run_metadata: 67669

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
67669	SRR17259775	SRX13438132	SRS11337553	SRP351293	PRJNA788929	CXCR4 CXCL12 axis promotes the efficient T cell reconstitution by the HSPCs immigration	GSE190921	Transcriptome Analysis	T cells are essentially involved in safeguarding homeostasis through fighting against the pathogens and malignant cells. T cell immunodeficiency especially their perturbation in the severe infection irradiation chemotherapy and thymic atrophy in ageing is detrimental. Therefore strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here we constructed a T cells ablation model in Tgcoro1a:DenNTR zebrafish via administrating a proper volume of metronidazole MTZ. T cells completely recovered at 6.5 days post treatment dpt. The nascent regenerated T cells were mainly derived from the immigration of hematopoietic stem/progenitor cells HSPCs in the kidney the functional homologue of BM. cxcr4b but not ccr9 nor ccr7 was drastically unregulated in the responsive HSPCs. Functional interference of CXCR4 via both genetic and chemical assays yielded limited influence in T lymphopoiesis but notably delayed T cells regeneration by a destroyed HSPCs migration. In contrast hematopoietic providing cxcr4b in Tg:coro1a:cxcr4b accelerates thymus replenishment of HSPCs. Correspondingly Cxcl12b the ligand of Cxcr4 exhibited impressive increment presentation in the thymic epithelial cells of injured animals. Interfering or overacting Cxcl12b in either cxcl12b / mutants or Tghsp70:cxcl12b recapitulated the similarly compromised or promoted T cells recovery as that seen in Cxcr4b scenario. Therefore CXCR4 CXCL12 axis plays a crucial role in promoting thymocyte reconstitution but did not influence T cell development. Our study discloses a special role of CXCR4 CXCL12 signaling in promoting T cells recovery and provides a promising target to mitigate T cell immunodeficiency. Overall design: 6 Smart seq data of kidney hematopoietic cells in DMSO and MTZ treated zebrafish		pubmed:35483564		DMSO treated zebrafish larval kiney hematopoietic cells rep3	GSM5734066		source name:kidney hematopoietic cells\|genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	DMSO treated zebrafish larval kiney hematopoietic cells rep3	Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2 Genome build: GRCz11	kidney hematopoietic cells		The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.		genotype:WT\|tissue:kidney\|age:3.5 dpt/9 dpf	GSM5734066	GSM5734066: DMSO treated zebrafish larval kiney hematopoietic cells rep3; Danio rerio; RNA Seq	GSM5734066		1	The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tgcoro1a:DenNTR transgenic larvae by a 405 nm laser in an LSM880 confocal microscope for 30 seconds. post photoconversion approximately eighty zebrafish larvae were collected mixed dissected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was re suspended in PBS followed by cell sorting using flow cytometry Moflo XDP Beckman. A cDNA library was generated from fifty red Dendra2+ cells by using the Smart seq2 protocol.	GEO Accession:GSM5734066	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP351293		loader:fastq load.py	DMSO-3_1.fq.gz DMSO-3_2.fq.gz	fastq fastq	11408306700.0	38027689.0	GSM5734066 r1	0:150 1:150	A:3247281964;C:2443184752;G:2483245163;T:3234534644;N:60177	150	150			3247281964	2443184752	2483245163	3234534644	60177	SRX13438132	SRS11337553	SRA1345009	GEO	Lili laboratory, southwest university	2	0.85938	0.85997	0.14372	0.14405	0.81406	0.8145	0.54289	0.54626	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		China	2021-12-14	Larval	Larval	Kidney	Renal System