metadata: run_metadata: 36 rows where experiment.library_selection = "cDNA", experiment.platform = "BGISEQ" and tissue

36 rows where experiment.library_selection = "cDNA", experiment.platform = "BGISEQ" and tissue_curation = "Liver"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.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.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
65887	65887	SRR15667963	SRX11964789	SRS9973857	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train overfeed 6	GSM5549117	source name:liver\|tissue:liver\|training:trained\|feed:overfeed\|gender:male\|strain:ABTL	liver train overfeed 6	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:overfeed\|gender:male\|strain:ABTL	GSM5549117	GSM5549117: liver train overfeed 6; Danio rerio; RNA Seq	GSM5549117		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549117	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L24B_1.fq.gz L24B_2.fq.gz	fastq fastq	4893222400.0	48932224.0	GSM5549117 r1	0:100 1:100	A:1299363606;C:1127714226;G:1149448002;T:1316696566;N:0	100	100	1299363606	1127714226	1149448002	1316696566	SRX11964789	SRS9973857	SRA1285419	GEO	ZMF, University Heidelberg	1	0.94811	0.06102	0.81306	0.58353	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65888	65888	SRR15667962	SRX11964788	SRS9973856	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train overfeed 5	GSM5549116	source name:liver\|tissue:liver\|training:trained\|feed:overfeed\|gender:male\|strain:ABTL	liver train overfeed 5	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:overfeed\|gender:male\|strain:ABTL	GSM5549116	GSM5549116: liver train overfeed 5; Danio rerio; RNA Seq	GSM5549116		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549116	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L23B_1.fq.gz L23B_2.fq.gz	fastq fastq	4864315800.0	48643158.0	GSM5549116 r1	0:100 1:100	A:1269157216;C:1139579077;G:1173873653;T:1281705854;N:0	100	100	1269157216	1139579077	1173873653	1281705854	SRX11964788	SRS9973856	SRA1285419	GEO	ZMF, University Heidelberg	1	0.94747	0.0487	0.81779	0.56304	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65889	65889	SRR15667961	SRX11964787	SRS9973855	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train overfeed 4	GSM5549115	source name:liver\|tissue:liver\|training:trained\|feed:overfeed\|gender:male\|strain:ABTL	liver train overfeed 4	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:overfeed\|gender:male\|strain:ABTL	GSM5549115	GSM5549115: liver train overfeed 4; Danio rerio; RNA Seq	GSM5549115		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549115	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L22B_1.fq.gz L22B_2.fq.gz	fastq fastq	4861767400.0	48617674.0	GSM5549115 r1	0:100 1:100	A:1272156595;C:1138672054;G:1163686667;T:1287252084;N:0	100	100	1272156595	1138672054	1163686667	1287252084	SRX11964787	SRS9973855	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95316	0.0514	0.82008	0.50642	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65890	65890	SRR15667960	SRX11964786	SRS9973854	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train overfeed 3	GSM5549114	source name:liver\|tissue:liver\|training:trained\|feed:overfeed\|gender:female\|strain:ABTL	liver train overfeed 3	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:overfeed\|gender:female\|strain:ABTL	GSM5549114	GSM5549114: liver train overfeed 3; Danio rerio; RNA Seq	GSM5549114		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549114	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L21B_1.fq.gz L21B_2.fq.gz	fastq fastq	4830571800.0	48305718.0	GSM5549114 r1	0:100 1:100	A:1279428022;C:1123545637;G:1144703564;T:1282894577;N:0	100	100	1279428022	1123545637	1144703564	1282894577	SRX11964786	SRS9973854	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95734	0.02001	0.8868	0.12725	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65891	65891	SRR15667959	SRX11964785	SRS9973853	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train overfeed 2	GSM5549113	source name:liver\|tissue:liver\|training:trained\|feed:overfeed\|gender:female\|strain:ABTL	liver train overfeed 2	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:overfeed\|gender:female\|strain:ABTL	GSM5549113	GSM5549113: liver train overfeed 2; Danio rerio; RNA Seq	GSM5549113		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549113	