run_metadata
67 rows where devstage_curation_coarse = "Multi-stage" and experiment.platform = "BGISEQ"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 30691 | 30691 | SRR28270998 | SRX23880961 | SRS20704477 | SRP494117 | PRJNA1085662 | Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells | PRJNA1085662 | Other | Roxithromycin ROX a commonly used macrolide antibiotic is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation ROX persists as a resilient environmental contaminant detectable in aquatic ecosystems and food products. However our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos significantly reducing hatch rates body lengths and increased malformation rates. Moreover ROX exposure adversely affected the locomotive capacity of zebrafish embryos and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons evident through reduced or irregular axonal lengths. Concurrently abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax bcl2 caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1 olig2 axon development cd82a mbpa plp1b sema5a and neuroimmunity aplnrb aplnra in zebrafish larvae. Furthermore the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis. | WT | strain:not provided|isolate:not provided|breed:not provided|cultivar:not provided|ecotype:not provided|age:not provided|dev stage:not provided|collection date:not provided|geo loc name:not provided|sex:not provided|tissue:Cerebrum|BioSampleModel:Model organism or animal | Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells | DANIO | DANIO | Illumina Second Generation Sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA_oligo_dT | SINGLE | BGISEQ | BGISEQ-500 | SRP494117 | WT_S1_L001_I1_001.fastq.gz | fastq | 7991376264.0 | 998922033.0 | WT S1 L001 I1 001.fastq.gz | 0:8 | A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175 | 8 | 2573734851 | 1426474966 | 1492966198 | 2498173074 | 27175 | SRX23880961 | SRS20704477 | SRA1820072 | shantou university|Neurobiology Center | shantou university | 1 | 0.0 | 0.0 | 1.0 | 8 | T | under 1.2% mapping rate | bgi | bgi | unknown | poly_a | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | China | 2024-03-11 | Undetermined | Multi-stage | Brain | Nervous System | |||||||||||||||||||||||||||||
| 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 | ||||||||||||
| 63586 | 63586 | SRR13951240 | SRX10330055 | SRS8449856 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep6 | GSM5169491 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169491 | GSM5169491: Zebrafish larvae WT acrolein treated rep6; Danio rerio; RNA Seq | GSM5169491 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169491 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAALRAAPEI-515_1.fq.gz V300079388_L3_HK500ZEBaopEAALRAAPEI-515_2.fq.gz | fastq fastq | 4980022200.0 | 49800222.0 | GSM5169491 r1 | 0:100 1:100 | A:1333773139;C:1140685596;G:1152592074;T:1352971391;N:0 | 100 | 100 | 1333773139 | 1140685596 | 1152592074 | 1352971391 | 0 | SRX10330055 | SRS8449856 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9486 | 0.11229 | 0.65967 | 0.47337 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63587 | 63587 | SRR13951239 | SRX10330054 | SRS8449858 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep5 | GSM5169490 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169490 | GSM5169490: Zebrafish larvae WT acrolein treated rep5; Danio rerio; RNA Seq | GSM5169490 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169490 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_1.fq.gz V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_2.fq.gz | fastq fastq | 4989256800.0 | 49892568.0 | GSM5169490 r1 | 0:100 1:100 | A:1333967860;C:1145275940;G:1156212626;T:1353800374;N:0 | 100 | 100 | 1333967860 | 1145275940 | 1156212626 | 1353800374 | 0 | SRX10330054 | SRS8449858 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94949 | 0.10728 | 0.65756 | 0.47006 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63588 | 63588 | SRR13951238 | SRX10330053 | SRS8449857 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep4 | GSM5169489 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169489 | GSM5169489: Zebrafish larvae WT acrolein treated rep4; Danio rerio; RNA Seq | GSM5169489 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169489 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_1.fq.gz V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_2.fq.gz | fastq fastq | 4991600600.0 | 49916006.0 | GSM5169489 r1 | 0:100 1:100 | A:1332160517;C:1148004219;G:1159807037;T:1351628827;N:0 | 100 | 100 | 1332160517 | 1148004219 | 1159807037 | 1351628827 | 0 | SRX10330053 | SRS8449857 