metadata: run_metadata: 18 rows where experiment.library_selection = "PCR", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and experiment.platform = "ILLUMINA"

18 rows where experiment.library_selection = "PCR", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and experiment.platform = "ILLUMINA"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
28513	28513	SRR31643557	SRX27006657	SRS23471106	SRP467901	PRJNA1026724	vertebrate lungs	PRJNA1026724	Other	We provide comprehensive datasets including RNA Seq and single cell RNA sequencing scRAN seq of multiple tissues for white spotted bamboo shark scRNA seq of multiple tissues of the African lungfish and Senegal bichir genome of the bearded dragon scRAN seq of African bullfrog lung and central bearded dragon lung and H3k27ac and H3k4me1 CUT&Tag sequencing data of chicken embryonic lungs from stage E9 to study the origin and evelution of vertebrate lungs.	pubmed:39953253			zebrafish	strain:Cyprinidae\|age:adult\|collection date:2021 09\|geo loc name:China: Wuhan city Wuhan Province\|sex:not collected\|tissue:swim bladder\|BioSampleModel:Model organism or animal	scRNA Seq of zebrafish :swim blader	zebrafish swimbladder	zebrafish swimbladder	sequencing for single cell gene expression	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP467901	Dr_Sb-3_S1_L003_R2_001.fastq.gz Dr_Sb-3_S1_L003_R1_001.fastq.gz Dr_Sb-2_S1_L001_R2_001.fastq.gz Dr_Sb-2_S1_L001_R1_001.fastq.gz Dr_Sb-1_S1_L001_R2_001.fastq.gz Dr_Sb-1_S1_L001_R1_001.fastq.gz	fastq fastq fastq fastq fastq fastq			Dr Sb 1 S1 L001 R1 001.fastq.gz										SRX27006657		SRA2029673	Northwestern Polytechnical University\|School of Ecology and Environment	Northwestern Polytechnical University															illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2024-12-08	Adult	Adult	Swim Bladder	Swim Bladder
33615	33615	SRR30272850	SRX25733949	SRS22373737	SRP526812	PRJNA1148907	Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio	PRJNA1148907	Other	The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS	pubmed:39947082		PFOS S2	Sample2	strain:Tgins:GFP zebrafish on an AB wildtype background\|age:72 hpf\|dev stage:protruding mouth stage\|collection date:2023 01 03\|geo loc name:USA: Massachusetts\|sex:NA\|tissue:whole body cells\|treatment:PFOS 16 uM\|BioSampleModel:Model organism or animal	PFOS	PFOS	PFOS	PFOS S2 scRNAseq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP526812	G194-S2-PFOS_S2_L001_R1_001.fastq.gz G194-S2-PFOS_S2_L001_R2_001.fastq.gz G194-S2-PFOS_S2_L002_R1_001.fastq.gz G194-S2-PFOS_S2_L002_R2_001.fastq.gz G194-S2-PFOS_S2_L003_R1_001.fastq.gz G194-S2-PFOS_S2_L003_R2_001.fastq.gz G194-S2-PFOS_S2_L004_R1_001.fastq.gz G194-S2-PFOS_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	21751958340.0	184338630.0	G194 S2 PFOS S2 L001 R1 001.fastq.gz	0:28 1:90	A:6239773453;C:4634671870;G:5196638658;T:5672561386;N:8312973	28	90	6239773453	4634671870	5196638658	5672561386	8312973	SRX25733949	SRS22373737	SRA1949185	University of Massachusetts Amherst\|Environmental Health Sciences	University of Massachusetts Amherst	2	0.01021	0.92344	0.00451	0.22962	0.99328	0.79847	0.28896	0.51751	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2024-08-16	Larval	Larval	Trunk	Surface Structure
33616	33616	SRR30272851	SRX25733948	SRS22373736	SRP526812	PRJNA1148907	Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio	PRJNA1148907	Other	The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS	pubmed:39947082		DMSO S1	Sample1	strain:Tgins:GFP zebrafish on an AB wildtype background\|age:72 hpf\|dev stage:protruding mouth stage\|collection date:2023 01 03\|geo loc name:USA: Massachusetts\|sex:NA\|tissue:whole body cells\|treatment:DMSO 0.01%\|BioSampleModel:Model organism or animal	DMSO	DMSO	DMSO	DMSO S1 scRNAseq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP526812	G194-S1-DMSO_S1_L001_R1_001.fastq.gz G194-S1-DMSO_S1_L001_R2_001.fastq.gz G194-S1-DMSO_S1_L002_R1_001.fastq.gz G194-S1-DMSO_S1_L002_R2_001.fastq.gz G194-S1-DMSO_S1_L003_R1_001.fastq.gz G194-S1-DMSO_S1_L003_R2_001.fastq.gz G194-S1-DMSO_S1_L004_R1_001.fastq.gz G194-S1-DMSO_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	21636838838.0	183363041.0	G194 S1 DMSO S1 L001 R1 001.fastq.gz	0:28 1:90	A:6175214014;C:4647929260;G:5248646646;T:5556827078;N:8221840	28	90	6175214014	4647929260	5248646646	5556827078	8221840	SRX25733948	SRS22373736	SRA1949185	University of Massachusetts Amherst\|Environmental Health Sciences	University of Massachusetts Amherst	2	0.01048	0.92488	0.00455	0.20966	0.99358	0.81464	0.28056	0.57876	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2024-08-16	Larval	Larval	Trunk	Surface Structure