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L20B_1.fq.gz L20B_2.fq.gz	fastq fastq	4798900200.0	47989002.0	GSM5549113 r1	0:100 1:100	A:1264903507;C:1122454994;G:1142785530;T:1268756169;N:0	100	100	1264903507	1122454994	1142785530	1268756169	SRX11964785	SRS9973853	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95953	0.02579	0.87251	0.20039	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65892	65892	SRR15667958	SRX11964784	SRS9973852	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train overfeed 1	GSM5549112	source name:liver\|tissue:liver\|training:trained\|feed:overfeed\|gender:female\|strain:ABTL	liver train overfeed 1	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:overfeed\|gender:female\|strain:ABTL	GSM5549112	GSM5549112: liver train overfeed 1; Danio rerio; RNA Seq	GSM5549112		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549112	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L19B_1.fq.gz L19B_2.fq.gz	fastq fastq	4834397800.0	48343978.0	GSM5549112 r1	0:100 1:100	A:1279393804;C:1125815329;G:1148443590;T:1280745077;N:0	100	100	1279393804	1125815329	1148443590	1280745077	SRX11964784	SRS9973852	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95933	0.02008	0.89483	0.14592	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65893	65893	SRR15667957	SRX11964783	SRS9973851	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train ctrl 6	GSM5549111	source name:liver\|tissue:liver\|training:trained\|feed:ctrl\|gender:male\|strain:ABTL	liver train ctrl 6	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:ctrl\|gender:male\|strain:ABTL	GSM5549111	GSM5549111: liver train ctrl 6; Danio rerio; RNA Seq	GSM5549111		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549111	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L18B_1.fq.gz L18B_2.fq.gz	fastq fastq	4821948400.0	48219484.0	GSM5549111 r1	0:100 1:100	A:1291565962;C:1101325255;G:1121237816;T:1307819367;N:0	100	100	1291565962	1101325255	1121237816	1307819367	SRX11964783	SRS9973851	SRA1285419	GEO	ZMF, University Heidelberg	1	0.94729	0.06306	0.81207	0.58228	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65894	65894	SRR15667956	SRX11964782	SRS9973850	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train ctrl 5	GSM5549110	source name:liver\|tissue:liver\|training:trained\|feed:ctrl\|gender:male\|strain:ABTL	liver train ctrl 5	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:ctrl\|gender:male\|strain:ABTL	GSM5549110	GSM5549110: liver train ctrl 5; Danio rerio; RNA Seq	GSM5549110		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549110	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L17B_1.fq.gz L17B_2.fq.gz	fastq fastq	4803628200.0	48036282.0	GSM5549110 r1	0:100 1:100	A:1284799467;C:1098135007;G:1120469212;T:1300224514;N:0	100	100	1284799467	1098135007	1120469212	1300224514	SRX11964782	SRS9973850	SRA1285419	GEO	ZMF, University Heidelberg	1	0.9496	0.0625	0.81456	0.59107	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65895	65895	SRR15667955	SRX11964781	SRS9973849	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train ctrl 4	GSM5549109	source name:liver\|tissue:liver\|training:trained\|feed:ctrl\|gender:male\|strain:ABTL	liver train ctrl 4	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:ctrl\|gender:male\|strain:ABTL	GSM5549109	GSM5549109: liver train ctrl 4; Danio rerio; RNA Seq	GSM5549109		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549109	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L16B_1.fq.gz L16B_2.fq.gz	fastq fastq	4810847400.0	48108474.0	GSM5549109 r1	0:100 1:100	A:1282522728;C:1105003262;G:1127602301;T:1295719109;N:0	100	100	1282522728	1105003262	1127602301	1295719109	SRX11964781	SRS9973849	SRA1285419	GEO	ZMF, University Heidelberg	1	0.94654	0.05935	0.81525	0.55406	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65896	65896	SRR15667954	SRX11964780	SRS9973848	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train ctrl 3	GSM5549108	source name:liver\|tissue:liver\|training:trained\|feed:ctrl\|gender:female\|strain:ABTL	liver train ctrl 3	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:ctrl\|gender:female\|strain:ABTL	GSM5549108	GSM5549108: liver train ctrl 3; Danio rerio; RNA Seq	GSM5549108		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549108	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L15B_1.fq.gz