metadata: run_metadata: 45 rows where devstage_curation = "Multi-stage" and tissue_curation

45 rows where devstage_curation = "Multi-stage" and tissue_curation_coarse = "Undetermined"

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.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.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
30662	30662	SRR28125659	SRX23770350	SRS20595835	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …		adult thy untreated	GSM8115869	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy untreated	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf		Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115869	GSM8115869: adult thy untreated; Danio rerio; RNA Seq	GSM8115869 r1	GSM8115869	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_untreated_S5_L001_R2_001.fastq.gz adult_thy_untreated_S5_L001_R1_001.fastq.gz adult_thy_untreated_S5_L001_I1_001.fastq.gz	fastq fastq fastq	61867658967.0	487146921.0	GSM8115869 r1	0:8 1:28 2:91	A:12933400034;C:9373762639;G:10188374364;T:11834295354;N:537420	8	28	91	12933400034	9373762639	10188374364	11834295354	537420	SRX23770350	SRS20595835			Oncology/Hematology, Boston Children's Hospital	1	0.90847	0.19603	0.76895	0.56494	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
30663	30663	SRR28125660	SRX23770349	SRS20595836	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …		adult thy liberase 2	GSM8115868	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy liberase 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf		Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115868	GSM8115868: adult thy liberase 2; Danio rerio; RNA Seq	GSM8115868 r1	GSM8115868	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_liberase_2_S7_L001_I1_001.fastq.gz adult_thy_liberase_2_S7_L001_R1_001.fastq.gz adult_thy_liberase_2_S7_L001_R2_001.fastq.gz	fastq fastq fastq	64816880653.0	510369139.0	GSM8115868 r1	0:8 1:28 2:91	A:12985717325;C:10400471721;G:10926930853;T:12129907262;N:564488	8	28	91	12985717325	10400471721	10926930853	12129907262	564488	SRX23770349	SRS20595836			Oncology/Hematology, Boston Children's Hospital	1	0.90014	0.13619	0.81103	0.54906	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
30664	30664	SRR28125661	SRX23770348	SRS20595834	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …		adult thy liberase 1	GSM8115867	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy liberase 1	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf		Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115867	GSM8115867: adult thy liberase 1; Danio rerio; RNA Seq	GSM8115867 r1	GSM8115867	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_liberase_1_S6_L001_I1_001.fastq.gz adult_thy_liberase_1_S6_L001_R1_001.fastq.gz adult_thy_liberase_1_S6_L001_R2_001.fastq.gz	fastq fastq fastq	62862684917.0	494981771.0	GSM8115867 r1	0:8 1:28 2:91	A:12631971877;C:10077821577;G:10579831603;T:11753169367;N:546737	8	28	91	12631971877	10077821577	10579831603	11753169367	546737	SRX23770348	SRS20595834			Oncology/Hematology, Boston Children's Hospital	1	0.89921	0.13602	0.814	0.55224	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
37961	37961	SRR1205174	SRX501301	SRS582373	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 5hr 3	GSM1357182	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:5hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	cntl neo 5hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:5hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357182	GSM1357182: cntl neo 5hr 3; Danio rerio; RNA Seq	GSM1357182		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357182	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_5_3.fastq.gz	fastq	1630216750.0	32604335.0	GSM1357182 r1	0:50 1:0	A:435441738;C:384703554;G:377838654;T:432163463;N:69341	50	0		435441738	384703554	377838654	432163463	69341	SRX501301	SRS582373	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93632	0.20492	0.67551	0.50281	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37962	37962	SRR1205173	SRX501300	SRS582372	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 5hr 2	GSM1357181	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:5hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	cntl neo 5hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:5hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357181	GSM1357181: cntl neo 5hr 2; Danio rerio; RNA Seq	GSM1357181		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357181	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_5_2.fastq.gz	fastq	1812797550.0	36255951.0	GSM1357181 r1	0:50 1:0	A:484800524;C:426109547;G:417833682;T:483968870;N:84927	50	0		484800524	426109547	417833682	483968870	84927	SRX501300	SRS582372	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93602	0.21513	0.67517	0.49404	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37963	37963	SRR1205172	SRX501299	SRS582371	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 5hr 1	GSM1357180	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:5hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	cntl neo 5hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:5hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357180	GSM1357180: cntl neo 5hr 1; Danio rerio; RNA Seq	GSM1357180		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357180	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_5_1.fastq.gz	fastq	1616736500.0	32334730.0	GSM1357180 r1	0:50 1:0	A:425328931;C:388105733;G:379129548;T:424100489;N:71799	50	0		425328931	388105733	379129548	424100489	71799	SRX501299	SRS582371	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.9361	0.23516	0.68091	0.50961	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37964	37964	SRR1205171	SRX501298	SRS582370	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 5hr 3	GSM1357179	