58873	58873	SRR11509894	SRX8082006	SRS6450124	SRP255712	PRJNA623798	Single cell lineage tracing on endogenous scarring sites scLOESS	PRJNA623798	Other	Lineage recording of zebrafish embryogenesis reveals early cell fate commitment		1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. 3 independent replicates in total.	Target specific Amplification of Single Cell cDNA Library	SCC	strain:AB line\|age:7dpf\|dev stage:larvae\|sex:not applicable\|tissue:Whole organism\|collection date:2018 07 26\|BioSampleModel:Model organism or animal	Single cell cDNA library Amplicon of zebrafish larva replicate 3	SCC replicate3	SCC replicate3	1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. PCR replicate 3.	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP255712	SCC-replicate3_R1.fq.gz SCC-replicate3_R2.fq.gz	fastq fastq	14811756300.0	49372521.0	SCC replicate3 R1.fq.gz	0:150 1:150	A:3255250699;C:3018244265;G:3088919277;T:5446140655;N:3201404	150	150	3255250699	3018244265	3088919277	5446140655	3201404	SRX8082006	SRS6450124	SRA1063780	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.01015	0.97122	0.00049	0.00158	0.99841	0.97569	0.54867	0.48858	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2020-04-10	Larval	Larval	Whole Organism	All anatomical structures
58874	58874	SRR11509895	SRX8082005	SRS6450124	SRP255712	PRJNA623798	Single cell lineage tracing on endogenous scarring sites scLOESS	PRJNA623798	Other	Lineage recording of zebrafish embryogenesis reveals early cell fate commitment		1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. 3 independent replicates in total.	Target specific Amplification of Single Cell cDNA Library	SCC	strain:AB line\|age:7dpf\|dev stage:larvae\|sex:not applicable\|tissue:Whole organism\|collection date:2018 07 26\|BioSampleModel:Model organism or animal	Single cell cDNA library Amplicon of zebrafish larva replicate 2	SCC replicate2	SCC replicate2	1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. PCR replicate 2.	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP255712	SCC-replicate2_R2.fq.gz SCC-replicate2_R1.fq.gz	fastq fastq	19858547700.0	66195159.0	SCC replicate2 R1.fq.gz	0:150 1:150	A:4363166112;C:4066433314;G:4155737160;T:7269480395;N:3730719	150	150	4363166112	4066433314	4155737160	7269480395	3730719	SRX8082005	SRS6450124	SRA1063780	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.025	0.97152	0.00079	0.00143	0.99746	0.97668	0.74358	0.46727	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2020-04-09	Larval	Larval	Whole Organism	All anatomical structures
58875	58875	SRR11509896	SRX8082004	SRS6450124	SRP255712	PRJNA623798	Single cell lineage tracing on endogenous scarring sites scLOESS	PRJNA623798	Other	Lineage recording of zebrafish embryogenesis reveals early cell fate commitment		1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. 3 independent replicates in total.	Target specific Amplification of Single Cell cDNA Library	SCC	strain:AB line\|age:7dpf\|dev stage:larvae\|sex:not applicable\|tissue:Whole organism\|collection date:2018 07 26\|BioSampleModel:Model organism or animal	Single cell cDNA library Amplicon of zebrafish larva replicate 1	SCC replicate1	SCC replicate1	1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles and purified amplicons were pooled into an equimolar mixture. PCR replicate 1.	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP255712	SCC-replicate1_R1.fq.gz SCC-replicate1_R2.fq.gz	fastq fastq	18191440200.0	60638134.0	SCC replicate1 R1.fq.gz	0:150 1:150	A:3994446536;C:3726446852;G:3814798796;T:6652431833;N:3316183	150	150	3994446536	3726446852	3814798796	6652431833	3316183	SRX8082004	SRS6450124	SRA1063780	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.03094	0.97334	0.00045	0.00127	0.99774	0.97824	0.80981	0.45378	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2020-04-09	Larval	Larval	Whole Organism	All anatomical structures
