metadata: run_metadata: 16 rows where devstage_curation = "Undetermined" and tissue

16 rows where devstage_curation = "Undetermined" and tissue_curation = "Spleen"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	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.study_ref	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.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
38293	38293	SRR1647684	SRX756919	SRS742121	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.	pubmed:25535281	24S	GSM1541908	source name:spleen\|tissue:spleen\|disease state:24h post SVCV infection	24S	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|disease state:24h post SVCV infection	GSM1541908	GSM1541908: 24S; Danio rerio; RNA Seq	GSM1541908		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541908	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP049663		24S_ATGTCA_L003_R1.fastq	fastq	1207014756.0	23666956.0	GSM1541908 r1	0:51	A:316359100;C:290453604;G:283305513;T:316815698;N:80841	51		316359100	290453604	283305513	316815698	80841	SRX756919	SRS742121	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.91158		0.09021		0.70867		0.46907		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
38294	38294	SRR1647683	SRX756918	SRS742119	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.	pubmed:25535281	6S	GSM1541907	source name:spleen\|tissue:spleen\|disease state:6h post SVCV infection	6S	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|disease state:6h post SVCV infection	GSM1541907	GSM1541907: 6S; Danio rerio; RNA Seq	GSM1541907		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541907	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP049663		6S_AGTTCC_L003_R1.fastq	fastq	1251006540.0	24529540.0	GSM1541907 r1	0:51	A:323805792;C:303846999;G:297418642;T:325862442;N:72665	51		323805792	303846999	297418642	325862442	72665	SRX756918	SRS742119	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.92105		0.09005		0.71273		0.46937		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
38295	38295	SRR1647682	SRX756917	SRS742118	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.	pubmed:25535281	0S	GSM1541906	source name:spleen\|tissue:spleen\|disease state:un infected	0S	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|disease state:un infected	GSM1541906	GSM1541906: 0S; Danio rerio; RNA Seq	GSM1541906		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541906	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP049663		0S_AGTCAA_L003_R1.fastq	fastq	1155087372.0	22648772.0	GSM1541906 r1	0:51	A:301183546;C:279328135;G:272663981;T:301834798;N:76912	51		301183546	279328135	272663981	301834798	76912	SRX756917	SRS742118	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.91841		0.09679		0.70546		0.47624		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
52200	52200	SRR8991406	SRX5770474	SRS4704583	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600	Spleen3	GSM3740959	source name:spleen\|strain:Tubingen\|genotype:wild type\|tissue:spleen	Spleen3	The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	spleen	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype:wild type\|tissue:spleen	GSM3740959	GSM3740959: Spleen3; Danio rerio; RNA Seq	GSM3740959		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3740959	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10	Spleen3.bam	bam	29617062386.0	98069743.0	GSM3740959 r1	0:151 1:151	A:7464139749;C:4972084318;G:5132144813;T:11970808438;N:77885068	151	151	7464139749	4972084318	5132144813	11970808438	77885068	SRX5770474	SRS4704583	SRA880843	GEO	Zhejiang University	2	0.0	0.7261	0.0	0.03774	1.0	0.86275		0.5339	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-04-30	Undetermined	Multi-stage	Spleen	Hematopoietic System
63895	63895	SRR14213371	SRX10579916	SRS8684384	SRP314470	PRJNA721381	RNA Seq from zebrafish adult tissues	GSE171906	Transcriptome Analysis	The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.	pubmed:34556579	Spleen3	GSM5237140	source name:zebrafish spleen\|genotype:wild type\|tissue:spleen\|strain:TLAB	Spleen3	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM	zebrafish spleen	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:spleen\|strain:TLAB	GSM5237140	GSM5237140: Spleen3; Danio rerio; RNA Seq	GSM5237140		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM5237140	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP314470		Spleen3.fastq	fastq	2469245600.0	24692456.0	GSM5237140 r1	0:100	A:595265067;C:649103304;G:625399353;T:599383209;N:94667	100		595265067	649103304	625399353	599383209	94667	SRX10579916	SRS8684384	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.9388		0.16508		0.75205		0.59719		100		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Spleen	Hematopoietic System
63896	63896	SRR14213370	SRX10579915	SRS8684383	SRP314470	PRJNA721381	RNA Seq from zebrafish adult tissues	GSE171906	Transcriptome Analysis	The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.	pubmed:34556579	Spleen2	GSM5237139	source name:zebrafish spleen\|genotype:wild type\|tissue:spleen\|strain:TLAB	Spleen2	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM	zebrafish spleen	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:spleen\|strain:TLAB	GSM5237139	GSM5237139: Spleen2; Danio rerio; RNA Seq	GSM5237139		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM5237139	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP314470		Spleen2.fastq	fastq	1372663100.0	13726631.0	GSM5237139 r1	0:100	A:303080845;C:392345861;G:369765807;T:307418421;N:52166	100		303080845	392345861	369765807	307418421	52166	SRX10579915	SRS8684383	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.96541		0.18478		0.78565		0.60522		100		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Spleen	Hematopoietic System
63897	63897	SRR14213369	SRX10579914	SRS8684382	SRP314470	PRJNA721381	RNA Seq from zebrafish adult tissues	GSE171906	Transcriptome Analysis	The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.	pubmed:34556579	Spleen1	GSM5237138	source name:zebrafish spleen\|genotype:wild type\|tissue:spleen\|strain:TLAB	Spleen1	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM	zebrafish spleen	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:spleen\|strain:TLAB	GSM5237138	GSM5237138: Spleen1; Danio rerio; RNA Seq	GSM5237138		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM5237138	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP314470		Spleen1.fastq	fastq	2268815600.0	22688156.0	GSM5237138 r1	0:100	A:570901318;C:562128594;G:552921437;T:582778510;N:85741	100		570901318	562128594	552921437	582778510	85741	SRX10579914	SRS8684382	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93633		0.14981		0.72825		0.52073		100		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Spleen	Hematopoietic System
