run_metadata
76 rows where experiment.platform = "BGISEQ", technology = "unknown" and tissue_curation = "Trunk"
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| Link | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 33164 | 33164 | SRR29809736 | SRX25309007 | SRS21984115 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 20mM STS 5 | GSM8393514 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 20mM STS 5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS | GSM8393514 | GSM8393514: pdx1 morpholino + 20mM STS 5; Danio rerio; RNA Seq | GSM8393514 r1 | GSM8393514 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 6_2.fq.gz 6_1.fq.gz | fastq fastq | 4827420200.0 | 24137101.0 | GSM8393514 r1 | 0:100 1:100 | A:1278807278;C:1130198430;G:1150325506;T:1268088986;N:0 | 100 | 100 | 1278807278 | 1130198430 | 1150325506 | 1268088986 | 0 | SRX25309007 | SRS21984115 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.9409 | 0.94542 | 0.08059 | 0.07981 | 0.69021 | 0.68887 | 0.47275 | 0.47095 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33165 | 33165 | SRR29809737 | SRX25309006 | SRS21984114 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 20mM STS 4 | GSM8393513 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 20mM STS 4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS | GSM8393513 | GSM8393513: pdx1 morpholino + 20mM STS 4; Danio rerio; RNA Seq | GSM8393513 r1 | GSM8393513 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 30_2.fq.gz 30_1.fq.gz | fastq fastq | 4240862400.0 | 21204312.0 | GSM8393513 r1 | 0:100 1:100 | A:1146088921;C:972830110;G:990127288;T:1131816081;N:0 | 100 | 100 | 1146088921 | 972830110 | 990127288 | 1131816081 | 0 | SRX25309006 | SRS21984114 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.93888 | 0.9444 | 0.08826 | 0.08671 | 0.70431 | 0.70212 | 0.48083 | 0.48199 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33166 | 33166 | SRR29809738 | SRX25309005 | SRS21984113 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 20mM STS 3 | GSM8393512 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 20mM STS 3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS | GSM8393512 | GSM8393512: pdx1 morpholino + 20mM STS 3; Danio rerio; RNA Seq | GSM8393512 r1 | GSM8393512 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 24_2.fq.gz 24_1.fq.gz | fastq fastq | 4822516400.0 | 24112582.0 | GSM8393512 r1 | 0:100 1:100 | A:1276866727;C:1130641795;G:1148897951;T:1266109927;N:0 | 100 | 100 | 1276866727 | 1130641795 | 1148897951 | 1266109927 | 0 | SRX25309005 | SRS21984113 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94126 | 0.94446 | 0.07837 | 0.07762 | 0.6911 | 0.69037 | 0.46251 | 0.4642 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33167 | 33167 | SRR29809739 | SRX25309004 | SRS21984112 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 20mM STS 2 | GSM8393511 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 20mM STS 2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS | GSM8393511 | GSM8393511: pdx1 morpholino + 20mM STS 2; Danio rerio; RNA Seq | GSM8393511 r1 | GSM8393511 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 18_2.fq.gz 18_1.fq.gz | fastq fastq | 4820332000.0 | 24101660.0 | GSM8393511 r1 | 0:100 1:100 | A:1306037553;C:1103383630;G:1122255994;T:1288654823;N:0 | 100 | 100 | 1306037553 | 1103383630 | 1122255994 | 1288654823 | 0 | SRX25309004 | SRS21984112 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94035 | 0.9445 | 0.08468 | 0.08417 | 0.71106 | 0.70897 | 0.47897 | 0.47969 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33168 | 33168 | SRR29809740 | SRX25309003 | SRS21984111 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 20mM STS 1 | GSM8393510 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 20mM STS 1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS | GSM8393510 | GSM8393510: pdx1 morpholino + 20mM STS 1; Danio rerio; RNA Seq | GSM8393510 r1 | GSM8393510 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 12_1.fq.gz 12_2.fq.gz | fastq fastq | 4825742600.0 | 24128713.0 | GSM8393510 r1 | 0:100 1:100 | A:1264457552;C:1145133600;G:1160084092;T:1256067356;N:0 | 100 | 100 | 1264457552 | 1145133600 | 1160084092 | 1256067356 | 0 | SRX25309003 | SRS21984111 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94613 | 0.9501 | 0.06915 | 0.06812 | 0.68941 | 0.68852 | 0.45659 | 0.45507 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33169 | 33169 | SRR29809741 | SRX25309002 | SRS21984110 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 15mM STS 5 | GSM8393509 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 15mM STS 5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS | GSM8393509 | GSM8393509: pdx1 morpholino + 15mM STS 5; Danio rerio; RNA Seq | GSM8393509 r1 | GSM8393509 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 5_2.fq.gz 5_1.fq.gz | fastq fastq | 4816068800.0 | 24080344.0 | GSM8393509 r1 | 0:100 1:100 | A:1278638535;C:1126555210;G:1141985166;T:1268889889;N:0 | 100 | 100 | 1278638535 | 1126555210 | 1141985166 | 1268889889 | 0 | SRX25309002 | SRS21984110 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.9414 | 0.94516 | 0.08012 | 0.07915 | 0.69284 | 0.69185 | 0.46526 | 0.46882 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33170 | 33170 | SRR29809742 | SRX25309001 | SRS21984109 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 15mM STS 4 | GSM8393508 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 15mM STS 4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS | GSM8393508 | GSM8393508: pdx1 morpholino + 15mM STS 4; Danio rerio; RNA Seq | GSM8393508 r1 | GSM8393508 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 29_2.fq.gz 29_1.fq.gz | fastq fastq | 4386218400.0 | 21931092.0 | GSM8393508 r1 | 0:100 1:100 | A:1181773341;C:1011246416;G:1025789654;T:1167408989;N:0 | 100 | 100 | 1181773341 | 1011246416 | 1025789654 | 1167408989 | 0 | SRX25309001 | SRS21984109 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94168 | 0.94587 | 0.08215 | 0.08003 | 0.69682 | 0.69544 | 0.47251 | 0.47607 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33171 | 33171 | SRR29809743 | SRX25309000 | SRS21984108 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 15mM STS 3 | GSM8393507 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 15mM STS 3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS | GSM8393507 | GSM8393507: pdx1 morpholino + 15mM STS 3; Danio rerio; RNA Seq | GSM8393507 r1 | GSM8393507 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 23_2.fq.gz 23_1.fq.gz | fastq fastq | 4808808800.0 | 24044044.0 | GSM8393507 r1 | 0:100 1:100 | A:1269564907;C:1132101674;G:1149286214;T:1257856005;N:0 | 100 | 100 | 1269564907 | 1132101674 | 1149286214 | 1257856005 | 0 | SRX25309000 | SRS21984108 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.9434 | 0.94774 | 0.07109 | 0.0703 | 0.69264 | 0.69183 | 0.45908 | 0.46455 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33172 | 33172 | SRR29809744 | SRX25308999 | SRS21984107 