run_metadata: 63109

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
63109	SRR13594957	SRX9989396	SRS8160231	SRP304100	PRJNA698538	Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing	GSE165888	Transcriptome Analysis	Plastic particles in water environment can adsorb heavy metals leading to combined toxicity to aquatic organisms. However current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs 50 µg/L lead Pb and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations including enterocytes macrophages neutrophils B cells T cells enteroendocrine cells and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However the Pb alone and combined exposures induced similar modes of action in the enterocytes including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.		pubmed:34861263		CK scRNA seq	GSM5057357		source name:intestine cells\|tissue:intestine single cell suspension\|age:16 wpf\|exposed pollutants:n1	CK scRNA seq	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcriptome. Only reads that are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells N see expect cells. Let m be a robust estimate of the maximum total UMI counts taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and if the reference contains multiple genomes for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix	intestine cells	Exposure solutions were prepared by adding 200μg/L PS NPs 50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days. post 21 d exposure zebrafish were collected and intestine were rapidly extracted on ice.	The isolated intestine tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.		tissue:intestine single cell suspension\|age:16 wpf\|exposed pollutants:n1	GSM5057357	GSM5057357: CK scRNA seq; Danio rerio; RNA Seq	GSM5057357		1	The isolated intestine tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.	GEO Accession:GSM5057357	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP304100			CK-5_S1_L003_R1_001.fastq.gz CK-5_S1_L003_R2_001.fastq.gz	fastq fastq	797925300.0	2659751.0	GSM5057357 r5	0:150 1:150	A:231261745;C:136517638;G:127031945;T:303086279;N:27693	150	150			231261745	136517638	127031945	303086279	27693	SRX9989396	SRS8160231	SRA1189975	GEO	School of the Environment, Nanjing university	2	0.01203	0.9069	0.0023	0.11051	0.99644	0.81884	0.53554	0.51319	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2021-02-01	Adult	Adult	Gut	Digestive System