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.95038 | 0.10485 | 0.65977 | 0.47668 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63589 | 63589 | SRR13951237 | SRX10330052 | SRS8449855 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep3 | GSM5169488 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169488 | GSM5169488: Zebrafish larvae WT acrolein treated rep3; Danio rerio; RNA Seq | GSM5169488 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169488 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_1.fq.gz V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_2.fq.gz | fastq fastq | 4931029800.0 | 49310298.0 | GSM5169488 r1 | 0:100 1:100 | A:1313566945;C:1137259809;G:1149091650;T:1331111396;N:0 | 100 | 100 | 1313566945 | 1137259809 | 1149091650 | 1331111396 | 0 | SRX10330052 | SRS8449855 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.95011 | 0.10594 | 0.65711 | 0.48179 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63590 | 63590 | SRR13951236 | SRX10330051 | SRS8449854 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep2 | GSM5169487 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169487 | GSM5169487: Zebrafish larvae WT acrolein treated rep2; Danio rerio; RNA Seq | GSM5169487 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169487 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_1.fq.gz V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_2.fq.gz | fastq fastq | 4934978600.0 | 49349786.0 | GSM5169487 r1 | 0:100 1:100 | A:1318738318;C:1133208442;G:1143616038;T:1339415802;N:0 | 100 | 100 | 1318738318 | 1133208442 | 1143616038 | 1339415802 | 0 | SRX10330051 | SRS8449854 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.948 | 0.10568 | 0.65685 | 0.45325 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63591 | 63591 | SRR13951235 | SRX10330050 | SRS8449851 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep1 | GSM5169486 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169486 | GSM5169486: Zebrafish larvae WT acrolein treated rep1; Danio rerio; RNA Seq | GSM5169486 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169486 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_1.fq.gz V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_2.fq.gz | fastq fastq | 4916868000.0 | 49168680.0 | GSM5169486 r1 | 0:100 1:100 | A:1319311116;C:1122812867;G:1129767432;T:1344976585;N:0 | 100 | 100 | 1319311116 | 1122812867 | 1129767432 | 1344976585 | 0 | SRX10330050 | SRS8449851 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94789 | 0.10769 | 0.65537 | 0.47629 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63592 | 63592 | SRR13951234 | SRX10330049 | SRS8449853 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep6 | GSM5169485 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169485 | GSM5169485: Zebrafish larvae WT rep6; Danio rerio; RNA Seq | GSM5169485 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169485 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_1.fq.gz V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_2.fq.gz | fastq fastq | 4918223600.0 | 49182236.0 | GSM5169485 r1 | 0:100 1:100 | A:1312501446;C:1129859893;G:1141743360;T:1334118901;N:0 | 100 | 100 | 1312501446 | 1129859893 | 1141743360 | 1334118901 | 0 | SRX10330049 | SRS8449853 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94736 | 0.10854 | 0.66095 | 0.46684 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63593 | 63593 | SRR13951251 | SRX10330048 | SRS8449849 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep5 | GSM5169484 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169484 | GSM5169484: Zebrafish larvae WT rep5; Danio rerio; RNA Seq | GSM5169484 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169484 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAERAAPEI-505_1.fq.gz V300079388_L2_HK500ZEBaopEAAERAAPEI-505_2.fq.gz | fastq fastq | 4921487400.0 | 49214874.0 | GSM5169484 r1 | 0:100 1:100 | A:1307773420;C:1137100007;G:1147334476;T:1329279497;N:0 | 100 | 100 | 1307773420 | 1137100007 | 1147334476 | 1329279497 | 0 | SRX10330048 | SRS8449849 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9488 | 0.10243 | 0.65596 | 0.47526 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63594 | 63594 | SRR13951250 | SRX10330047 | SRS8449847 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep4 | GSM5169483 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169483 | GSM5169483: Zebrafish larvae WT rep4; Danio rerio; RNA Seq | GSM5169483 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169483 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAADRAAPEI-504_1.fq.gz V300079388_L2_HK500ZEBaopEAADRAAPEI-504_2.fq.gz | fastq fastq | 4902200200.0 | 49022002.0 | GSM5169483 r1 | 0:100 1:100 | A:1302490426;C:1131663107;G:1148042501;T:1320004166;N:0 | 100 | 100 | 1302490426 | 1131663107 | 1148042501 | 1320004166 | 0 | SRX10330047 | SRS8449847 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9486 | 0.10416 | 0.66133 | 0.45959 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63595 | 63595 | SRR13951249 | SRX10330046 | SRS8449846 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep3 | GSM5169482 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169482 | GSM5169482: Zebrafish larvae WT rep3; Danio rerio; RNA Seq | GSM5169482 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169482 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAACRAAPEI-503_1.fq.gz V300079388_L2_HK500ZEBaopEAACRAAPEI-503_2.fq.gz | fastq fastq | 4932506000.0 | 49325060.0 | GSM5169482 r1 | 0:100 1:100 | A:1314021251;C:1136250372;G:1148046464;T:1334187913;N:0 | 100 | 100 | 1314021251 | 1136250372 | 1148046464 | 1334187913 | 0 | SRX10330046 | SRS8449846 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.95001 | 0.10334 | 0.66003 | 0.474 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63596 | 63596 | SRR13951248 | SRX10330045 | SRS8449848 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep2 | GSM5169481 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169481 | GSM5169481: Zebrafish larvae WT rep2; Danio rerio; RNA Seq | GSM5169481 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169481 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAABRAAPEI-502_1.fq.gz V300079388_L2_HK500ZEBaopEAABRAAPEI-502_2.fq.gz | fastq fastq | 4938494000.0 | 49384940.0 | GSM5169481 r1 | 0:100 1:100 | A:1313976068;C:1139517379;G:1153604159;T:1331396394;N:0 | 100 | 100 | 1313976068 | 1139517379 | 1153604159 | 1331396394 | 0 | SRX10330045 | SRS8449848 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94864 | 0.10252 | 0.65957 | 0.47642 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63597 | 63597 | SRR13951247 | SRX10330044 | SRS8449845 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep1 | GSM5169480 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169480 | GSM5169480: Zebrafish larvae WT rep1; Danio rerio; RNA Seq | GSM5169480 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169480 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAARAAPEI-501_1.fq.gz V300079388_L2_HK500ZEBaopEAAARAAPEI-501_2.fq.gz | fastq fastq | 4920498800.0 | 49204988.0 | GSM5169480 r1 | 0:100 1:100 | A:1312070030;C:1133298664;G:1141858537;T:1333271569;N:0 | 100 | 100 | 1312070030 | 1133298664 | 1141858537 | 1333271569 | 0 | SRX10330044 | SRS8449845 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94865 | 0.10459 | 0.65965 | 0.46788 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63598 | 63598 | SRR13951246 | SRX10330043 | SRS8449844 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep6 | GSM5169479 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169479 | GSM5169479: Zebrafish larvae akr1a1a KO rep6; Danio rerio; RNA Seq | GSM5169479 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169479 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAARRAAPEI-521_1.fq.gz V300079388_L3_HK500ZEBaopEAARRAAPEI-521_2.fq.gz | fastq fastq | 4983441000.0 | 49834410.0 | GSM5169479 r1 | 0:100 1:100 | A:1322739180;C:1153664354;G:1168919194;T:1338118272;N:0 | 100 | 100 | 1322739180 | 1153664354 | 1168919194 | 1338118272 | 0 | SRX10330043 | SRS8449844 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9473 | 0.09632 | 0.66419 | 0.46649 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63599 | 63599 | SRR13951245 | SRX10330042 | SRS8449843 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep5 | GSM5169478 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169478 | GSM5169478: Zebrafish larvae akr1a1a KO rep5; Danio rerio; RNA Seq | GSM5169478 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169478 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_1.fq.gz V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_2.fq.gz | fastq fastq | 4979727600.0 | 49797276.0 | GSM5169478 r1 | 0:100 1:100 | A:1324141918;C:1150666829;G:1165518713;T:1339400140;N:0 | 100 | 100 | 1324141918 | 1150666829 | 1165518713 | 1339400140 | 0 | SRX10330042 | SRS8449843 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94914 | 0.09649 | 0.66377 | 0.47093 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63600 | 63600 | SRR13951244 | SRX10330041 | SRS8449852 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep4 | GSM5169477 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169477 | GSM5169477: Zebrafish larvae akr1a1a KO