run_metadata: 55673

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
55673	SRR10721218	SRX7397865	SRS5845643	SRP237948	PRJNA596232	RNA sequencing of zebrafish asxl1+/+ and asxl1 /	GSE142214	Transcriptome Analysis	ASXL1 gene is one of the most frequently mutated genes in malignant myeloid diseases. In patients ASXL1 mutations are usually heterozygous frameshift or non sense mutations leading to C terminal truncation. Here we generated an endogenous C terminal truncated Asxl1 mutant in zebrafish which is more comparable to human malignant leukemia patients. Our data showed that at embryonic stage neutrophil differentiation was explicitly blocked in our mutant. To understand the basis for the impairment of neutrophil differentiation in zebrafish asxl1 mutants we performed RNA seq of asxl1 mutants at 3dpf and their littermate controls. Similar with the phenotype we observed the expression of neutrophil markers were all included in down regulated genes. Nonetheless the expression of myeloid progenitor marker and macrophage marker were not impaired in asxl1 mutants. We also found inflammatory cytokine and matrix metalloproteinases were upregulated post mutated asxl1. It suggests that neutrophil deficiency may stimulate the expression of some inflammatory cytokines and enhances the inflammatory responds. Therefore transcriptome analysis mainly represented the disruption of neutrophil development. Overall design: 3 dpf dpf asxl1+/+ and asxl1 / embryos from asxl1+/ intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit. Sequencing was done on an Illumina NovaSeq sequencing platform to obtain 150bp 2 ´ 150 bp		pubmed:33483612		asxl1 MUT B	GSM4222803		tissue:3dpf embryo's tail\|Stage:3dpf\|genotype:asxl1 /	asxl1 MUT B	The reads were mapped onto the GRCz11 zebrafish reference genome using STAR Dobin et al. 2013. Raw read counts were for each gene were calculated with Ensembl annotation by Featurecounts Liao et al. 2014 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include feature counts for each Sample	3dpf embryo's tail	No treatments were applied prior to RNA extraction	3 dpf dpf asxl1+/+ and asxl1 / embryos from asxl1+/ intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.	Zebrafish were raised and maintained under standard conditions. Embryos were raised at 28.5°C and incubated in “egg water” containing 0.002% methylene blue as a fungicide. Embryos were collected and morphologically staged as described Kimmel et al. 1995. The mutants were based on an AB background.	Stage:3dpf\|genotype:asxl1 /	GSM4222803	GSM4222803: asxl1 MUT B; Danio rerio; RNA Seq	GSM4222803		1	3 dpf dpf asxl1+/+ and asxl1 / embryos from asxl1+/ intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.	GEO Accession:GSM4222803	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP237948			asxl1_MUT_B_1.fq.gz asxl1_MUT_B_2.fq.gz	fastq fastq	8539660200.0	28465534.0	GSM4222803 r1	0:150 1:150	A:2250292446;C:2015024018;G:2096676101;T:2177532680;N:134955	150	150			2250292446	2015024018	2096676101	2177532680	134955	SRX7397865	SRS5845643	SRA1013371	GEO	Laboratory of Developmental Biology and Regenerative Medicine, School of Medicine, South China University of Technology	2	0.9519	0.95085	0.07684	0.07685	0.71135	0.7138	0.43808	0.44748	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		China	2019-12-17	Larval	Larval	Tail	Multi-system