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 15mM STS 2 | GSM8393506 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 15mM STS 2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS | GSM8393506 | GSM8393506: pdx1 morpholino + 15mM STS 2; Danio rerio; RNA Seq | GSM8393506 r1 | GSM8393506 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 17_1.fq.gz 17_2.fq.gz | fastq fastq | 4805883400.0 | 24029417.0 | GSM8393506 r1 | 0:100 1:100 | A:1299291748;C:1102517917;G:1122450422;T:1281623313;N:0 | 100 | 100 | 1299291748 | 1102517917 | 1122450422 | 1281623313 | 0 | SRX25308999 | SRS21984107 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94253 | 0.9461 | 0.08371 | 0.08155 | 0.70589 | 0.70423 | 0.4853 | 0.47925 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33173 | 33173 | SRR29809745 | SRX25308998 | SRS21984106 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 15mM STS 1 | GSM8393505 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 15mM STS 1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS | GSM8393505 | GSM8393505: pdx1 morpholino + 15mM STS 1; Danio rerio; RNA Seq | GSM8393505 r1 | GSM8393505 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 11_1.fq.gz 11_2.fq.gz | fastq fastq | 4812111600.0 | 24060558.0 | GSM8393505 r1 | 0:100 1:100 | A:1269803704;C:1133657948;G:1150461915;T:1258188033;N:0 | 100 | 100 | 1269803704 | 1133657948 | 1150461915 | 1258188033 | 0 | SRX25308998 | SRS21984106 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94311 | 0.94708 | 0.07444 | 0.07235 | 0.69266 | 0.69158 | 0.46689 | 0.46584 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33174 | 33174 | SRR29809746 | SRX25308997 | SRS21984105 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 0mM STS 5 | GSM8393504 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 0mM STS 5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS | GSM8393504 | GSM8393504: pdx1 morpholino + 0mM STS 5; Danio rerio; RNA Seq | GSM8393504 r1 | GSM8393504 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 4_2.fq.gz 4_1.fq.gz | fastq fastq | 4804978800.0 | 24024894.0 | GSM8393504 r1 | 0:100 1:100 | A:1266882676;C:1131396187;G:1149418875;T:1257281062;N:0 | 100 | 100 | 1266882676 | 1131396187 | 1149418875 | 1257281062 | 0 | SRX25308997 | SRS21984105 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94345 | 0.94707 | 0.07428 | 0.0741 | 0.6898 | 0.68856 | 0.4653 | 0.46918 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33175 | 33175 | SRR29809747 | SRX25308996 | SRS21984104 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 0mM STS 4 | GSM8393503 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 0mM STS 4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS | GSM8393503 | GSM8393503: pdx1 morpholino + 0mM STS 4; Danio rerio; RNA Seq | GSM8393503 r1 | GSM8393503 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 28_1.fq.gz 28_2.fq.gz | fastq fastq | 4464066400.0 | 22320332.0 | GSM8393503 r1 | 0:100 1:100 | A:1209155509;C:1023407835;G:1040239673;T:1191263383;N:0 | 100 | 100 | 1209155509 | 1023407835 | 1040239673 | 1191263383 | 0 | SRX25308996 | SRS21984104 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.934 | 0.93723 | 0.08814 | 0.08601 | 0.69834 | 0.69798 | 0.47533 | 0.47611 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33176 | 33176 | SRR29809748 | SRX25308995 | SRS21984103 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 0mM STS 3 | GSM8393502 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 0mM STS 3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS | GSM8393502 | GSM8393502: pdx1 morpholino + 0mM STS 3; Danio rerio; RNA Seq | GSM8393502 r1 | GSM8393502 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 22_1.fq.gz 22_2.fq.gz | fastq fastq | 4613819800.0 | 23069099.0 | GSM8393502 r1 | 0:100 1:100 | A:1218890904;C:1084874278;G:1104087523;T:1205967095;N:0 | 100 | 100 | 1218890904 | 1084874278 | 1104087523 | 1205967095 | 0 | SRX25308995 | SRS21984103 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.9426 | 0.94852 | 0.07601 | 0.07487 | 0.69197 | 0.69075 | 0.45872 | 0.45856 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33177 | 33177 | SRR29809749 | SRX25308994 | SRS21984102 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 0mM STS 2 | GSM8393501 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 0mM STS 2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS | GSM8393501 | GSM8393501: pdx1 morpholino + 0mM STS 2; Danio rerio; RNA Seq | GSM8393501 r1 | GSM8393501 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 16_1.fq.gz 16_2.fq.gz | fastq fastq | 4818005000.0 | 24090025.0 | GSM8393501 r1 | 0:100 1:100 | A:1291680744;C:1114433015;G:1134463270;T:1277427971;N:0 | 100 | 100 | 1291680744 | 1114433015 | 1134463270 | 1277427971 | 0 | SRX25308994 | SRS21984102 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.93988 | 0.94257 | 0.08614 | 0.08554 | 0.69376 | 0.69367 | 0.47178 | 0.47111 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33178 | 33178 | SRR29809750 | SRX25308993 | SRS21984101 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | pdx1 morpholino + 0mM STS 1 | GSM8393500 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing | pdx1 morpholino + 0mM STS 1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS | GSM8393500 | GSM8393500: pdx1 morpholino + 0mM STS 1; Danio rerio; RNA Seq | GSM8393500 r1 | GSM8393500 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 10_2.fq.gz 10_1.fq.gz | fastq fastq | 4827935800.0 | 24139679.0 | GSM8393500 r1 | 0:100 1:100 | A:1267823750;C:1143323623;G:1156194469;T:1260593958;N:0 | 100 | 100 | 1267823750 | 1143323623 | 1156194469 | 1260593958 | 0 | SRX25308993 | SRS21984101 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94483 | 0.94829 | 0.07178 | 0.07025 | 0.69077 | 0.69025 | 0.46181 | 0.45982 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33179 | 33179 | SRR29809751 | SRX25308992 | SRS21984100 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 20mM STS 5 | GSM8393499 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 20mM STS 5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS | GSM8393499 | GSM8393499: Control morpholino + 20mM STS 5; Danio rerio; RNA Seq | GSM8393499 r1 | GSM8393499 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 9_1.fq.gz 9_2.fq.gz | fastq fastq | 4822379000.0 | 24111895.0 | GSM8393499 r1 | 0:100 1:100 | A:1262977318;C:1145277730;G:1159167028;T:1254956924;N:0 | 100 | 100 | 1262977318 | 1145277730 | 1159167028 | 1254956924 | 0 | SRX25308992 | SRS21984100 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94642 | 0.94964 | 0.06863 | 0.0674 | 0.69288 | 0.69252 | 0.4574 | 0.44372 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33180 | 33180 | SRR29809752 | SRX25308991 | SRS21984099 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 20mM STS 4 | GSM8393498 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 20mM STS 4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS | GSM8393498 | GSM8393498: Control morpholino + 20mM STS 4; Danio rerio; RNA Seq | GSM8393498 r1 | GSM8393498 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 3_1.fq.gz 3_2.fq.gz | fastq fastq | 4803150200.0 | 24015751.0 | GSM8393498 r1 | 0:100 1:100 | A:1253239300;C:1144350399;G:1158671984;T:1246888517;N:0 | 100 | 100 | 1253239300 | 1144350399 | 1158671984 | 1246888517 | 0 | SRX25308991 | SRS21984099 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94606 | 0.95015 | 0.06543 | 0.06441 | 0.68676 | 0.68611 | 0.44857 | 0.44396 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33181 | 33181 | SRR29809753 | SRX25308990 | SRS21984098 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 20mM STS 3 | GSM8393497 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 20mM STS 3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS | GSM8393497 | GSM8393497: Control morpholino + 20mM STS 3; Danio rerio; RNA Seq | GSM8393497 r1 | GSM8393497 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 27_1.fq.gz 27_2.fq.gz | fastq fastq | 4277827200.0 | 21389136.0 | GSM8393497 r1 | 0:100 1:100 | A:1142589086;C:997230367;G:1005771965;T:1132235782;N:0 | 100 | 100 | 1142589086 | 997230367 | 1005771965 | 1132235782 | 0 | SRX25308990 | SRS21984098 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94201 | 0.94596 | 0.07754 | 0.07484 | 0.69794 | 0.69617 | 0.46286 | 0.45985 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33182 | 33182 | SRR29809754 | SRX25308989 | SRS21984097 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 20mM STS 2 | GSM8393496 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 20mM STS 2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS | GSM8393496 | GSM8393496: Control morpholino + 20mM STS 2; Danio rerio; RNA Seq | GSM8393496 r1 | GSM8393496 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 21_2.fq.gz 21_1.fq.gz | fastq fastq | 4019456600.0 | 20097283.0 | GSM8393496 r1 | 0:100 1:100 | A:1053249649;C:953992221;G:968100759;T:1044113971;N:0 | 100 | 100 | 1053249649 | 953992221 | 968100759 | 1044113971 | 0 | SRX25308989 | SRS21984097 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94377 | 0.95125 | 0.06861 | 0.06745 | 0.68676 | 0.68523 | 0.45049 | 0.45168 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33183 | 33183 | SRR29809755 | SRX25308988 | SRS21984096 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 20mM STS 1 | GSM8393495 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 20mM STS 1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS | GSM8393495 | GSM8393495: Control morpholino + 20mM STS 1; Danio rerio; RNA Seq | GSM8393495 r1 | GSM8393495 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 15_1.fq.gz 15_2.fq.gz | fastq fastq | 4829679200.0 | 24148396.0 | GSM8393495 r1 | 0:100 1:100 | A:1292193191;C:1119414896;G:1140502241;T:1277568872;N:0 | 100 | 100 | 1292193191 | 1119414896 | 1140502241 | 1277568872 | 0 | SRX25308988 | SRS21984096 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.9423 | 0.9467 | 0.07958 | 0.07808 | 0.69763 | 0.69658 | 0.46406 | 0.46623 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33184 | 33184 | SRR29809756 | SRX25308987 | SRS21984095 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 15mM STS 5 | GSM8393494 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 15mM STS 5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS | GSM8393494 | GSM8393494: Control morpholino + 15mM STS 5; Danio rerio; RNA Seq | GSM8393494 r1 | GSM8393494 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 8_2.fq.gz 8_1.fq.gz | fastq fastq | 4803709800.0 | 24018549.0 | GSM8393494 r1 | 0:100 1:100 | A:1253733589;C:1143748058;G:1158768340;T:1247459813;N:0 | 100 | 100 | 1253733589 | 1143748058 | 1158768340 | 1247459813 | 0 | SRX25308987 | SRS21984095 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94718 | 0.94926 | 0.06582 | 0.06461 | 0.68791 | 0.68738 | 0.44759 | 0.44517 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33185 | 33185 | SRR29809757 | SRX25308986 | SRS21984094 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 15mM STS 4 | GSM8393493 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 15mM STS 4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS | GSM8393493 | GSM8393493: Control morpholino + 15mM STS 4; Danio rerio; RNA Seq | GSM8393493 r1 | GSM8393493 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 26_1.fq.gz 26_2.fq.gz | fastq fastq | 4816718000.0 | 24083590.0 | GSM8393493 r1 | 0:100 1:100 | A:1278966223;C:1129131703;G:1144234415;T:1264385659;N:0 | 100 | 100 | 1278966223 | 1129131703 | 1144234415 | 1264385659 | 0 | SRX25308986 | SRS21984094 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94278 | 0.94713 | 0.07235 | 0.0704 | 0.69895 | 0.698 | 0.4536 | 0.45416 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33186 | 33186 | SRR29809758 | SRX25308985 | SRS21984093 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 15mM STS 3 | GSM8393492 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 15mM STS 3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS | GSM8393492 | GSM8393492: Control morpholino + 15mM STS 3; Danio rerio; RNA Seq | GSM8393492 r1 | GSM8393492 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 20_2.fq.gz 20_1.fq.gz | fastq fastq | 4825880400.0 | 24129402.0 | GSM8393492 r1 | 0:100 1:100 | A:1263053657;C:1147908238;G:1161094243;T:1253824262;N:0 | 100 | 100 | 1263053657 | 1147908238 | 1161094243 | 1253824262 | 0 | SRX25308985 | SRS21984093 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94642 | 0.95164 | 0.06472 | 0.06312 | 0.69035 | 0.68909 | 0.44854 | 0.44216 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33187 | 33187 | SRR29809759 | SRX25308984 | SRS21984092 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 15mM STS 2 | GSM8393491 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 15mM STS 2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS | GSM8393491 | GSM8393491: Control morpholino + 15mM STS 2; Danio rerio; RNA Seq | GSM8393491 r1 | GSM8393491 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 2_1.fq.gz 2_2.fq.gz | fastq fastq | 4805985200.0 | 24029926.0 | GSM8393491 r1 | 0:100 1:100 | A:1255841114;C:1143278337;G:1157783615;T:1249082134;N:0 | 100 | 100 | 1255841114 | 1143278337 | 1157783615 | 1249082134 | 0 | SRX25308984 | SRS21984092 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94666 | 0.94794 | 0.06553 | 0.06456 | 0.69181 | 0.69175 | 0.4359 | 0.44559 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33188 | 33188 | SRR29809760 | SRX25308983 | SRS21984091 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 15mM STS 1 | GSM8393490 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 15mM STS 1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS | GSM8393490 | GSM8393490: Control morpholino + 15mM STS 1; Danio rerio; RNA Seq | GSM8393490 r1 | GSM8393490 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 14_1.fq.gz 14_2.fq.gz | fastq fastq | 4553465000.0 | 22767325.0 | GSM8393490 r1 | 0:100 1:100 | A:1209891078;C:1063666819;G:1082075995;T:1197831108;N:0 | 100 | 100 | 1209891078 | 1063666819 | 1082075995 | 1197831108 | 0 | SRX25308983 | SRS21984091 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.9432 | 0.94661 | 0.07696 | 0.07599 | 0.69763 | 0.69721 | 0.46463 | 0.46425 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33189 | 33189 | SRR29809761 | SRX25308982 | SRS21984090 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 0mM STS 5 | GSM8393489 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 0mM STS 5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS | GSM8393489 | GSM8393489: Control morpholino + 0mM STS 5; Danio rerio; RNA Seq | GSM8393489 r1 | GSM8393489 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 7_1.fq.gz 7_2.fq.gz | fastq fastq | 4813770200.0 | 24068851.0 | GSM8393489 r1 | 0:100 1:100 | A:1251918123;C:1151936172;G:1164458418;T:1245457487;N:0 | 100 | 100 | 1251918123 | 1151936172 | 1164458418 | 1245457487 | 0 | SRX25308982 | SRS21984090 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.95021 | 0.95271 | 0.06538 | 0.06376 | 0.69171 | 0.68996 | 0.44317 | 0.4435 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33190 | 33190 | SRR29809762 | SRX25308981 | SRS21984089 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 0mM STS 4 | GSM8393488 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 0mM STS 4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS | GSM8393488 | GSM8393488: Control morpholino + 0mM STS 4; Danio rerio; RNA Seq | GSM8393488 r1 | GSM8393488 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 25_1.fq.gz 25_2.fq.gz | fastq fastq | 4810346800.0 | 24051734.0 | GSM8393488 r1 | 0:100 1:100 | A:1275301780;C:1127999390;G:1144547869;T:1262497761;N:0 | 100 | 100 | 1275301780 | 1127999390 | 1144547869 | 1262497761 | 0 | SRX25308981 | SRS21984089 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94519 | 0.94834 | 0.06949 | 0.06803 | 0.69552 | 0.69524 | 0.44741 | 0.45052 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33191 | 33191 | SRR29809763 | SRX25308980 | SRS21984088 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 0mM STS 3 | GSM8393487 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 0mM STS 3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS | GSM8393487 | GSM8393487: Control morpholino + 0mM STS 3; Danio rerio; RNA Seq | GSM8393487 r1 | GSM8393487 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 19_1.fq.gz 19_2.fq.gz | fastq fastq | 4811704200.0 | 24058521.0 | GSM8393487 r1 | 0:100 1:100 | A:1257129134;C:1146835083;G:1160663520;T:1247076463;N:0 | 100 | 100 | 1257129134 | 1146835083 | 1160663520 | 1247076463 | 0 | SRX25308980 | SRS21984088 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94691 | 0.95082 | 0.06344 | 0.06212 | 0.69014 | 0.69059 | 0.45386 | 0.43864 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33192 | 33192 | SRR29809764 | SRX25308979 | SRS21984087 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 0mM STS 2 | GSM8393486 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 0mM STS 2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS | GSM8393486 | GSM8393486: Control morpholino + 0mM STS 2; Danio rerio; RNA Seq | GSM8393486 r1 | GSM8393486 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 13_1.fq.gz 13_2.fq.gz | fastq fastq | 4616178800.0 | 23080894.0 | GSM8393486 r1 | 0:100 1:100 | A:1225429879;C:1079094541;G:1096304865;T:1215349515;N:0 | 100 | 100 | 1225429879 | 1079094541 | 1096304865 | 1215349515 | 0 | SRX25308979 | SRS21984087 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94498 | 0.9498 | 0.07635 | 0.075 | 0.69319 | 0.6927 | 0.46598 | 0.466 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 33193 | 33193 | SRR29809765 | SRX25308978 | SRS21984086 | SRP519612 | PRJNA1135151 | The effect of sodium thiosulfate on hyperglycemic zebrafish larvae | GSE272119 | Transcriptome Analysis | We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed. | pubmed:39264236 | Control morpholino + 0mM STS 1 | GSM8393485 | source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing | Control morpholino + 0mM STS 1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17 | larvae | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS | GSM8393485 | GSM8393485: Control morpholino + 0mM STS 1; Danio rerio; RNA Seq | GSM8393485 r1 | GSM8393485 | 1 | RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP519612 | 1_1.fq.gz 1_2.fq.gz | fastq fastq | 4823953400.0 | 24119767.0 | GSM8393485 r1 | 0:100 1:100 | A:1270954678;C:1137736456;G:1155516940;T:1259745326;N:0 | 100 | 100 | 1270954678 | 1137736456 | 1155516940 | 1259745326 | 0 | SRX25308978 | SRS21984086 | SRA1923353 | ZMF, University Heidelberg | ZMF, University Heidelberg | 2 | 0.94325 | 0.94699 | 0.06928 | 0.06864 | 0.69372 | 0.69307 | 0.44844 | 0.45647 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2024-07-12 | Multi-stage | Multi-stage | Trunk | Surface Structure | ||||||||||||
| 35980 | 35980 | SRR33796117 | SRX29017800 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P2000 1 | P2000 1 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P2000_1_1.fq.gz P2000_1_2.fq.gz | fastq fastq | 6682157100.0 | 22273857.0 | P2000 1 1.fq.gz | 0:150 1:150 | A:1750970707;C:1591819991;G:1593263349;T:1746103053;N:0 | 150 | 150 | 1750970707 | 1591819991 | 1593263349 | 1746103053 | 0 | SRX29017800 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35981 | 35981 | SRR33796118 | SRX29017799 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P1000 3 | P1000 3 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P1000_3_1.fq.gz P1000_3_2.fq.gz | fastq fastq | 6596943000.0 | 21989810.0 | P1000 3 1.fq.gz | 0:150 1:150 | A:1725528987;C:1574140428;G:1576046656;T:1721226929;N:0 | 150 | 150 | 1725528987 | 1574140428 | 1576046656 | 1721226929 | 0 | SRX29017799 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35982 | 35982 | SRR33796119 | SRX29017798 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P1000 2 | P1000 2 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P1000_2_1.fq.gz P1000_2_2.fq.gz | fastq fastq | 6677331000.0 | 22257770.0 | P1000 2 1.fq.gz | 0:150 1:150 | A:1758237128;C:1582217484;G:1584403835;T:1752472553;N:0 | 150 | 150 | 1758237128 | 1582217484 | 1584403835 | 1752472553 | 0 | SRX29017798 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35983 | 35983 | SRR33796120 | SRX29017797 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P1000 1 | P1000 1 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P1000_1_1.fq.gz P1000_1_2.fq.gz | fastq fastq | 6771926100.0 | 22573087.0 | P1000 1 1.fq.gz | 0:150 1:150 | A:1788071352;C:1600799117;G:1602227700;T:1780827931;N:0 | 150 | 150 | 1788071352 | 1600799117 | 1602227700 | 1780827931 | 0 | SRX29017797 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35984 | 35984 | SRR33796121 | SRX29017796 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P500 3 | P500 3 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P500_3_1.fq.gz P500_3_2.fq.gz | fastq fastq | 6691956300.0 | 22306521.0 | P500 3 1.fq.gz | 0:150 1:150 | A:1763763611;C:1584417511;G:1585842124;T:1757933054;N:0 | 150 | 150 | 1763763611 | 1584417511 | 1585842124 | 1757933054 | 0 | SRX29017796 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35985 | 35985 | SRR33796122 | SRX29017795 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P500 2 | P500 2 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P500_2_1.fq.gz P500_2_2.fq.gz | fastq fastq | 6720858300.0 | 22402861.0 | P500 2 1.fq.gz | 0:150 1:150 | A:1752279513;C:1609781801;G:1611483135;T:1747313851;N:0 | 150 | 150 | 1752279513 | 1609781801 | 1611483135 | 1747313851 | 0 | SRX29017795 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35986 | 35986 | SRR33796123 | SRX29017794 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P500 1 | P500 1 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P500_1_1.fq.gz P500_1_2.fq.gz | fastq fastq | 6820862100.0 | 22736207.0 | P500 1 1.fq.gz | 0:150 1:150 | A:1812260874;C:1601860387;G:1602603805;T:1804137034;N:0 | 150 | 150 | 1812260874 | 1601860387 | 1602603805 | 1804137034 | 0 | SRX29017794 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35987 | 35987 | SRR33796124 | SRX29017793 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | MX 3 | MX 3 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | MX_3_1.fq.gz MX_3_2.fq.gz | fastq fastq | 6795327600.0 | 22651092.0 | MX 3 1.fq.gz | 0:150 1:150 | A:1768016462;C:1630727253;G:1632326554;T:1764257331;N:0 | 150 | 150 | 1768016462 | 1630727253 | 1632326554 | 1764257331 | 0 | SRX29017793 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35988 | 35988 | SRR33796125 | SRX29017792 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P2000 3 | P2000 3 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P2000_3_1.fq.gz P2000_3_2.fq.gz | fastq fastq | 6620786400.0 | 22069288.0 | P2000 3 1.fq.gz | 0:150 1:150 | A:1736628496;C:1574653543;G:1577791512;T:1731712849;N:0 | 150 | 150 | 1736628496 | 1574653543 | 1577791512 | 1731712849 | 0 | SRX29017792 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35989 | 35989 | SRR33796126 | SRX29017791 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | P2000 2 | P2000 2 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | P2000_2_1.fq.gz P2000_2_2.fq.gz | fastq fastq | 6613914000.0 | 22046380.0 | P2000 2 1.fq.gz | 0:150 1:150 | A:1733574880;C:1575483348;G:1576793005;T:1728062767;N:0 | 150 | 150 | 1733574880 | 1575483348 | 1576793005 | 1728062767 | 0 | SRX29017791 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35990 | 35990 | SRR33796127 | SRX29017790 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | MX 2 | MX 2 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | MX_2_1.fq.gz MX_2_2.fq.gz | fastq fastq | 6769929300.0 | 22566431.0 | MX 2 1.fq.gz | 0:150 1:150 | A:1773923783;C:1611785261;G:1615111695;T:1769108561;N:0 | 150 | 150 | 1773923783 | 1611785261 | 1615111695 | 1769108561 | 0 | SRX29017790 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 35991 | 35991 | SRR33796128 | SRX29017789 | SRS25233880 | SRP589371 | PRJNA1256770 | Danio rerio Raw sequence reads | PRJNA1256770 | Whole Genome Sequencing | Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish. | Model organism or animal sample from Danio rerio | Zebrafish treatment with polysaccharides | strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: embryo whole body | MX 1 | MX 1 | Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads. | RNA-Seq | TRANSCRIPTOMIC | cDNA_randomPriming | PAIRED | BGISEQ | MGISEQ-2000RS | SRP589371 | MX_1_1.fq.gz MX_1_2.fq.gz | fastq fastq | 6715295400.0 | 22384318.0 | MX 1 1.fq.gz | 0:150 1:150 | A:1774590051;C:1584963102;G:1587348964;T:1768393283;N:0 | 150 | 150 | 1774590051 | 1584963102 | 1587348964 | 1768393283 | 0 | SRX29017789 | SRS25233880 | SRA2141272 | West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine | West Anhui Universiaty | B | B | biological fallback assumption | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2025-06-02 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||||||
| 48054 | 48054 | SRR7008006 | SRX3940581 | SRS3171382 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | MO26h rep1 | MO26h 1 | Sample3 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 1|BioSampleModel:Model organism or animal | RNA seq of fsd1 morphants1 | MO26h 1 | MO26h 1 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | MO26h_1_1.fq.gz | fastq | 1193983450.0 | 23879669.0 | MO26h 1 1.fq.gz | 0:50 | A:313344068;C:282899939;G:291404437;T:306051122;N:283884 | 50 | 313344068 | 282899939 | 291404437 | 306051122 | 283884 | SRX3940581 | SRS3171382 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.95658 | 0.07921 | 0.70307 | 0.47586 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||||||||
| 48055 | 48055 | SRR7008007 | SRX3940580 | SRS3171381 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | MO26h rep2 | MO26h 2 | Sample4 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 2|BioSampleModel:Model organism or animal | RNA seq of fsd1 morphants2 | MO26h 2 | MO26h 2 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | MO26h_2_1.fq.gz | fastq | 1199524600.0 | 23990492.0 | MO26h 2 1.fq.gz | 0:50 | A:318726410;C:282721669;G:287606979;T:310182197;N:287345 | 50 | 318726410 | 282721669 | 287606979 | 310182197 | 287345 | SRX3940580 | SRS3171381 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.9541 | 0.08695 | 0.70404 | 0.47195 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||||||||
| 48056 | 48056 | SRR7008008 | SRX3940579 | SRS3171379 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | WT26h rep1 | WT26h 1 | Sample1 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 1|BioSampleModel:Model organism or animal | RNA seq of normal embryos1 | WT26h 1 | WT26h 1 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | WT26h_1_1.fq.gz | fastq | 1200268650.0 | 24005373.0 | WT26h 1 1.fq.gz | 0:50 | A:315743815;C:284447849;G:295772915;T:303964473;N:339598 | 50 | 315743815 | 284447849 | 295772915 | 303964473 | 339598 | SRX3940579 | SRS3171379 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.95659 | 0.07726 | 0.70425 | 0.47269 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||||||||
| 48057 | 48057 | SRR7008009 | SRX3940578 | SRS3171380 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | WT26h rep2 | WT26h 2 | Sample2 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 2|BioSampleModel:Model organism or animal | RNA seq of normal embryos2 | WT26h 2 | WT26h 2 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | WT26h_2_1.fq.gz | fastq | 1199179850.0 | 23983597.0 | WT26h 2 1.fq.gz | 0:50 | A:316605984;C:281184572;G:292581373;T:308419476;N:388445 | 50 | 316605984 | 281184572 | 292581373 | 308419476 | 388445 | SRX3940578 | SRS3171380 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.95377 | 0.08617 | 0.70508 | 0.4775 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||||||||