L15B_2.fq.gz	fastq fastq	4985037400.0	49850374.0	GSM5549108 r1	0:100 1:100	A:1350433123;C:1126555415;G:1149552334;T:1358496528;N:0	100	100	1350433123	1126555415	1149552334	1358496528	SRX11964780	SRS9973848	SRA1285419	GEO	ZMF, University Heidelberg	1	0.94223	0.05241	0.81753	0.38734	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65897	65897	SRR15667953	SRX11964779	SRS9973847	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train ctrl 2	GSM5549107	source name:liver\|tissue:liver\|training:trained\|feed:ctrl\|gender:female\|strain:ABTL	liver train ctrl 2	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:ctrl\|gender:female\|strain:ABTL	GSM5549107	GSM5549107: liver train ctrl 2; Danio rerio; RNA Seq	GSM5549107		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549107	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L14B_1.fq.gz L14B_2.fq.gz	fastq fastq	4804454800.0	48044548.0	GSM5549107 r1	0:100 1:100	A:1265573746;C:1124189778;G:1148662079;T:1266029197;N:0	100	100	1265573746	1124189778	1148662079	1266029197	SRX11964779	SRS9973847	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95891	0.02268	0.88392	0.17772	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65898	65898	SRR15667952	SRX11964778	SRS9973846	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver train ctrl 1	GSM5549106	source name:liver\|tissue:liver\|training:trained\|feed:ctrl\|gender:female\|strain:ABTL	liver train ctrl 1	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:trained\|feed:ctrl\|gender:female\|strain:ABTL	GSM5549106	GSM5549106: liver train ctrl 1; Danio rerio; RNA Seq	GSM5549106		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549106	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L13B_1.fq.gz L13B_2.fq.gz	fastq fastq	4822830200.0	48228302.0	GSM5549106 r1	0:100 1:100	A:1276481281;C:1123835516;G:1144873235;T:1277640168;N:0	100	100	1276481281	1123835516	1144873235	1277640168	SRX11964778	SRS9973846	SRA1285419	GEO	ZMF, University Heidelberg	1	0.96141	0.0197	0.89388	0.1349	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65899	65899	SRR15667951	SRX11964777	SRS9973845	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl overfeed 6	GSM5549105	source name:liver\|tissue:liver\|training:ctrl\|feed:overfeed\|gender:female\|strain:ABTL	liver ctrl overfeed 6	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:overfeed\|gender:female\|strain:ABTL	GSM5549105	GSM5549105: liver ctrl overfeed 6; Danio rerio; RNA Seq	GSM5549105		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549105	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L9B_1.fq.gz L9B_2.fq.gz	fastq fastq	4818164600.0	48181646.0	GSM5549105 r1	0:100 1:100	A:1279585168;C:1117941633;G:1137085086;T:1283552713;N:0	100	100	1279585168	1117941633	1137085086	1283552713	SRX11964777	SRS9973845	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95794	0.0217	0.8772	0.13327	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65900	65900	SRR15667950	SRX11964776	SRS9973844	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl overfeed 5	GSM5549104	source name:liver\|tissue:liver\|training:ctrl\|feed:overfeed\|gender:female\|strain:ABTL	liver ctrl overfeed 5	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:overfeed\|gender:female\|strain:ABTL	GSM5549104	GSM5549104: liver ctrl overfeed 5; Danio rerio; RNA Seq	GSM5549104		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549104	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L8B_1.fq.gz L8B_2.fq.gz	fastq fastq	4815366200.0	48153662.0	GSM5549104 r1	0:100 1:100	A:1274920749;C:1122213902;G:1140211257;T:1278020292;N:0	100	100	1274920749	1122213902	1140211257	1278020292	SRX11964776	SRS9973844	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95864	0.02123	0.88805	0.13863	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65901	65901	SRR15667949	SRX11964775	SRS9973843	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl overfeed 4	GSM5549103	source name:liver\|tissue:liver\|training:ctrl\|feed:overfeed\|gender:female\|strain:ABTL	liver ctrl overfeed 4	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:overfeed\|gender:female\|strain:ABTL	GSM5549103	GSM5549103: liver ctrl overfeed 4; Danio rerio; RNA Seq	GSM5549103		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549103	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L7B_1.fq.gz L7B_2.fq.gz	fastq fastq	