run_metadata: 74782

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
74782	SRR24042933	SRX19844906	SRS17204004	SRP430475	PRJNA951376	Spic is required for the differentiation of metaphocyte progenitor cells	GSE228732	Transcriptome Analysis	Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings	parent bioproject:PRJNA951389	pubmed:37148242		mutant gill 3	GSM7135706		source name:gill\|tissue:gill\|strain:Tgspic:EGFP; mpeg1:DsRedx\|cell type:spic:EGFP+mpeg1:DsRedx cells\|genotype:mutant\|Stage:adult	mutant gill 3	Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample	gill		The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.		tissue:gill\|strain:Tgspic:EGFP; mpeg1:DsRedx\|cell type:spic:EGFP+mpeg1:DsRedx cells\|genotype:mutant\|Stage:adult	GSM7135706	GSM7135706: mutant gill 3; Danio rerio; RNA Seq	GSM7135706 r1	GSM7135706	1	The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP430475		loader:fastq load.py	mut_gill_3_R1.fq.gz mut_gill_3_R2.fq.gz	fastq fastq	5914269900.0	19714233.0	GSM7135706 r1	0:150 1:150	A:1744887146;C:1199785696;G:1139441688;T:1829560268;N:595102	150	150			1744887146	1199785696	1139441688	1829560268	595102	SRX19844906	SRS17204004	SRA1614434	WEN lab, Life Science, Hong Kong University of Science and Technology	WEN lab, Life Science, Hong Kong University of Science and Technology	2	0.81829	0.82058	0.35062	0.34936	0.82822	0.82818	0.45594	0.45957	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq		China	2023-04-02	Adult	Adult	Gill	Respiratory System