| 71636 | 71636 | SRR21869755 | SRX17856945 | SRS15377990 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE L 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 10|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221019 | AT20221019 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | BHEE_L_1_1.fq.gz BHEE_L_1_2.fq.gz | fastq fastq | 6801171000.0 | 45341140.0 | BHEE L 1 1.fq.gz | 0:150 1:150 | A:1888974247;C:1508524578;G:1489908963;T:1913517780;N:245432 | 150 | 150 | 1888974247 | 1508524578 | 1489908963 | 1913517780 | 245432 | SRX17856945 | SRS15377990 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.9335 | 0.13981 | 0.68002 | 0.4788 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71637 | 71637 | SRR21869756 | SRX17856944 | SRS15377989 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA H 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 9|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221018 | AT20221018 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | TBBPA_H_3_1.fq.gz TBBPA_H_3_2.fq.gz | fastq fastq | 6951086400.0 | 46340576.0 | TBBPA H 3 1.fq.gz | 0:150 1:150 | A:1880119007;C:1592162094;G:1577584281;T:1900616606;N:604412 | 150 | 150 | 1880119007 | 1592162094 | 1577584281 | 1900616606 | 604412 | SRX17856944 | SRS15377989 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93943 | 0.10589 | 0.67689 | 0.47979 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71638 | 71638 | SRR21869757 | SRX17856943 | SRS15377988 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA H 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 8|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221017 | AT20221017 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | TBBPA_H_2_2.fq.gz TBBPA_H_2_1.fq.gz | fastq fastq | 6795391800.0 | 45302612.0 | TBBPA H 2 1.fq.gz | 0:150 1:150 | A:1857631184;C:1537732087;G:1520731548;T:1879126916;N:170065 | 150 | 150 | 1857631184 | 1537732087 | 1520731548 | 1879126916 | 170065 | SRX17856943 | SRS15377988 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.939 | 0.11307 | 0.67562 | 0.48002 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71639 | 71639 | SRR21869758 | SRX17856942 | SRS15377987 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA H 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 7|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221016 | AT20221016 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | TBBPA_H_1_1.fq.gz TBBPA_H_1_2.fq.gz | fastq fastq | 6725010600.0 | 44833404.0 | TBBPA H 1 1.fq.gz | 0:150 1:150 | A:1843421900;C:1516907852;G:1500976839;T:1863525958;N:178051 | 150 | 150 | 1843421900 | 1516907852 | 1500976839 | 1863525958 | 178051 | SRX17856942 | SRS15377987 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93897 | 0.11644 | 0.67919 | 0.47402 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71640 | 71640 | SRR21869759 | SRX17856941 | SRS15377986 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA L 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 6|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221015 | AT20221015 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | TBBPA_L_3_1.fq.gz TBBPA_L_3_2.fq.gz | fastq fastq | 6808286400.0 | 45388576.0 | TBBPA L 3 1.fq.gz | 0:150 1:150 | A:1858988152;C:1543294665;G:1528035258;T:1877760196;N:208129 | 150 | 150 | 1858988152 | 1543294665 | 1528035258 | 1877760196 | 208129 | SRX17856941 | SRS15377986 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93964 | 0.11186 | 0.67537 | 0.47243 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71641 | 71641 | SRR21869760 | SRX17856940 | SRS15377985 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA L 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 5|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221014 | AT20221014 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | TBBPA_L_2_1.fq.gz TBBPA_L_2_2.fq.gz | fastq fastq | 6774228000.0 | 45161520.0 | TBBPA L 2 1.fq.gz | 0:150 1:150 | A:1848399114;C:1536937930;G:1519456780;T:1869169891;N:264285 | 150 | 150 | 1848399114 | 1536937930 | 1519456780 | 1869169891 | 264285 | SRX17856940 | SRS15377985 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.94025 | 0.11637 | 0.67462 | 0.47263 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71642 | 71642 | SRR21869761 | SRX17856939 | SRS15377984 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA L 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 4|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221013 | AT20221013 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | TBBPA_L_1_2.fq.gz TBBPA_L_1_1.fq.gz | fastq fastq | 6921381900.0 | 46142546.0 | TBBPA L 1 1.fq.gz | 0:150 1:150 | A:1884200037;C:1574208410;G:1563278291;T:1899461955;N:233207 | 150 | 150 | 1884200037 | 1574208410 | 1563278291 | 1899461955 | 233207 | SRX17856939 | SRS15377984 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.94086 | 0.10976 | 0.67645 | 0.47784 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71643 | 71643 | SRR21869762 | SRX17856938 | SRS15377982 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE H 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 15|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221124 | AT20221124 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | BHEE_H_3.fq.gz | fastq | 533428889.0 | 23211223.0 | BHEE H 3.fq.gz | 0:22.98 | A:120057830;C:104713991;G:142506271;T:166150296;N:501 | 22 | 120057830 | 104713991 | 142506271 | 166150296 | 501 | SRX17856938 | SRS15377982 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.79272 | 0.10596 | 0.92431 | 0.52918 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71644 | 71644 | SRR21869763 | SRX17856937 | SRS15377981 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE H 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 14|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221123 | AT20221123 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | BHEE_H_2.fq.gz | fastq | 542237520.0 | 23757627.0 | BHEE H 2.fq.gz | 0:22.82 | A:118608004;C:107602147;G:146341292;T:169685803;N:274 | 22 | 118608004 | 107602147 | 146341292 | 169685803 | 274 | SRX17856937 | SRS15377981 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.78829 | 0.10064 | 0.91346 | 0.52625 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71645 | 71645 | SRR21869764 | SRX17856936 | SRS15377980 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE H 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 13|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221122 | AT20221122 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | BHEE_H_1.fq.gz | fastq | 553437966.0 | 24068768.0 | BHEE H 1.fq.gz | 0:22.99 | A:123764056;C:109954264;G:151884637;T:167834745;N:264 | 22 | 123764056 | 109954264 | 151884637 | 167834745 | 264 | SRX17856936 | SRS15377980 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.70849 | 0.09465 | 0.91768 | 0.52194 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71646 | 71646 | SRR21869765 | SRX17856935 | SRS15377979 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE L 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 12|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221121 | AT20221121 