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:5hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	gfp neo 5hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:5hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357179	GSM1357179: gfp neo 5hr 3; Danio rerio; RNA Seq	GSM1357179		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357179	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_5_3.fastq.gz	fastq	1856512100.0	37130242.0	GSM1357179 r1	0:50 1:0	A:492227117;C:440944515;G:431529818;T:491731276;N:79374	50	0		492227117	440944515	431529818	491731276	79374	SRX501298	SRS582370	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93677	0.28732	0.71435	0.50496	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37965	37965	SRR1205170	SRX501297	SRS582369	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 5hr 2	GSM1357178	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:5hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	gfp neo 5hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:5hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357178	GSM1357178: gfp neo 5hr 2; Danio rerio; RNA Seq	GSM1357178		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357178	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_5_2.fastq.gz	fastq	1605154400.0	32103088.0	GSM1357178 r1	0:50 1:0	A:431076570;C:373656204;G:367046732;T:433299718;N:75176	50	0		431076570	373656204	367046732	433299718	75176	SRX501297	SRS582369	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93022	0.29198	0.69656	0.47675	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37966	37966	SRR1205169	SRX501296	SRS582368	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 5hr 1	GSM1357177	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:5hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	gfp neo 5hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:5hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357177	GSM1357177: gfp neo 5hr 1; Danio rerio; RNA Seq	GSM1357177		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357177	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_5_1.fastq.gz	fastq	1902899900.0	38057998.0	GSM1357177 r1	0:50 1:0	A:511489376;C:443148505;G:433716076;T:514461324;N:84619	50	0		511489376	443148505	433716076	514461324	84619	SRX501296	SRS582368	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.92977	0.29647	0.69583	0.48582	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37967	37967	SRR1205168	SRX501295	SRS582367	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 3hr 3	GSM1357176	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:3hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	cntl neo 3hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:3hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357176	GSM1357176: cntl neo 3hr 3; Danio rerio; RNA Seq	GSM1357176		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357176	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_3_3.fastq.gz	fastq	1555198750.0	31103975.0	GSM1357176 r1	0:50 1:0	A:416734314;C:365733903;G:359113904;T:413549150;N:67479	50	0		416734314	365733903	359113904	413549150	67479	SRX501295	SRS582367	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93432	0.21789	0.67363	0.49063	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37968	37968	SRR1205167	SRX501294	SRS582366	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 3hr 2	GSM1357175	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:3hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	cntl neo 3hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:3hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357175	GSM1357175: cntl neo 3hr 2; Danio rerio; RNA Seq	GSM1357175		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357175	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_3_2.fastq.gz	fastq	1701011300.0	34020226.0	GSM1357175 r1	0:50 1:0	A:453767169;C:401144167;G:392795706;T:453224665;N:79593	50	0		453767169	401144167	392795706	453224665	79593	SRX501294	SRS582366	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93437	0.19214	0.66884	0.48995	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37969	37969	SRR1205166	SRX501293	SRS582365	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 3hr 1	GSM1357174	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:3hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	cntl neo 3hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:3hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357174	GSM1357174: cntl neo 3hr 1; Danio rerio; RNA Seq	GSM1357174		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357174	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_3_1.fastq.gz	fastq	1228792200.0	24575844.0	GSM1357174 r1	0:50 1:0	A:328509222;C:288306723;G:283185002;T:328736353;N:54900	50	0		328509222	288306723	283185002	328736353	54900	SRX501293	SRS582365	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93269	0.21003	0.66592	0.48875	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37970	37970	SRR1205165	SRX501292	SRS582364	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 3hr 3	GSM1357173	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:3hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	gfp neo 3hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:3hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357173	GSM1357173: gfp neo 3hr 3; Danio rerio; RNA Seq	GSM1357173		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357173	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_3_3.fastq.gz	fastq	1406657700.0	28133154.0	GSM1357173 r1	0:50 1:0	A:379997165;C:326224852;G:320555458;T:379818406;N:61819	50	0		379997165	326224852	320555458	379818406	61819	SRX501292	SRS582364	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.9327	0.3167	0.70709	0.48722	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37971	