run_metadata: 69499

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
69499	SRR18745505	SRX14845525	SRS12600427	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.		pubmed:36496511		IT325 P2 1	GSM6043270		source name:whole kidney marrow WKM\|tissue:whole kidney marrow WKM\|age:3 month\|genotype/variation:IT325 Mutant WKM cells	IT325 P2 1	For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2 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 collection. A ventral midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm 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	GSM6043270	GSM6043270: IT325 P2 1; Danio rerio; RNA Seq	GSM6043270 r1	GSM6043270	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× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP370089			IT325_P2_1_R1.fastq.gz IT325_P2_1_R2.fastq.gz	fastq fastq	2126689200.0	21266892.0	GSM6043270 r1	0:30 1:70	A:516252796;C:374159868;G:388671448;T:843235579;N:4369509	30	70			516252796	374159868	388671448	843235579	4369509	SRX14845525	SRS12600427	SRA1403848	Sagar, Department of Internal Medicine II, University Medical Center Freiburg	Sagar, Department of Internal Medicine II, University Medical Center Freiburg	2	0.64115	0.86798	0.58644	0.22539	0.99188	0.82065	0.79141	0.64477	30	70	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	celseq		Germany	2022-04-13	Adult	Adult	Kidney	Renal System