run_metadata: 4421

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
4421	ERR1427362	ERX1497894	ERS1183196	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#35	SAMEA4012086	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012086\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#35\|broker name:ArrayExpress\|common name:zebrafish\|fsc:26079\|gfp:93\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#35\|ssc:4930\|tissue:Heart\|well:C5									Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#35	LCK 7#35	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 26079:fsc\|Experimental Factor: 4930:ssc\|Experimental Factor: 93:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_35_mod.bam LCK_7_35.cram	bam cram			E MTAB 4617:LCK 7#35	0:125 1:125	A:139844227;C:137312069;G:126169914;T:149207606;N:69934	125	125			139844227	137312069	126169914	149207606	69934	ERX1497894		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.19648	0.19308	0.05501	0.05463	0.98149	0.982	0.60289	0.60804	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq		Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System