4806451200.0	48064512.0	GSM5549103 r1	0:100 1:100	A:1272428504;C:1119437887;G:1139899400;T:1274685409;N:0	100	100	1272428504	1119437887	1139899400	1274685409	SRX11964775	SRS9973843	SRA1285419	GEO	ZMF, University Heidelberg	1	0.9605	0.02337	0.87625	0.17173	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65902	65902	SRR15667948	SRX11964774	SRS9973842	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl overfeed 3	GSM5549102	source name:liver\|tissue:liver\|training:ctrl\|feed:overfeed\|gender:male\|strain:ABTL	liver ctrl overfeed 3	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:overfeed\|gender:male\|strain:ABTL	GSM5549102	GSM5549102: liver ctrl overfeed 3; Danio rerio; RNA Seq	GSM5549102		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549102	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L12B_1.fq.gz L12B_2.fq.gz	fastq fastq	4808986200.0	48089862.0	GSM5549102 r1	0:100 1:100	A:1282711930;C:1106482446;G:1126540026;T:1293251798;N:0	100	100	1282711930	1106482446	1126540026	1293251798	SRX11964774	SRS9973842	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95163	0.05783	0.80872	0.56282	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65903	65903	SRR15667947	SRX11964773	SRS9973841	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl overfeed 2	GSM5549101	source name:liver\|tissue:liver\|training:ctrl\|feed:overfeed\|gender:male\|strain:ABTL	liver ctrl overfeed 2	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:overfeed\|gender:male\|strain:ABTL	GSM5549101	GSM5549101: liver ctrl overfeed 2; Danio rerio; RNA Seq	GSM5549101		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549101	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L11B_1.fq.gz L11B_2.fq.gz	fastq fastq	4813626000.0	48136260.0	GSM5549101 r1	0:100 1:100	A:1280868095;C:1108012462;G:1126540954;T:1298204489;N:0	100	100	1280868095	1108012462	1126540954	1298204489	SRX11964773	SRS9973841	SRA1285419	GEO	ZMF, University Heidelberg	1	0.94831	0.05349	0.81513	0.57243	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65904	65904	SRR15667946	SRX11964772	SRS9973840	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl overfeed 1	GSM5549100	source name:liver\|tissue:liver\|training:ctrl\|feed:overfeed\|gender:male\|strain:ABTL	liver ctrl overfeed 1	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:overfeed\|gender:male\|strain:ABTL	GSM5549100	GSM5549100: liver ctrl overfeed 1; Danio rerio; RNA Seq	GSM5549100		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549100	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L10B_1.fq.gz L10B_2.fq.gz	fastq fastq	4810219200.0	48102192.0	GSM5549100 r1	0:100 1:100	A:1291986049;C:1097301072;G:1114733041;T:1306199038;N:0	100	100	1291986049	1097301072	1114733041	1306199038	SRX11964772	SRS9973840	SRA1285419	GEO	ZMF, University Heidelberg	1	0.9477	0.06719	0.80762	0.56967	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65905	65905	SRR15667945	SRX11964771	SRS9973839	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl ctrl 6	GSM5549099	source name:liver\|tissue:liver\|training:ctrl\|feed:ctrl\|gender:male\|strain:ABTL	liver ctrl ctrl 6	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:ctrl\|gender:male\|strain:ABTL	GSM5549099	GSM5549099: liver ctrl ctrl 6; Danio rerio; RNA Seq	GSM5549099		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549099	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L6B_1.fq.gz L6B_2.fq.gz	fastq fastq	4800718000.0	48007180.0	GSM5549099 r1	0:100 1:100	A:1258342638;C:1122320482;G:1144931913;T:1275122967;N:0	100	100	1258342638	1122320482	1144931913	1275122967	SRX11964771	SRS9973839	SRA1285419	GEO	ZMF, University Heidelberg	1	0.953	0.05324	0.81257	0.58562	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65906	65906	SRR15667944	SRX11964770	SRS9973838	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl ctrl 5	GSM5549098	source name:liver\|tissue:liver\|training:ctrl\|feed:ctrl\|gender:male\|strain:ABTL	liver ctrl ctrl 5	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:ctrl\|gender:male\|strain:ABTL	GSM5549098	GSM5549098: liver ctrl ctrl 5; Danio rerio; RNA Seq	GSM5549098		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549098	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L5B_1.fq.gz L5B_2.fq.gz	fastq fastq	4806088800.0	48060888.0	GSM5549098 r1	0:100 1:100	A:1271888694;C:1114093824;G:1133421540;T:1286684742;N:0	