37971	SRR1205164	SRX501291	SRS582363	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 3hr 2	GSM1357172	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:3hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	gfp neo 3hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:3hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357172	GSM1357172: gfp neo 3hr 2; Danio rerio; RNA Seq	GSM1357172		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357172	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_3_2.fastq.gz	fastq	1409177900.0	28183558.0	GSM1357172 r1	0:50 1:0	A:377366991;C:329654609;G:322942817;T:379147506;N:65977	50	0		377366991	329654609	322942817	379147506	65977	SRX501291	SRS582363	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.92559	0.27573	0.69968	0.48668	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37972	37972	SRR1205163	SRX501290	SRS582362	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 3hr 1	GSM1357171	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:3hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	gfp neo 3hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:3hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Apr2012	GSM1357171	GSM1357171: gfp neo 3hr 1; Danio rerio; RNA Seq	GSM1357171		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357171	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_3_1.fastq.gz	fastq	1364255100.0	27285102.0	GSM1357171 r1	0:50 1:0	A:367031933;C:317262942;G:311363762;T:368536308;N:60155	50	0		367031933	317262942	311363762	368536308	60155	SRX501290	SRS582362	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93433	0.34822	0.70504	0.49052	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37973	37973	SRR1205162	SRX501289	SRS582361	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp nt 1hr 3	GSM1357170	tissue:GFP positive cells from 5 dpf larvae\|drug:no drug\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	gfp nt 1hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:no drug\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357170	GSM1357170: gfp nt 1hr 3; Danio rerio; RNA Seq	GSM1357170		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357170	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_nt_1_3.fastq.gz	fastq	2032585500.0	40651710.0	GSM1357170 r1	0:50 1:0	A:540423336;C:478257444;G:470055372;T:543729414;N:119934	50	0		540423336	478257444	470055372	543729414	119934	SRX501289	SRS582361	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93511	0.2696	0.70425	0.49291	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37974	37974	SRR1205161	SRX501288	SRS582360	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp nt 1hr 2	GSM1357169	tissue:GFP positive cells from 5 dpf larvae\|drug:no drug\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	gfp nt 1hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:no drug\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357169	GSM1357169: gfp nt 1hr 2; Danio rerio; RNA Seq	GSM1357169		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357169	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_nt_1_2.fastq.gz	fastq	1562346650.0	31246933.0	GSM1357169 r1	0:50 1:0	A:414164641;C:369142355;G:361974997;T:416978503;N:86154	50	0		414164641	369142355	361974997	416978503	86154	SRX501288	SRS582360	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93897	0.31695	0.70991	0.50448	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37975	37975	SRR1205160	SRX501287	SRS582359	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp nt 1hr 1	GSM1357168	tissue:GFP positive cells from 5 dpf larvae\|drug:no drug\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	gfp nt 1hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:no drug\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357168	GSM1357168: gfp nt 1hr 1; Danio rerio; RNA Seq	GSM1357168		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357168	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_nt_1_1.fastq.gz	fastq	1689050050.0	33781001.0	GSM1357168 r1	0:50 1:0	A:453271567;C:394505701;G:386090706;T:455068897;N:113179	50	0		453271567	394505701	386090706	455068897	113179	SRX501287	SRS582359	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93627	0.28408	0.70585	0.48065	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37976	37976	SRR1205159	SRX501286	SRS582358	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 1hr 3	GSM1357167	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	gfp neo 1hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357167	GSM1357167: gfp neo 1hr 3; Danio rerio; RNA Seq	GSM1357167		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357167	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_1_3.fastq.gz	fastq	1611919200.0	32238384.0	GSM1357167 r1	0:50 1:0	A:428150047;C:380113504;G:372605259;T:430955158;N:95232	50	0		428150047	380113504	372605259	430955158	95232	SRX501286	SRS582358	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.94024	0.31287	0.71601	0.50103	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37977	37977	SRR1205158	SRX501285	SRS582357	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 1hr 2	GSM1357166	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	gfp neo 1hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357166	GSM1357166: gfp neo 1hr 2; Danio rerio; RNA Seq	GSM1357166		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357166	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_1_2.fastq.gz	fastq	1653679950.0	33073599.0	GSM1357166 r1	0:50 1:0	A:439492851;C:388625865;G:381772828;T:443698911;N:89495	50	0		439492851	388625865	381772828	443698911	89495	SRX501285	SRS582357	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.94345	0.38847	0.7357	0.50373	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37978	37978	SRR1205157	SRX501284	SRS582356	