{"database": "metadata", "table": "run_metadata", "rows": [[69503, "SRR18745509", "SRX14845521", "SRS12600423", "SRP370089", "PRJNA826497", "Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish", "GSE200756", "Transcriptome Analysis", "The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.", null, "pubmed:36496511", null, "IT325 P1 10", "GSM6043266", null, "source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells", "IT325 P1 10", "For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2\u200b was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.", "whole kidney marrow WKM", "No Treatment was performed.", "Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney\u00a0collection. A\u00a0ventral  midline incision was made\u00a0and kidney were dissected and placed into ice cold 0.9\u00d7 PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 \u03bcm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol", "Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.", "tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells", "GSM6043266", "GSM6043266: IT325 P1 10; Danio rerio; RNA Seq", "GSM6043266 r1", "GSM6043266", "1", "Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9\u00d7 PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 \u03bcm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP370089", null, null, "IT325_P1_10_R1.fastq.gz IT325_P1_10_R2.fastq.gz", "fastq fastq", 1586719700.0, 15867197.0, "GSM6043266 r1", "0:30 1:70", "A:401941369;C:273093096;G:285633018;T:621609734;N:4442483", 30, 70, null, null, 401941369, 273093096, 285633018, 621609734, 4442483, "SRX14845521", "SRS12600423", "SRA1403848", "Sagar, Department of Internal Medicine II, University Medical Center Freiburg", "Sagar, Department of Internal Medicine II, University Medical Center Freiburg", 2, 0.4951, 0.81744, 0.4671, 0.28736, 0.99247, 0.8337, 0.59663, 0.70252, 30, 70, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2022-04-13", "Adult", "Adult", "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": ["69503"], "units": {}, "query_ms": 15.284023999811325}