run_metadata: 64268

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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
64268	SRR14428594	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354		scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502		tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell three prime Library produces a standard Illumina BCL data output folder. The BCL data includes the paired end Read 1 containing the 16 bp 10x Barcode and 10 bp UMI and Read 2 and the sample index in the i7 index read.	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP318543		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L002 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L002 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L002 R2 001.fastq.gz	SU4_DRT_S2_L002_I1_001.fastq.gz SU4_DRT_S2_L002_R1_001.fastq.gz SU4_DRT_S2_L002_R2_001.fastq.gz	fastq fastq fastq	7355984272.0	57921136.0	GSM5282502 r2	0:8 1:28 2:91	A:2029150464;C:1629831151;G:1703134376;T:1991639472;N:2228809	8	28	91		2029150464	1629831151	1703134376	1991639472	2228809	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93751		0.14654		0.80048		0.53568		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x		United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system