100	100	1271888694	1114093824	1133421540	1286684742	SRX11964770	SRS9973838	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95001	0.05792	0.807	0.56126	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65907	65907	SRR15667943	SRX11964769	SRS9973837	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl ctrl 4	GSM5549097	source name:liver\|tissue:liver\|training:ctrl\|feed:ctrl\|gender:male\|strain:ABTL	liver ctrl ctrl 4	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:ctrl\|gender:male\|strain:ABTL	GSM5549097	GSM5549097: liver ctrl ctrl 4; Danio rerio; RNA Seq	GSM5549097		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549097	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L4B_1.fq.gz L4B_2.fq.gz	fastq fastq	4793658200.0	47936582.0	GSM5549097 r1	0:100 1:100	A:1278328591;C:1101882376;G:1120230481;T:1293216752;N:0	100	100	1278328591	1101882376	1120230481	1293216752	SRX11964769	SRS9973837	SRA1285419	GEO	ZMF, University Heidelberg	1	0.94635	0.06821	0.77814	0.57203	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65908	65908	SRR15667942	SRX11964768	SRS9973836	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl ctrl 3	GSM5549096	source name:liver\|tissue:liver\|training:ctrl\|feed:ctrl\|gender:female\|strain:ABTL	liver ctrl ctrl 3	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:ctrl\|gender:female\|strain:ABTL	GSM5549096	GSM5549096: liver ctrl ctrl 3; Danio rerio; RNA Seq	GSM5549096		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549096	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L3B_1.fq.gz L3B_2.fq.gz	fastq fastq	4826663000.0	48266630.0	GSM5549096 r1	0:100 1:100	A:1279595092;C:1123953174;G:1141367365;T:1281747369;N:0	100	100	1279595092	1123953174	1141367365	1281747369	SRX11964768	SRS9973836	SRA1285419	GEO	ZMF, University Heidelberg	1	0.9594	0.02127	0.88463	0.12493	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65909	65909	SRR15667941	SRX11964767	SRS9973835	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl ctrl 2	GSM5549095	source name:liver\|tissue:liver\|training:ctrl\|feed:ctrl\|gender:female\|strain:ABTL	liver ctrl ctrl 2	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:ctrl\|gender:female\|strain:ABTL	GSM5549095	GSM5549095: liver ctrl ctrl 2; Danio rerio; RNA Seq	GSM5549095		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549095	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L2B_1.fq.gz L2B_2.fq.gz	fastq fastq	4825604600.0	48256046.0	GSM5549095 r1	0:100 1:100	A:1280321186;C:1120511740;G:1138899889;T:1285871785;N:0	100	100	1280321186	1120511740	1138899889	1285871785	SRX11964767	SRS9973835	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95896	0.0192	0.88899	0.11515	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
65910	65910	SRR15667940	SRX11964766	SRS9973834	SRP334698	PRJNA758884	Metabolic and transcriptional adaptations improve physical performance of zebrafish	GSE183023	Transcriptome Analysis	Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish	pubmed:34679716	liver ctrl ctrl 1	GSM5549094	source name:liver\|tissue:liver\|training:ctrl\|feed:ctrl\|gender:female\|strain:ABTL	liver ctrl ctrl 1	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.	liver	Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.	tissue:liver\|training:ctrl\|feed:ctrl\|gender:female\|strain:ABTL	GSM5549094	GSM5549094: liver ctrl ctrl 1; Danio rerio; RNA Seq	GSM5549094		1	Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5549094	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP334698	L1B_1.fq.gz L1B_2.fq.gz	fastq fastq	4829756800.0	48297568.0	GSM5549094 r1	0:100 1:100	A:1282017434;C:1119791375;G:1138880812;T:1289067179;N:0	100	100	1282017434	1119791375	1138880812	1289067179	SRX11964766	SRS9973834	SRA1285419	GEO	ZMF, University Heidelberg	1	0.95838	0.03146	0.8479	0.28451	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-08-30	Juvenile	Juvenile	Liver	Liver and Biliary System