61523	61523	SRR12858253	SRX9325184	SRS7549492	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Day	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Day\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Day	3Day 2 S6	3Day 2 S6	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Day_2_S6_L004_R1_001.fastq.gz 3Day_2_S6_L004_R2_001.fastq.gz	fastq fastq	76033651818.0	251767059.0	3Day 2 S6 L004 R1 001.fastq.gz	0:151 1:151	A:35535267340;C:11863415027;G:11773502422;T:16858157612;N:3309417	151	151	35535267340	11863415027	11773502422	16858157612	3309417	SRX9325184	SRS7549492	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.86148	0.0	0.22304	1.0	0.7582		0.53846	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61524	61524	SRR12858254	SRX9325183	SRS7549492	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Day	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Day\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Day	3Day 1 S5	3Day 1 S5	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Day_1_S5_L004_R1_001.fastq.gz 3Day_1_S5_L004_R2_001.fastq.gz	fastq fastq	59092751626.0	195671363.0	3Day 1 S5 L004 R1 001.fastq.gz	0:151 1:151	A:27630588655;C:9241106126;G:9168471456;T:13050007147;N:2578242	151	151	27630588655	9241106126	9168471456	13050007147	2578242	SRX9325183	SRS7549492	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.86271	0.0	0.22343	1.0	0.76023		0.54977	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61525	61525	SRR12858255	SRX9325182	SRS7549493	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Hour	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Hour\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Hours	3Hour 4 S12	3Hour 4 S12	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Hour_4_S12_L004_R1_001.fastq.gz 3Hour_4_S12_L004_R2_001.fastq.gz	fastq fastq	72128136780.0	238834890.0	3Hour 4 S12 L004 R1 001.fastq.gz	0:151 1:151	A:33932689920;C:11046769968;G:10941298685;T:16204223580;N:3154627	151	151	33932689920	11046769968	10941298685	16204223580	3154627	SRX9325182	SRS7549493	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.84197	0.0	0.22466	1.0	0.78441		0.56868	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61526	61526	SRR12858256	SRX9325181	SRS7549493	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Hour	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Hour\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Hours	3Hour 3 S11	3Hour 3 S11	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Hour_3_S11_L004_R1_001.fastq.gz 3Hour_3_S11_L004_R2_001.fastq.gz	fastq fastq	80705527190.0	267236845.0	3Hour 3 S11 L004 R1 001.fastq.gz	0:151 1:151	A:37985436560;C:12358793423;G:12237346212;T:18120396893;N:3554102	151	151	37985436560	12358793423	12237346212	18120396893	3554102	SRX9325181	SRS7549493	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.84472	0.0	0.22522	1.0	0.78293		0.57384	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61527	61527	SRR12858257	SRX9325180	SRS7549493	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Hour	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Hour\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Hours	3Hour 2 S10	3Hour 2 S10	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Hour_2_S10_L004_R1_001.fastq.gz 3Hour_2_S10_L004_R2_001.fastq.gz	fastq fastq	76448858632.0	253141916.0	3Hour 2 S10 L004 R1 001.fastq.gz	0:151 1:151	A:35936389130;C:11685225790;G:11595239085;T:17228685305;N:3319322	151	151	35936389130	11685225790	11595239085	17228685305	3319322	SRX9325180	SRS7549493	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.84222	0.0	0.22514	1.0	0.78309		0.56453	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61528	61528	SRR12858258	SRX9325179	SRS7549493	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Hour	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Hour\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Hours	3Hour 1 S9	3Hour 1 S9	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Hour_1_S9_L004_R1_001.fastq.gz 3Hour_1_S9_L004_R2_001.fastq.gz	fastq fastq	74702264584.0	247358492.0	3Hour 1 S9 L004 R1 001.fastq.gz	0:151 1:151	A:35096290154;C:11422923493;G:11335995120;T:16843790763;N:3265054	151	151	35096290154	11422923493	11335995120	16843790763	3265054	SRX9325179	SRS7549493	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.84313	0.0	0.2256	1.0	0.78514		0.57158	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61529	61529	SRR12858259	SRX9325178	SRS7549491	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish intranasal PBS	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal PBS\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal PBS	Control 4 S4	Control 4 S4	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	Control_4_S4_L004_R1_001.fastq.gz Control_4_S4_L004_R2_001.fastq.gz	fastq fastq	63748002502.0	211086101.0	Control 4 S4 L004 R1 001.fastq.gz	0:151 1:151	A:29580785771;C:10210575747;G:10201571462;T:13752296624;N:2772898	151	151	29580785771	