{"database": "metadata", "table": "run_metadata", "rows": [[67670, "SRR17259774", "SRX13438131", "SRS11337554", "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", null, "pubmed:35483564", null, "DMSO treated zebrafish larval kiney hematopoietic cells rep2", "GSM5734065", null, "source name:kidney hematopoietic cells|genotype:WT|tissue:kidney|age:3.5 dpt/9 dpf", "DMSO treated zebrafish larval kiney hematopoietic cells rep2", "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", null, "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 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C 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.", null, "genotype:WT|tissue:kidney|age:3.5 dpt/9 dpf", "GSM5734065", "GSM5734065: DMSO treated zebrafish larval kiney hematopoietic cells rep2; Danio rerio; RNA Seq", "GSM5734065", null, "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 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C 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:GSM5734065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP351293", null, "loader:fastq load.py", "DMSO-2_1.fq.gz DMSO-2_2.fq.gz", "fastq fastq", 11556992700.0, 38523309.0, "GSM5734065 r1", "0:150 1:150", "A:3286230684;C:2481190727;G:2527388699;T:3262121371;N:61219", 150, 150, null, null, 3286230684, 2481190727, 2527388699, 3262121371, 61219, "SRX13438131", "SRS11337554", "SRA1345009", "GEO", "Lili laboratory, southwest university", 2, 0.89912, 0.8983, 0.14258, 0.14322, 0.81341, 0.81408, 0.5562, 0.55202, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2021-12-14", "Larval", "Larval", "Kidney", "Renal System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["67670"], "units": {}, "query_ms": 8.20512097561732}