70080	70080	SRR19445938	SRX15499122	SRS13214006	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 / 6	GSM6205029	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:KO	Glo2 / 6	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:KO	GSM6205029	GSM6205029: Glo2 / 6; Danio rerio; RNA Seq	GSM6205029 r1	GSM6205029	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	12.1_1.fq.gz 12.1_2.fq.gz	fastq fastq	4163038200.0	41630382.0	GSM6205029 r1	0:100 1:100	A:1080428167;C:982538284;G:1004098821;T:1095972928;N:0	100	100	1080428167	982538284	1004098821	1095972928	SRX15499122	SRS13214006	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95934	0.04773	0.80028	0.52892	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70081	70081	SRR19445939	SRX15499121	SRS13214005	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 +/+ 6	GSM6205028	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:WT	Glo2 +/+ 6	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:WT	GSM6205028	GSM6205028: Glo2 +/+ 6; Danio rerio; RNA Seq	GSM6205028 r1	GSM6205028	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	11.1_1.fq.gz 11.1_2.fq.gz	fastq fastq	4170292600.0	41702926.0	GSM6205028 r1	0:100 1:100	A:1081431596;C:983791100;G:1012532071;T:1092537833;N:0	100	100	1081431596	983791100	1012532071	1092537833	SRX15499121	SRS13214005	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95587	0.0499	0.80805	0.50421	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70082	70082	SRR19445940	SRX15499120	SRS13214004	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 / 5	GSM6205027	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:KO	Glo2 / 5	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:KO	GSM6205027	GSM6205027: Glo2 / 5; Danio rerio; RNA Seq	GSM6205027 r1	GSM6205027	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	10.1_1.fq.gz 10.1_2.fq.gz	fastq fastq	4165964600.0	41659646.0	GSM6205027 r1	0:100 1:100	A:1087548367;C:975174787;G:1002623835;T:1100617611;N:0	100	100	1087548367	975174787	1002623835	1100617611	SRX15499120	SRS13214004	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95351	0.05573	0.80229	0.5231	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70083	70083	SRR19445941	SRX15499119	SRS13214003	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 +/+ 5	GSM6205026	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:WT	Glo2 +/+ 5	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:WT	GSM6205026	GSM6205026: Glo2 +/+ 5; Danio rerio; RNA Seq	GSM6205026 r1	GSM6205026	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	9.1_1.fq.gz 9.1_2.fq.gz	fastq fastq	4161803400.0	41618034.0	GSM6205026 r1	0:100 1:100	A:1084378904;C:978685192;G:1004569873;T:1094169431;N:0	100	100	1084378904	978685192	1004569873	1094169431	SRX15499119	SRS13214003	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95218	0.04867	0.80732	0.52859	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70084	70084	SRR19445942	SRX15499118	SRS13214002	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 / 4	GSM6205025	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:KO	Glo2 / 4	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:KO	GSM6205025	GSM6205025: Glo2 / 4; Danio rerio; RNA Seq	GSM6205025 r1	GSM6205025	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	8.1_1.fq.gz 8.1_2.fq.gz	fastq fastq	4152089400.0	41520894.0	GSM6205025 r1	0:100 1:100	A:1071439906;C:981252736;G:1021757559;T:1077639199;N:0	100	100	1071439906	981252736	1021757559	1077639199	SRX15499118	SRS13214002	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94509	0.04233	0.82031	0.5193	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70085	70085	SRR19445943	SRX15499117	SRS13214001	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 +/+ 4	GSM6205024	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:WT	Glo2 +/+ 4	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:WT	GSM6205024	GSM6205024: Glo2 +/+ 4; Danio rerio; RNA Seq	GSM6205024 r1	GSM6205024	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	7.1_1.fq.gz 7.1_2.fq.gz	fastq fastq	4164307200.0	41643072.0	GSM6205024 r1	0:100 1:100	A:1089101337;C:971144234;G:1001055993;T:1103005636;N:0	100	100	1089101337	971144234	1001055993	1103005636	SRX15499117	SRS13214001	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95715	0.05232	0.8062	0.52299	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70086	70086	SRR19445944	SRX15499116	SRS13214000	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 / 3	GSM6205023	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:KO	Glo2 / 3	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:KO	GSM6205023	GSM6205023: Glo2 / 3; Danio rerio; RNA Seq	GSM6205023 r1	GSM6205023	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	6.1_1.fq.gz 6.1_2.fq.gz	fastq fastq	4160202200.0	41602022.0	