run_metadata: 59203

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
59203	SRR11777183	SRX8330061	SRS6649548	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227		dominant 1	GSM4547700		tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547700	GSM4547700: dominant 1; Danio rerio; RNA Seq	GSM4547700		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547700	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP261272		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample6 S6 L001 I1 001.fastq.gz read2PairFiles=sample6 S6 L001 R1 001.fastq.gz read3PairFiles=sample6 S6 L001 R2 001.fastq.gz	sample6_S6_L001_R2_001.fastq.gz sample6_S6_L001_R1_001.fastq.gz sample6_S6_L001_I1_001.fastq.gz	fastq fastq fastq	35787988152.0	284031652.0	GSM4547700 r2	0:8 1:26 2:92	A:9781991861;C:8320736351;G:8552750572;T:9130655372;N:1853996	8	26	92		9781991861	8320736351	8552750572	9130655372	1853996	SRX8330061	SRS6649548	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95998		0.0809		0.84891		0.53314		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system