rep4; Danio rerio; RNA Seq | GSM5169477 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169477 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_1.fq.gz V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_2.fq.gz | fastq fastq | 4978998800.0 | 49789988.0 | GSM5169477 r1 | 0:100 1:100 | A:1333355936;C:1140285632;G:1151126213;T:1354231019;N:0 | 100 | 100 | 1333355936 | 1140285632 | 1151126213 | 1354231019 | 0 | SRX10330041 | SRS8449852 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94594 | 0.10032 | 0.66194 | 0.48009 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63601 | 63601 | SRR13951243 | SRX10330040 | SRS8449842 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep3 | GSM5169476 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169476 | GSM5169476: Zebrafish larvae akr1a1a KO rep3; Danio rerio; RNA Seq | GSM5169476 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169476 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAORAAPEI-518_1.fq.gz V300079388_L3_HK500ZEBaopEAAORAAPEI-518_2.fq.gz | fastq fastq | 4978639200.0 | 49786392.0 | GSM5169476 r1 | 0:100 1:100 | A:1331238273;C:1143633964;G:1152228372;T:1351538591;N:0 | 100 | 100 | 1331238273 | 1143633964 | 1152228372 | 1351538591 | 0 | SRX10330040 | SRS8449842 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94616 | 0.1007 | 0.66054 | 0.46712 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63602 | 63602 | SRR13951242 | SRX10330039 | SRS8449850 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep2 | GSM5169475 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169475 | GSM5169475: Zebrafish larvae akr1a1a KO rep2; Danio rerio; RNA Seq | GSM5169475 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169475 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAANRAAPEI-517_1.fq.gz V300079388_L3_HK500ZEBaopEAANRAAPEI-517_2.fq.gz | fastq fastq | 4967553600.0 | 49675536.0 | GSM5169475 r1 | 0:100 1:100 | A:1324408005;C:1143569026;G:1158003192;T:1341573377;N:0 | 100 | 100 | 1324408005 | 1143569026 | 1158003192 | 1341573377 | 0 | SRX10330039 | SRS8449850 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94688 | 0.09559 | 0.66158 | 0.4794 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63603 | 63603 | SRR13951241 | SRX10330038 | SRS8449841 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep1 | GSM5169474 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169474 | GSM5169474: Zebrafish larvae akr1a1a KO rep1; Danio rerio; RNA Seq | GSM5169474 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169474 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_1.fq.gz V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_2.fq.gz | fastq fastq | 4967500800.0 | 49675008.0 | GSM5169474 r1 | 0:100 1:100 | A:1323753410;C:1144795675;G:1158403216;T:1340548499;N:0 | 100 | 100 | 1323753410 | 1144795675 | 1158403216 | 1340548499 | 0 | SRX10330038 | SRS8449841 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94765 | 0.09715 | 0.66018 | 0.4542 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 65128 | 65128 | SRR14935651 | SRX11248280 | SRS9294818 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep9 | GSM5406802 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep9 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406802 | GSM5406802: kidney pdx1 heterozygous ko rep9; Danio rerio; RNA Seq | GSM5406802 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406802 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_18_R1_001.fastq.gz 8724R1_18_R2_001.fastq.gz | fastq fastq | 11176979232.0 | 37097872.0 | GSM5406802 r1 | 0:150.64 1:150.65 | A:2835225993;C:2589629327;G:2820499304;T:2931557102;N:67506 | 150 | 150 | 2835225993 | 2589629327 | 2820499304 | 2931557102 | 67506 | SRX11248280 | SRS9294818 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87724 | 0.87448 | 0.31729 | 0.31569 | 0.73716 | 0.73933 | 0.62206 | 0.62398 | 151 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65129 | 65129 | SRR14935650 | SRX11248279 | SRS9294817 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep8 | GSM5406801 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep8 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406801 | GSM5406801: kidney pdx1 heterozygous ko rep8; Danio rerio; RNA Seq | GSM5406801 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406801 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_17_R1_001.fastq.gz 8724R1_17_R2_001.fastq.gz | fastq fastq | 11394814456.0 | 37822298.0 | GSM5406801 r1 | 0:150.65 1:150.62 | A:2870553528;C:2617084802;G:2858252766;T:3048861279;N:62081 | 150 | 150 | 2870553528 | 2617084802 | 2858252766 | 3048861279 | 62081 | SRX11248279 | SRS9294817 