run_metadata: 66718

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
66718	SRR16490737	SRX12693840	SRS10644723	SRP342163	PRJNA772751	Single cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species	GSE186158	Other	We utilized single cell RNA sequencing scRNA seq to carry out comparative transcriptome analysis in various immune cells from the spleens across seven vertebrate species. Overall design: High dimensional single cell RNA sequencing 10X Genomics was used to profile the transcriptomes of total immune cells isolated from seven organism spleens.		pubmed:36871615		Fish	GSM5639492		tissue:Fish splenocytes\|cell type:Splenocytes	Fish	The 10x Genomics Cell Ranger 3.0.1 version pipeline was used to demultiplex raw files into FASTQ files extract barcodes and UMI filter and map reads to the corresponding reference genome and generate a matrix containing UMI counts. A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings. Genome build: Fish:GRCz11 Frog:Xenopus laevis v2 Mouse:GRCm38 Rat:Rnor 6.0 Pig:Sscrofa11 Monkey:Mmul 8 Human:GRCh38 Supplementary files format and content: Supplementary files format and content: filtered feature bc matrix.tar contains counts matrix stored in the Market Exchange Format for sparse matrices.	Fish splenocytes	Splenocytes were sorted from the spleens of seven vertebrate species	Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer 2% FBS in PBS then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK Ammonium Chloride Potassium Lysing Buffer to remove the red blood cells. post washing with 10 ml cold FACS buffer the remaining cells were stained with 7AAD Part 76332; Lot B226294 Biolegend for 30 min at 4 °C then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter BD Biosciences. Sorted 7AAD cells with a viability higher than 90% were used for 10X genomics scRNA seq. Finally libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit 300 cycles. RNA libraries were prepared for sequencing using standard Illumina protocols		cell type:Splenocytes	GSM5639492	GSM5639492: Fish; Danio rerio; RNA Seq	GSM5639492 r1	GSM5639492	1	Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer 2% FBS in PBS then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK Ammonium Chloride Potassium Lysing Buffer to remove the red blood cells. post washing with 10 ml cold FACS buffer the remaining cells were stained with 7AAD Part 76332; Lot B226294 Biolegend for 30 min at 4 °C then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter BD Biosciences. Sorted 7AAD cells with a viability higher than 90% were used for 10X genomics scRNA seq. Finally libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit 300 cycles. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP342163			fish5_S1_L002_R1_001.fastq.gz fish5_S1_L002_R2_001.fastq.gz	fastq fastq	128052138306.0	424013703.0	GSM5639492 r1	0:151 1:151	A:31857061588;C:30793041207;G:30850699878;T:34545754656;N:5580977	151	151			31857061588	30793041207	30850699878	34545754656	5580977	SRX12693840	SRS10644723	SRA1377133	xian jiaotong university	xian jiaotong university	2	0.06618	0.94142	0.01504	0.09555	0.96631	0.81266	0.69482	0.58057	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2021-10-19	Undetermined	Undetermined	Multi-tissue	Multi-system