10210575747	10201571462	13752296624	2772898	SRX9325178	SRS7549491	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.87565	0.0	0.22003	1.0	0.76808		0.5449	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61530	61530	SRR12858260	SRX9325177	SRS7549491	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish intranasal PBS	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal PBS\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal PBS	Control 3 S3	Control 3 S3	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	Control_3_S3_L004_R1_001.fastq.gz Control_3_S3_L004_R2_001.fastq.gz	fastq fastq	59006583476.0	195386038.0	Control 3 S3 L004 R1 001.fastq.gz	0:151 1:151	A:27374753929;C:9460015806;G:9444431483;T:12724779257;N:2603001	151	151	27374753929	9460015806	9444431483	12724779257	2603001	SRX9325177	SRS7549491	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.87809	0.0	0.22265	1.0	0.77141		0.54249	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61531	61531	SRR12858261	SRX9325176	SRS7549492	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Day	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Day\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Day	3Day 2 S8	3Day 2 S8	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Day_4_S8_L004_R1_001.fastq.gz 3Day_4_S8_L004_R2_001.fastq.gz	fastq fastq	84540262488.0	279934644.0	3Day 4 S8 L004 R1 001.fastq.gz	0:151 1:151	A:39522904023;C:13210312500;G:13112786947;T:18690553925;N:3705093	151	151	39522904023	13210312500	13112786947	18690553925	3705093	SRX9325176	SRS7549492	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.86134	0.0	0.22228	1.0	0.75741		0.53967	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61532	61532	SRR12858262	SRX9325175	SRS7549492	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish Intranasal rSpike 3Day	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal 100ng r Spike 3Day\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal r Spike 3Day	3Day 3 S7	3Day 3 S7	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	3Day_3_S7_L004_R1_001.fastq.gz 3Day_3_S7_L004_R2_001.fastq.gz	fastq fastq	72504765812.0	240082006.0	3Day 3 S7 L004 R1 001.fastq.gz	0:151 1:151	A:33922644753;C:11322044063;G:11218554755;T:16038363159;N:3159082	151	151	33922644753	11322044063	11218554755	16038363159	3159082	SRX9325175	SRS7549492	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.86092	0.0	0.22194	1.0	0.75941		0.54693	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61533	61533	SRR12858263	SRX9325174	SRS7549491	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish intranasal PBS	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal PBS\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal PBS	Control 2 S2	Control 2 S2	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	Control_2_S2_L004_R1_001.fastq.gz Control_2_S2_L004_R2_001.fastq.gz	fastq fastq	64254998894.0	212764897.0	Control 2 S2 L004 R1 001.fastq.gz	0:151 1:151	A:29800534511;C:10295273086;G:10286925663;T:13869445548;N:2820086	151	151	29800534511	10295273086	10286925663	13869445548	2820086	SRX9325174	SRS7549491	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.87826	0.0	0.22134	1.0	0.77195		0.54341	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System
61534	61534	SRR12858264	SRX9325173	SRS7549491	SRP287979	PRJNA668529	Single Cell Olfactory Organ of Zebrafish exposed to r Spike from SARS CoV 2	PRJNA668529	Other	Captured fresh cells with 10x genomic chromium then sequenced with illumina NovaSeq				Zebrafish intranasal PBS	strain:AB\|age:3 Months\|sex:female and male\|tissue:Olfactory Rosette\|treatment:Intranasal PBS\|BioSampleModel:Model organism or animal	Single cell zebrafish olfactory organ: intranasal PBS	Control 1 S1	Control 1 S1	Followed Chromium Next GEM Single Cell 3 Reagent Kits v3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287979	Control_1_S1_L004_R1_001.fastq.gz Control_1_S1_L004_R2_001.fastq.gz	fastq fastq	69676036606.0	230715353.0	Control 1 S1 L004 R1 001.fastq.gz	0:151 1:151	A:32349942335;C:11154687198;G:11132501059;T:15035845934;N:3060080	151	151	32349942335	11154687198	11132501059	15035845934	3060080	SRX9325173	SRS7549491	SRA1141422	University of New Mexico\|Biology	University of New Mexico	2	0.0	0.87698	0.0	0.2194	1.0	0.7685		0.53763	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Mexico	2020-10-21	Adult	Adult	Brain	Nervous System

Advanced export

JSON shape: default, array, newline-delimited

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;