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | BHEE_L_3.fq.gz | fastq | 534633614.0 | 23823089.0 | BHEE L 3.fq.gz | 0:22.44 | A:117363754;C:102332510;G:134833529;T:180103711;N:110 | 22 | 117363754 | 102332510 | 134833529 | 180103711 | 110 | SRX17856935 | SRS15377979 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.91988 | 0.08325 | 0.94073 | 0.53253 | 23 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71647 | 71647 | SRR21869766 | SRX17856934 | SRS15377978 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE L 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 11|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221120 | AT20221120 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | BHEE_L_2.fq.gz | fastq | 544854900.0 | 24226737.0 | BHEE L 2.fq.gz | 0:22.49 | A:119782823;C:104902871;G:136756907;T:183412172;N:127 | 22 | 119782823 | 104902871 | 136756907 | 183412172 | 127 | SRX17856934 | SRS15377978 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93474 | 0.08179 | 0.9345 | 0.52916 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71648 | 71648 | SRR21869767 | SRX17856933 | SRS15377990 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE L 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 10|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221119 | AT20221119 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | BHEE_L_1.fq.gz | fastq | 536871966.0 | 23768969.0 | BHEE L 1.fq.gz | 0:22.59 | A:117321330;C:102381550;G:133641788;T:183527144;N:154 | 22 | 117321330 | 102381550 | 133641788 | 183527144 | 154 | SRX17856933 | SRS15377990 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.94042 | 0.08986 | 0.93141 | 0.51821 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71649 | 71649 | SRR21869768 | SRX17856932 | SRS15377989 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA H 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 9|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221118 | AT20221118 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | TBBPA_H_3.fq.gz | fastq | 528430937.0 | 23464221.0 | TBBPA H 3.fq.gz | 0:22.52 | A:115261465;C:101477007;G:136961367;T:174730904;N:194 | 22 | 115261465 | 101477007 | 136961367 | 174730904 | 194 | SRX17856932 | SRS15377989 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.89616 | 0.09929 | 0.93042 | 0.5004 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71650 | 71650 | SRR21869769 | SRX17856931 | SRS15377988 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA H 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 8|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221117 | AT20221117 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | TBBPA_H_2.fq.gz | fastq | 523343500.0 | 22888420.0 | TBBPA H 2.fq.gz | 0:22.86 | A:114272050;C:101352294;G:133914155;T:173804699;N:302 | 22 | 114272050 | 101352294 | 133914155 | 173804699 | 302 | SRX17856931 | SRS15377988 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.90842 | 0.10759 | 0.92088 | 0.53284 | 20 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71651 | 71651 | SRR21869770 | SRX17856930 | SRS15377987 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA H 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 7|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221116 | AT20221116 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | TBBPA_H_1.fq.gz | fastq | 538481195.0 | 23517366.0 | TBBPA H 1.fq.gz | 0:22.90 | A:117132485;C:106262580;G:143962997;T:171122739;N:394 | 22 | 117132485 | 106262580 | 143962997 | 171122739 | 394 | SRX17856930 | SRS15377987 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.83673 | 0.10787 | 0.91238 | 0.53365 | 21 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71652 | 71652 | SRR21869771 | SRX17856929 | SRS15377986 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA L 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 6|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221115 | AT20221115 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | TBBPA_L_3.fq.gz | fastq | 536529124.0 | 23817957.0 | TBBPA L 3.fq.gz | 0:22.53 | A:115664153;C:104457844;G:136444705;T:179962303;N:119 | 22 | 115664153 | 104457844 | 136444705 | 179962303 | 119 | SRX17856929 | SRS15377986 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.86178 | 0.09041 | 0.93624 | 0.4992 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71653 | 71653 | SRR21869772 | SRX17856928 | SRS15377983 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | Control 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 3|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221012 | AT20221012 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | Control_3_1.fq.gz Control_3_2.fq.gz | fastq fastq | 6649034700.0 | 44326898.0 | Control 3 1.fq.gz | 0:150 1:150 | A:1818740838;C:1502937390;G:1485401626;T:1841692100;N:262746 | 150 | 150 | 1818740838 | 1502937390 | 1485401626 | 1841692100 | 262746 | SRX17856928 | SRS15377983 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.938 | 0.1166 | 0.66543 | 0.48941 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71654 | 71654 | SRR21869773 | SRX17856927 | SRS15377985 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA L 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 5|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221114 | AT20221114 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | TBBPA_L_2.fq.gz | fastq | 525712427.0 | 23458446.0 | TBBPA L 2.fq.gz | 0:22.41 | A:115172158;C:103930973;G:133832634;T:172776555;N:107 | 22 | 115172158 | 103930973 | 133832634 | 172776555 | 107 | SRX17856927 | SRS15377985 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.87223 | 0.08526 | 0.93845 | 0.54116 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71655 | 71655 | SRR21869774 | SRX17856926 | SRS15377984 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | TBBPA L 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 4|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221113 | AT20221113 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | TBBPA_L_1.fq.gz | fastq | 527804519.0 | 23370082.0 | TBBPA L 1.fq.gz | 0:22.58 | A:114266025;C:102477479;G:134403120;T:176657729;N:166 | 22 | 114266025 | 102477479 | 134403120 | 176657729 | 166 | SRX17856926 | SRS15377984 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.89339 | 0.09635 | 0.92608 | 0.48415 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71656 | 71656 | SRR21869775 | SRX17856925 | SRS15377983 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | Control 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 3|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221112 | AT20221112 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | Control_3.fq.gz | fastq | 535579212.0 | 23899710.0 | Control 3.fq.gz | 0:22.41 | A:117125157;C:106586085;G:133001456;T:178866289;N:225 | 22 | 117125157 | 106586085 | 133001456 | 178866289 | 225 | SRX17856925 | SRS15377983 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.89094 | 0.06851 | 0.94807 | 0.54835 | 23 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71657 | 71657 | SRR21869776 | SRX17856924 | SRS15377977 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | Control 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 2|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221111 | AT20221111 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | Control_2.fq.gz | fastq | 528466892.0 | 23430674.0 | Control 2.fq.gz | 0:22.55 | A:116361274;C:103960709;G:132758802;T:175385846;N:261 | 22 | 116361274 | 103960709 | 132758802 | 175385846 | 261 | SRX17856924 | SRS15377977 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.89063 | 0.07453 | 0.94255 | 0.54503 | 21 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71658 | 71658 | SRR21869777 | SRX17856923 | SRS15377976 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | Control 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 1|BioSampleModel:Model organism or animal | miRNA Seq of zebrafish larvae | AT20221110 | AT20221110 | miRNA Seq of zebrafish larvae | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | BGISEQ | BGISEQ-500 | SRP402080 | loader:fastq load.py | Control_1.fq.gz | fastq | 517484481.0 | 23046792.0 | Control 1.fq.gz | 0:22.45 | A:114187486;C:101456491;G:129311971;T:172528320;N:213 | 22 | 114187486 | 101456491 | 129311971 | 172528320 | 213 | SRX17856923 | SRS15377976 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.89811 | 0.07533 | 0.93198 | 0.55322 | 22 | B | usable mapping rate | bgi | bgi | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71659 | 71659 | SRR21869778 | SRX17856922 | SRS15377982 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE H 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 15|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221024 | AT20221024 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | BHEE_H_3_1.fq.gz BHEE_H_3_2.fq.gz | fastq fastq | 6884798700.0 | 45898658.0 | BHEE H 3 1.fq.gz | 0:150 1:150 | A:1866404874;C:1573550459;G:1557181628;T:1887479557;N:182182 | 150 | 150 | 1866404874 | 1573550459 | 1557181628 | 1887479557 | 182182 | SRX17856922 | SRS15377982 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.94047 | 0.10782 | 0.67939 | 0.46829 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71660 | 71660 | SRR21869779 | SRX17856921 | SRS15377981 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE H 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 14|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221023 | AT20221023 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | BHEE_H_2_1.fq.gz BHEE_H_2_2.fq.gz | fastq fastq | 6909787800.0 | 46065252.0 | BHEE H 2 1.fq.gz | 0:150 1:150 | A:1885404557;C:1566069244;G:1552991479;T:1905049514;N:273006 | 150 | 150 | 1885404557 | 1566069244 | 1552991479 | 1905049514 | 273006 | SRX17856921 | SRS15377981 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93913 | 0.1148 | 0.68057 | 0.48135 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71661 | 71661 | SRR21869780 | SRX17856920 | SRS15377980 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE H 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 13|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221022 | AT20221022 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | BHEE_H_1_1.fq.gz BHEE_H_1_2.fq.gz | fastq fastq | 6732629100.0 | 44884194.0 | BHEE H 1 1.fq.gz | 0:150 1:150 | A:1847364286;C:1516868611;G:1502080906;T:1866125318;N:189979 | 150 | 150 | 1847364286 | 1516868611 | 1502080906 | 1866125318 | 189979 | SRX17856920 | SRS15377980 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93635 | 0.12452 | 0.68795 | 0.45878 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71662 | 71662 | SRR21869781 | SRX17856919 | SRS15377979 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE L 3 | replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 12|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221021 | AT20221021 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | BHEE_L_3_2.fq.gz BHEE_L_3_1.fq.gz | fastq fastq | 7006678200.0 | 46711188.0 | BHEE L 3 1.fq.gz | 0:150 1:150 | A:1916044576;C:1583765437;G:1567414975;T:1939187929;N:265283 | 150 | 150 | 1916044576 | 1583765437 | 1567414975 | 1939187929 | 265283 | SRX17856919 | SRS15377979 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93694 | 0.12086 | 0.67712 | 0.47941 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71663 | 71663 | SRR21869782 | SRX17856918 | SRS15377978 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | BHEE L 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 11|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221020 | AT20221020 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | BHEE_L_2_1.fq.gz BHEE_L_2_2.fq.gz | fastq fastq | 6735918300.0 | 44906122.0 | BHEE L 2 1.fq.gz | 0:150 1:150 | A:1857641267;C:1506371574;G:1491507978;T:1880130050;N:267431 | 150 | 150 | 1857641267 | 1506371574 | 1491507978 | 1880130050 | 267431 | SRX17856918 | SRS15377978 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93519 | 0.13194 | 0.67677 | 0.47877 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71664 | 71664 | SRR21869783 | SRX17856917 | SRS15377977 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | Control 2 | replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 2|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221011 | AT20221011 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | Control_2_2.fq.gz Control_2_1.fq.gz | fastq fastq | 6852696300.0 | 45684642.0 | Control 2 1.fq.gz | 0:150 1:150 | A:1884613769;C:1539134365;G:1524511981;T:1904229008;N:207177 | 150 | 150 | 1884613769 | 1539134365 | 1524511981 | 1904229008 | 207177 | SRX17856917 | SRS15377977 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93613 | 0.12084 | 0.66809 | 0.49052 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||||||||||
| 71665 | 71665 | SRR21869784 | SRX17856916 | SRS15377976 | SRP402080 | PRJNA889683 | miRNA mRNA sequencing of zebrafish embryos | PRJNA889683 | Other | miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE | Control 1 | replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 1|BioSampleModel:Model organism or animal | RNA Seq of zebrafish larvae | AT20221010 | AT20221010 | RNA Seq of zebrafish larvae | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | BGISEQ | BGISEQ-500 | SRP402080 | Control_1_2.fq.gz Control_1_1.fq.gz | fastq fastq | 6880244100.0 | 45868294.0 | Control 1 1.fq.gz | 0:150 1:150 | A:1897293267;C:1539803870;G:1527831180;T:1915045017;N:270766 | 150 | 150 | 1897293267 | 1539803870 | 1527831180 | 1915045017 | 270766 | SRX17856916 | SRS15377976 | SRA1518395 | Jiangsu University|School of Environment and Safety Engineering | Jiangsu University | 1 | 0.93542 | 0.12732 | 0.66916 | 0.48712 | 150 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2022-10-12 | Larval | Larval | Trunk | Surface Structure |
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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");;