71972	71972	SRR22163682	SRX18142568	SRS15644032	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			C3	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:control\|replicate:replicate3\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	C3	C3	control group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		C3.R1.fastq.gz C3.R2.fastq.gz	fastq fastq	6777299176.0	22441388.0	C3.R1.fastq.gz	0:151 1:151	A:1869146927;C:1513142912;G:1565477798;T:1829395893;N:135646	151	151	1869146927	1513142912	1565477798	1829395893	135646	SRX18142568	SRS15644032	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.91581	0.91452	0.09416	0.09344	0.71167	0.71338	0.50247	0.50311	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71973	71973	SRR22163683	SRX18142567	SRS15644031	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			C2	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:control\|replicate:replicate2\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	C2	C2	control group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		C2.R1.fastq.gz C2.R2.fastq.gz	fastq fastq	6956425644.0	23034522.0	C2.R1.fastq.gz	0:151 1:151	A:1847551873;C:1616308106;G:1662475314;T:1829952767;N:137584	151	151	1847551873	1616308106	1662475314	1829952767	137584	SRX18142567	SRS15644031	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93033	0.9312	0.056	0.05619	0.71261	0.71376	0.4668	0.47014	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71974	71974	SRR22163684	SRX18142566	SRS15644030	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			C1	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:control\|replicate:replicate1\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	C1	C1	control group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		C1.R1.fastq.gz C1.R2.fastq.gz	fastq fastq	6218689172.0	20591686.0	C1.R1.fastq.gz	0:151 1:151	A:1651743119;C:1444992966;G:1490934383;T:1630891482;N:127222	151	151	1651743119	1444992966	1490934383	1630891482	127222	SRX18142566	SRS15644030	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93571	0.93627	0.03427	0.0346	0.73336	0.73401	0.47064	0.47601	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71975	71975	SRR22163685	SRX18142565	SRS15644029	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			B3	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:challenge\|replicate:replicate3\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	B3	B3	challenge group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		B3.R1.fastq.gz B3.R2.fastq.gz	fastq fastq	7958268062.0	26351881.0	B3.R1.fastq.gz	0:151 1:151	A:2067039750;C:1894612680;G:1943559820;T:2052891379;N:164433	151	151	2067039750	1894612680	1943559820	2052891379	164433	SRX18142565	SRS15644029	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93754	0.93809	0.03309	0.03347	0.71762	0.71731	0.49012	0.4888	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71976	71976	SRR22163686	SRX18142564	SRS15644028	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			B2	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:challenge\|replicate:replicate2\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	B2	B2	challenge group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		B2.R1.fastq.gz B2.R2.fastq.gz	fastq fastq	7071097158.0	23414229.0	B2.R1.fastq.gz	0:151 1:151	A:1862299896;C:1658740196;G:1713471478;T:1836444697;N:140891	151	151	1862299896	1658740196	1713471478	1836444697	140891	SRX18142564	SRS15644028	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.94335	0.94369	0.04139	0.04172	0.80405	0.80415	0.39649	0.39674	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71977	71977	SRR22163687	SRX18142563	SRS15644027	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			B1	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:challenge\|replicate:replicate1\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	B1	B1	challenge group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		B1.R1.fastq.gz B1.R2.fastq.gz	fastq fastq	7597788178.0	25158239.0	B1.R1.fastq.gz	0:151 1:151	A:1986638730;C:1797302173;G:1839273564;T:1974418679;N:155032	151	151	1986638730	1797302173	1839273564	1974418679	155032	SRX18142563	SRS15644027	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93891	0.93921	0.04922	0.04888	0.74552	0.74501	0.48725	0.49058	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71978	71978	SRR22163688	SRX18142562	SRS15644026	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			A3	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:treatment\|replicate:replicate3\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	A3	A3	treatment group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		A3.R1.fastq.gz A3.R2.fastq.gz	fastq fastq	8674550152.0	28723676.0	A3.R1.fastq.gz	0:151 1:151	A:2234032232;C:2083164440;G:2128058461;T:2229111717;N:183302	151	151	2234032232	2083164440	2128058461	2229111717	183302	SRX18142562	SRS15644026	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93839	0.93828	0.01889	0.01887	0.73639	0.73724	0.48841	0.47397	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71979	71979	SRR22163689	SRX18142561	SRS15644025	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			A2	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:treatment\|replicate:replicate2\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	A2	A2	treatment group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		A2.R1.fastq.gz A2.R2.fastq.gz	fastq fastq	7383660816.0	24449208.0	A2.R1.fastq.gz	0:151 1:151	A:1917884453;C:1759507724;G:1796259178;T:1909857526;N:151935	151	151	1917884453	1759507724	1796259178	1909857526	151935	SRX18142561	SRS15644025	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93853	0.93854	0.02662	0.02663	0.71435	0.7149	0.49509	0.49212	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71980	71980	SRR22163690	SRX18142560	SRS15644024	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.			A1	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:treatment\|replicate:replicate1\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio	A1	A1	treatment group			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990		A1.R1.fastq.gz A1.R2.fastq.gz	fastq fastq	7734454352.0	25610776.0	A1.R1.fastq.gz	0:151 1:151	A:2031967267;C:1817027018;G:1866115793;T:2019187811;N:156463	151	151	2031967267	1817027018	1866115793	2019187811	156463	SRX18142560	SRS15644024	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93755	0.93728	0.03692	0.03688	0.71664	0.71693	0.48577	0.48719	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System

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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");;