run_metadata: 63444

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
63444	SRR13796911	SRX10181144	SRS8330083	SRP308406	PRJNA705198	Inflammation potentiates JMML like blood defects in Shp2 mutant Noonan syndrome	GSE167787	Transcriptome Analysis	Hematopoietic stem and progenitor cells derived from a zebrafish model of Noonan syndrome carrying a patient associated Shp2 D61G mutation display an expansion of monocyte/macrophage progenitors with an inflammatory gene expression signature. Overall design: CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:35535491		SBF 9	GSM5112478		source name:CHT\|tissue:Hematopoietic stem and progenitor cells\|developmental stage:5dpf\|sort day:2\|genotype:Ptpn11a D61G hom	SBF 9	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Genome build: zV9 Danio Rerio Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Supplementary files format and content: transcriptCounts.tsv	CHT		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Hematopoietic stem and progenitor cells\|developmental stage:5dpf\|sort day:2\|genotype:Ptpn11a D61G hom	GSM5112478	GSM5112478: SBF 9; Danio rerio; RNA Seq	GSM5112478		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5112478	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP308406			HUB-SF-009_HC3G3BGX9_S1_L004_R1_001.fastq.gz HUB-SF-009_HC3G3BGX9_S1_L004_R2_001.fastq.gz	fastq fastq	1839478166.0	21389281.0	GSM5112478 r4	0:26 1:60	A:451446429;C:337220595;G:370055154;T:679895438;N:860550	26	60			451446429	337220595	370055154	679895438	860550	SRX10181144	SRS8330083	SRA1200709	GEO	Hubrecht Institute	2	0.10617	0.88085	0.09686	0.21868	0.98498	0.81718	0.62816	0.5696	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq		Netherlands	2021-02-26	Larval	Larval	Blood	Hematopoietic System