GSM6205023 r1	0:100 1:100	A:1078397784;C:984320163;G:1006828922;T:1090655331;N:0	100	100	1078397784	984320163	1006828922	1090655331	SRX15499116	SRS13214000	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95752	0.04539	0.8072	0.5241	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70087	70087	SRR19445945	SRX15499115	SRS13213999	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 +/+ 3	GSM6205022	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:WT	Glo2 +/+ 3	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:WT	GSM6205022	GSM6205022: Glo2 +/+ 3; Danio rerio; RNA Seq	GSM6205022 r1	GSM6205022	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	5.1_1.fq.gz 5.1_2.fq.gz	fastq fastq	4165235600.0	41652356.0	GSM6205022 r1	0:100 1:100	A:1072104475;C:989511105;G:1023359503;T:1080260517;N:0	100	100	1072104475	989511105	1023359503	1080260517	SRX15499115	SRS13213999	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95194	0.03798	0.82087	0.54781	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70088	70088	SRR19445946	SRX15499114	SRS13213998	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 / 2	GSM6205021	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:KO	Glo2 / 2	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:KO	GSM6205021	GSM6205021: Glo2 / 2; Danio rerio; RNA Seq	GSM6205021 r1	GSM6205021	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	4.1_1.fq.gz 4.1_2.fq.gz	fastq fastq	4171018400.0	41710184.0	GSM6205021 r1	0:100 1:100	A:1073769040;C:990042636;G:1019695979;T:1087510745;N:0	100	100	1073769040	990042636	1019695979	1087510745	SRX15499114	SRS13213998	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95183	0.04539	0.81134	0.51505	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70089	70089	SRR19445947	SRX15499113	SRS13213997	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 +/+ 2	GSM6205020	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:WT	Glo2 +/+ 2	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:WT	GSM6205020	GSM6205020: Glo2 +/+ 2; Danio rerio; RNA Seq	GSM6205020 r1	GSM6205020	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	3.1_1.fq.gz 3.1_2.fq.gz	fastq fastq	4145841000.0	41458410.0	GSM6205020 r1	0:100 1:100	A:1051425067;C:998554505;G:1029593084;T:1066268344;N:0	100	100	1051425067	998554505	1029593084	1066268344	SRX15499113	SRS13213997	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.96363	0.03563	0.81994	0.49336	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70090	70090	SRR19445948	SRX15499112	SRS13213996	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 / 1	GSM6205019	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:KO	Glo2 / 1	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:KO	GSM6205019	GSM6205019: Glo2 / 1; Danio rerio; RNA Seq	GSM6205019 r1	GSM6205019	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	2.1_1.fq.gz 2.1_2.fq.gz	fastq fastq	4147644400.0	41476444.0	GSM6205019 r1	0:100 1:100	A:1103014496;C:947498522;G:988532296;T:1108599086;N:0	100	100	1103014496	947498522	988532296	1108599086	SRX15499112	SRS13213996	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94203	0.05616	0.81268	0.5326	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System
70091	70091	SRR19445949	SRX15499111	SRS13213995	SRP377632	PRJNA843695	Loss of Glo2 alters the glucose metabolism in zebrafish	GSE205085	Transcriptome Analysis	Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.	pubmed:36535130	Glo2 +/+ 1	GSM6205018	source name:Tgfli1:EGFP\|tissue:whole liver\|trained:no\|genotype:WT	Glo2 +/+ 1	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 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Tgfli1:EGFP		Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:whole liver\|trained:no\|genotype:WT	GSM6205018	GSM6205018: Glo2 +/+ 1; Danio rerio; RNA Seq	GSM6205018 r1	GSM6205018	1	Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP377632	1.1_1.fq.gz 1.1_2.fq.gz	fastq fastq	4155343800.0	41553438.0	GSM6205018 r1	0:100 1:100	A:1072547817;C:985284919;G:1008557411;T:1088953653;N:0	100	100	1072547817	985284919	1008557411	1088953653	SRX15499111	SRS13213995	SRA1428824	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.96135	0.04666	0.80543	0.51213	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2022-05-30	Undetermined	Larval	Liver	Liver and Biliary System

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