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.88351 | 0.88116 | 0.29453 | 0.29339 | 0.72908 | 0.73012 | 0.59959 | 0.60047 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65130 | 65130 | SRR14935649 | SRX11248278 | SRS9294816 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep7 | GSM5406800 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep7 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406800 | GSM5406800: kidney pdx1 heterozygous ko rep7; Danio rerio; RNA Seq | GSM5406800 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406800 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_16_R1_001.fastq.gz 8724R1_16_R2_001.fastq.gz | fastq fastq | 10795664046.0 | 35825557.0 | GSM5406800 r1 | 0:150.66 1:150.68 | A:2699673063;C:2430598463;G:2795587348;T:2869745840;N:59332 | 150 | 150 | 2699673063 | 2430598463 | 2795587348 | 2869745840 | 59332 | SRX11248278 | SRS9294816 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87086 | 0.8686 | 0.31803 | 0.31528 | 0.73517 | 0.73752 | 0.60984 | 0.61136 | 151 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65131 | 65131 | SRR14935648 | SRX11248277 | SRS9294815 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep6 | GSM5406799 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406799 | GSM5406799: kidney pdx1 heterozygous ko rep6; Danio rerio; RNA Seq | GSM5406799 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406799 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_15_R1_001.fastq.gz 8724R1_15_R2_001.fastq.gz | fastq fastq | 10760871119.0 | 35714100.0 | GSM5406799 r1 | 0:150.66 1:150.65 | A:2739382001;C:2429434631;G:2669749643;T:2922244501;N:60343 | 150 | 150 | 2739382001 | 2429434631 | 2669749643 | 2922244501 | 60343 | SRX11248277 | SRS9294815 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.8687 | 0.86692 | 0.3287 | 0.32779 | 0.73405 | 0.73486 | 0.60891 | 0.61291 | 151 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65132 | 65132 | SRR14935647 | SRX11248276 | SRS9294814 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep5 | GSM5406798 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406798 | GSM5406798: kidney pdx1 heterozygous ko rep5; Danio rerio; RNA Seq | GSM5406798 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406798 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_14_R1_001.fastq.gz 8724R1_14_R2_001.fastq.gz | fastq fastq | 10649537104.0 | 35349599.0 | GSM5406798 r1 | 0:150.64 1:150.62 | A:2731221488;C:2409467117;G:2701711963;T:2807076164;N:60372 | 150 | 150 | 2731221488 | 2409467117 | 2701711963 | 2807076164 | 60372 | SRX11248276 | SRS9294814 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87441 | 0.87237 | 0.29421 | 0.29338 | 0.72693 | 0.72955 | 0.5953 | 0.59497 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65133 | 65133 | SRR14935646 | SRX11248275 | SRS9294813 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep4 | GSM5406797 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406797 | GSM5406797: kidney pdx1 heterozygous ko rep4; Danio rerio; RNA Seq | GSM5406797 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406797 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_13_R1_001.fastq.gz 8724R1_13_R2_001.fastq.gz | fastq fastq | 10694204698.0 | 35493814.0 | GSM5406797 r1 | 0:150.66 1:150.64 | A:2702728213;C:2453895836;G:2650869868;T:2886649326;N:61455 | 150 | 150 | 2702728213 | 2453895836 | 2650869868 | 2886649326 | 61455 | SRX11248275 | SRS9294813 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87706 | 0.87455 | 0.30298 | 0.30085 | 0.73492 | 0.73499 | 0.60664 | 0.61545 | 149 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65134 | 65134 | SRR14935645 | SRX11248274 | SRS9294812 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep3 | GSM5406796 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406796 | GSM5406796: kidney pdx1 heterozygous ko rep3; Danio rerio; RNA Seq | GSM5406796 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406796 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_12_R1_001.fastq.gz 8724R1_12_R2_001.fastq.gz | fastq fastq | 10345053183.0 | 34342254.0 | GSM5406796 r1 | 0:150.63 1:150.60 | A:2688355747;C:2362640622;G:2528888231;T:2765108367;N:60216 | 150 | 150 | 2688355747 | 2362640622 | 2528888231 | 2765108367 | 60216 | SRX11248274 | SRS9294812 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.86578 | 0.86485 | 0.32858 | 0.32741 | 0.74022 | 0.74192 | 0.6202 | 0.62802 | 150 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65135 | 65135 | SRR14935644 | SRX11248273 | SRS9294811 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep2 | GSM5406795 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406795 | GSM5406795: kidney pdx1 heterozygous ko rep2; Danio rerio; RNA Seq | GSM5406795 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406795 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_11_R1_001.fastq.gz 8724R1_11_R2_001.fastq.gz | fastq fastq | 10918902659.0 | 36232610.0 | GSM5406795 r1 | 0:150.67 1:150.68 | A:2720295545;C:2469360250;G:2821457214;T:2907726754;N:62896 | 150 | 150 | 2720295545 | 2469360250 | 2821457214 | 2907726754 | 62896 | SRX11248273 | SRS9294811 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87461 | 0.87362 | 0.33405 | 0.33405 | 0.74024 | 0.73994 | 0.60898 | 0.60832 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65136 | 65136 | SRR14935643 | SRX11248272 | SRS9294810 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep1 | GSM5406794 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406794 | GSM5406794: kidney pdx1 heterozygous ko rep1; Danio rerio; RNA Seq | GSM5406794 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406794 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_10_R1_001.fastq.gz 8724R1_10_R2_001.fastq.gz | fastq fastq | 11557818156.0 | 38359672.0 | GSM5406794 r1 | 0:150.63 1:150.67 | A:2923769735;C:2594538133;G:2968671202;T:3070777088;N:61998 | 150 | 150 | 2923769735 | 2594538133 | 2968671202 | 3070777088 | 61998 | SRX11248272 | SRS9294810 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.8705 | 0.86891 | 0.33241 | 0.3311 | 0.7363 | 0.73835 | 0.61699 | 0.62373 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65137 | 65137 | SRR14935642 | SRX11248271 | SRS9294809 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney wildtype rep3 | GSM5406793 | source name:total kidney|genotype:WT|tissue:kidney | kidney wildtype rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:WT|tissue:kidney | GSM5406793 | GSM5406793: kidney wildtype rep3; Danio rerio; RNA Seq | GSM5406793 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406793 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_3_R1_001.fastq.gz 8724R1_3_R2_001.fastq.gz | fastq fastq | 10759333910.0 | 35709735.0 | GSM5406793 r1 | 0:150.63 1:150.67 | A:2742030248;C:2405074908;G:2740896620;T:2871268925;N:63209 | 150 | 150 | 2742030248 | 2405074908 | 2740896620 | 2871268925 | 63209 | SRX11248271 | SRS9294809 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87736 | 0.875 | 0.29165 | 0.29063 | 0.73261 | 0.73361 | 0.51754 | 0.51714 | 150 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65138 | 65138 | SRR14935641 | SRX11248270 | SRS9294808 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney wildtype rep2 | GSM5406792 | source name:total kidney|genotype:WT|tissue:kidney | kidney wildtype rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:WT|tissue:kidney | GSM5406792 | GSM5406792: kidney wildtype rep2; Danio rerio; RNA Seq | GSM5406792 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406792 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_2_R1_001.fastq.gz 8724R1_2_R2_001.fastq.gz | fastq fastq | 11014631579.0 | 36552301.0 | GSM5406792 r1 | 0:150.65 1:150.68 | A:2786726244;C:2457413219;G:2801015846;T:2969414816;N:61454 | 150 | 150 | 2786726244 | 2457413219 | 2801015846 | 2969414816 | 61454 | SRX11248270 | SRS9294808 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87866 | 0.87699 | 0.31394 | 0.31278 | 0.73588 | 0.73726 | 0.61713 | 0.61801 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65139 | 65139 | SRR14935640 | SRX11248269 | SRS9294807 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney wildtype rep1 | GSM5406791 | source name:total kidney|genotype:WT|tissue:kidney | kidney wildtype rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:WT|tissue:kidney | GSM5406791 | GSM5406791: kidney wildtype rep1; Danio rerio; RNA Seq | GSM5406791 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406791 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_1_R1_001.fastq.gz 8724R1_1_R2_001.fastq.gz | fastq fastq | 10413411371.0 | 34567408.0 | GSM5406791 r1 | 0:150.65 1:150.60 | A:2697353558;C:2358512324;G:2568693377;T:2788789911;N:62201 | 150 | 150 | 2697353558 | 2358512324 | 2568693377 | 2788789911 | 62201 | SRX11248269 | SRS9294807 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.86943 | 0.8664 | 0.31108 | 0.30889 | 0.73815 | 0.74034 | 0.56789 | 0.60471 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65852 | 65852 | SRR15657174 | SRX11954177 | SRS9963999 | SRP334492 | PRJNA758398 | Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq] | GSE182945 | Transcriptome Analysis | Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq. | parent bioproject:PRJNA758396 | embryo Cu 0.156uM 96hpf | GSM5543529 | tissue:embryo Cu 0.156uM 96hpf|cell type:embryos at 96hpf whose parents were exposed to 0.156μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | embryo Cu 0.156uM 96hpf | Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample | embryo Cu 0.156uM 96hpf | 50 60 embryos F1 from each group | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | embryos F1 cultured in normal water environment | cell type:embryos at 96hpf hours post fertilization|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | GSM5543529 | GSM5543529: embryo Cu 0.156uM 96hpf; Danio rerio; RNA Seq | GSM5543529 | 1 | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | GEO Accession:GSM5543529 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | MGISEQ-2000RS | SRP334492 | Cu_0.156uM_96hpf_R1.fastq.gz Cu_0.156uM_96hpf_R2.fastq.gz | fastq fastq | 7167443000.0 | 71674430.0 | GSM5543529 r1 | 0:100 1:100 | A:1930084120;C:1646651059;G:1623549050;T:1966203424;N:955347 | 100 | 100 | 1930084120 | 1646651059 | 1623549050 | 1966203424 | 955347 | SRX11954177 | SRS9963999 | SRA1284991 | GEO | college of informatics, Huazhong Agricultural University | 1 | 0.94339 | 0.113 | 0.6549 | 0.4857 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2021-08-27 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 65853 | 65853 | SRR15657173 | SRX11954176 | SRS9963998 | SRP334492 | PRJNA758398 | Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq] | GSE182945 | Transcriptome Analysis | Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq. | parent bioproject:PRJNA758396 | embryo Cu 0.156uM 24hpf | GSM5543528 | tissue:embryo Cu 0.156uM 24hpf|cell type:embryos at 24hpf whose parents were exposed to 0.156μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | embryo Cu 0.156uM 24hpf | Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample | embryo Cu 0.156uM 24hpf | 50 60 embryos F1 from each group | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | embryos F1 cultured in normal water environment | cell type:embryos at 24hpf hours post fertilization|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | GSM5543528 | GSM5543528: embryo Cu 0.156uM 24hpf; Danio rerio; RNA Seq | GSM5543528 | 1 | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | GEO Accession:GSM5543528 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | MGISEQ-2000RS | SRP334492 | Cu_0.156uM_24hpf_R1.fastq.gz Cu_0.156uM_24hpf_R2.fastq.gz | fastq fastq | 7164832400.0 | 71648324.0 | GSM5543528 r1 | 0:100 1:100 | A:1929135591;C:1646939515;G:1617401036;T:1970900148;N:456110 | 100 | 100 | 1929135591 | 1646939515 | 1617401036 | 1970900148 | 456110 | SRX11954176 | SRS9963998 | SRA1284991 | GEO | college of informatics, Huazhong Agricultural University | 1 | 0.94344 | 0.10713 | 0.68919 | 0.47118 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2021-08-27 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 65854 | 65854 | SRR15657172 | SRX11954175 | SRS9963997 | SRP334492 | PRJNA758398 | Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq] | GSE182945 | Transcriptome Analysis | Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq. | parent bioproject:PRJNA758396 | embryo Cu 0.078uM 96hpf | GSM5543527 | tissue:embryo Cu 0.078uM 96hpf|cell type:embryos at 96hpf whose parents were exposed to 0.078μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | embryo Cu 0.078uM 96hpf | Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample | embryo Cu 0.078uM 96hpf | 50 60 embryos F1 from each group | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | embryos F1 cultured in normal water environment | cell type:embryos at 96hpf hours post fertilization|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | GSM5543527 | GSM5543527: embryo Cu 0.078uM 96hpf; Danio rerio; RNA Seq | GSM5543527 | 1 | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | GEO Accession:GSM5543527 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | MGISEQ-2000RS | SRP334492 | Cu_0.078uM_96hpf_R1.fastq.gz Cu_0.078uM_96hpf_R2.fastq.gz | fastq fastq | 7135774800.0 | 71357748.0 | GSM5543527 r1 | 0:100 1:100 | A:1928230196;C:1633490990;G:1605871113;T:1967776814;N:405687 | 100 | 100 | 1928230196 | 1633490990 | 1605871113 | 1967776814 | 405687 | SRX11954175 | SRS9963997 | SRA1284991 | GEO | college of informatics, Huazhong Agricultural University | 1 | 0.94191 | 0.11803 | 0.65614 | 0.48225 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2021-08-27 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 65855 | 65855 | SRR15657171 | SRX11954174 | SRS9963995 | SRP334492 | PRJNA758398 | Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq] | GSE182945 | Transcriptome Analysis | Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq. | parent bioproject:PRJNA758396 | embryo Cu 0.078uM 24hpf | GSM5543526 | tissue:embryo Cu 0.078uM 24hpf|cell type:embryos at 24hpf whose parents were exposed to 0.078μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | embryo Cu 0.078uM 24hpf | Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample | embryo Cu 0.078uM 24hpf | 50 60 embryos F1 from each group | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | embryos F1 cultured in normal water environment | cell type:embryos at 24hpf hours post fertilization|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | GSM5543526 | GSM5543526: embryo Cu 0.078uM 24hpf; Danio rerio; RNA Seq | GSM5543526 | 1 | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | GEO Accession:GSM5543526 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | MGISEQ-2000RS | SRP334492 | Cu_0.078uM_24hpf_R1.fastq.gz Cu_0.078uM_24hpf_R2.fastq.gz | fastq fastq | 6934019600.0 | 69340196.0 | GSM5543526 r1 | 0:100 1:100 | A:1865548284;C:1597354050;G:1569395022;T:1901304271;N:417973 | 100 | 100 | 1865548284 | 1597354050 | 1569395022 | 1901304271 | 417973 | SRX11954174 | SRS9963995 | SRA1284991 | GEO | college of informatics, Huazhong Agricultural University | 1 | 0.94389 | 0.10356 | 0.68726 | 0.47794 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2021-08-27 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 65856 | 65856 | SRR15657170 | SRX11954173 | SRS9963996 | SRP334492 | PRJNA758398 | Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq] | GSE182945 | Transcriptome Analysis | Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq. | parent bioproject:PRJNA758396 | embryo Control 96hpf | GSM5543525 | tissue:embryo Control 96hpf|cell type:embryos at 96hpf whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | embryo Control 96hpf | Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample | embryo Control 96hpf | 50 60 embryos F1 from each group | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | embryos F1 cultured in normal water environment | cell type:embryos at 96hpf hours post fertilization|treatment:embryos whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | GSM5543525 | GSM5543525: embryo Control 96hpf; Danio rerio; RNA Seq | GSM5543525 | 1 | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | GEO Accession:GSM5543525 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | MGISEQ-2000RS | SRP334492 | Control_96hpf_R1.fastq.gz Control_96hpf_R2.fastq.gz | fastq fastq | 6698614400.0 | 66986144.0 | GSM5543525 r1 | 0:100 1:100 | A:1816763075;C:1526218454;G:1496202651;T:1858550518;N:879702 | 100 | 100 | 1816763075 | 1526218454 | 1496202651 | 1858550518 | 879702 | SRX11954173 | SRS9963996 | SRA1284991 | GEO | college of informatics, Huazhong Agricultural University | 1 | 0.93836 | 0.12432 | 0.65504 | 0.47564 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2021-08-27 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 65857 | 65857 | SRR15657169 | SRX11954172 | SRS9963994 | SRP334492 | PRJNA758398 | Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq] | GSE182945 | Transcriptome Analysis | Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq. | parent bioproject:PRJNA758396 | embryo Control 24hpf | GSM5543524 | tissue:embryo Control 24hpf|cell type:embryos at 24hpf whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | embryo Control 24hpf | Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample | embryo Control 24hpf | 50 60 embryos F1 from each group | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | embryos F1 cultured in normal water environment | cell type:embryos at 24hpf hours post fertilization|treatment:embryos whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish | GSM5543524 | GSM5543524: embryo Control 24hpf; Danio rerio; RNA Seq | GSM5543524 | 1 | RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute | GEO Accession:GSM5543524 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | MGISEQ-2000RS | SRP334492 | Control_24hpf_R1.fastq.gz Control_24hpf_R2.fastq.gz | fastq fastq | 6911559200.0 | 69115592.0 | GSM5543524 r1 | 0:100 1:100 | A:1858569189;C:1592355971;G:1564572369;T:1895593185;N:468486 | 100 | 100 | 1858569189 | 1592355971 | 1564572369 | 1895593185 | 468486 | SRX11954172 | SRS9963994 | SRA1284991 | GEO | college of informatics, Huazhong Agricultural University | 1 | 0.93745 | 0.09795 | 0.69059 | 0.48209 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2021-08-27 | Multi-stage | Multi-stage | Embryo Imprecise | All anatomical structures |
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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");;