S1 L004 R2 001.fastq.gz	KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	69380677872.0	312525576.0	GSM7709161 r1	0:10 1:10 2:101 3:101	A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567	10	10	101	101	16018222868	11704492905	12161620273	23245625739	204567	SRX21361064	SRS18605556	SRA1692494	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	SangesLab Computational Genomics, NEUROSCIENCE, SISSA	2	0.00071	0.93976	0.0001	0.12725	0.99945	0.78457	0.75	0.50121	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x		Italy	2023-08-14	Pharyngula	Embryo	Pharyngeal Arch	Multi-system