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	gfp neo 1hr 1	GSM1357165	tissue:GFP positive cells from 5 dpf larvae\|drug:neomycin\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	gfp neo 1hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP positive cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:1hr\|gfp status:positive\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357165	GSM1357165: gfp neo 1hr 1; Danio rerio; RNA Seq	GSM1357165		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357165	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	gfp_neo_1_1.fastq.gz	fastq	1873022200.0	37460444.0	GSM1357165 r1	0:50 1:0	A:501397145;C:438845045;G:428481612;T:504171995;N:126403	50	0		501397145	438845045	428481612	504171995	126403	SRX501284	SRS582356	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.933	0.24769	0.70591	0.50587	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37979	37979	SRR1205156	SRX501283	SRS582355	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl nt 1hr 3	GSM1357164	tissue:GFP negative cells from 5 dpf larvae\|drug:no drug\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	cntl nt 1hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:no drug\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357164	GSM1357164: cntl nt 1hr 3; Danio rerio; RNA Seq	GSM1357164		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357164	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_nt_1_3.fastq.gz	fastq	1523970250.0	30479405.0	GSM1357164 r1	0:50 1:0	A:404458518;C:360948466;G:353690676;T:404782977;N:89613	50	0		404458518	360948466	353690676	404782977	89613	SRX501283	SRS582355	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93995	0.21232	0.66772	0.48499	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37980	37980	SRR1205155	SRX501282	SRS582354	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl nt 1hr 2	GSM1357163	tissue:GFP negative cells from 5 dpf larvae\|drug:no drug\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	cntl nt 1hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:no drug\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357163	GSM1357163: cntl nt 1hr 2; Danio rerio; RNA Seq	GSM1357163		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357163	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_nt_1_2.fastq.gz	fastq	1649622150.0	32992443.0	GSM1357163 r1	0:50 1:0	A:434980357;C:392949654;G:385359402;T:436242531;N:90206	50	0		434980357	392949654	385359402	436242531	90206	SRX501282	SRS582354	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.94128	0.24395	0.67549	0.50787	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37981	37981	SRR1205154	SRX501281	SRS582353	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl nt 1hr 1	GSM1357162	tissue:GFP negative cells from 5 dpf larvae\|drug:no drug\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	cntl nt 1hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:no drug\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357162	GSM1357162: cntl nt 1hr 1; Danio rerio; RNA Seq	GSM1357162		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357162	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_nt_1_1.fastq.gz	fastq	1953710600.0	39074212.0	GSM1357162 r1	0:50 1:0	A:518489677;C:462970545;G:452495723;T:519623507;N:131148	50	0		518489677	462970545	452495723	519623507	131148	SRX501281	SRS582353	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93818	0.2175	0.66229	0.50468	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37982	37982	SRR1205153	SRX501280	SRS582352	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 1hr 3	GSM1357161	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	cntl neo 1hr 3	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357161	GSM1357161: cntl neo 1hr 3; Danio rerio; RNA Seq	GSM1357161		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357161	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_1_3.fastq.gz	fastq	1934085200.0	38681704.0	GSM1357161 r1	0:50 1:0	A:513203802;C:458221455;G:449581302;T:512967391;N:111250	50	0		513203802	458221455	449581302	512967391	111250	SRX501280	SRS582352	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93811	0.22613	0.66671	0.49681	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37983	37983	SRR1205152	SRX501279	SRS582351	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 1hr 2	GSM1357160	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	cntl neo 1hr 2	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357160	GSM1357160: cntl neo 1hr 2; Danio rerio; RNA Seq	GSM1357160		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357160	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_1_2.fastq.gz	fastq	1836127900.0	36722558.0	GSM1357160 r1	0:50 1:0	A:485828745;C:436091545;G:426562682;T:487543575;N:101353	50	0		485828745	436091545	426562682	487543575	101353	SRX501279	SRS582351	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93856	0.23223	0.67154	0.5021	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
37984	37984	SRR1205151	SRX501278	SRS582350	SRP040561	PRJNA242641	Gene expression analysis of hair cell regeneration in the zebrafish lateral line	GSE56176	Transcriptome Analysis	Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However non mammalian animals e.g. birds amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration because these cells can be acutely killed by exposure to neomycin post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1 3 and 5 hours post neomycin treatment as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin dissociated and FACS sorted into GFP positive and GFP negative populations at xxx 3 and 5 hours following treatment along with a mock treated 1 hr control. The experiment was performed in triplicate for a total of 24 samples.	pubmed:24706903	cntl neo 1hr 1	GSM1357159	tissue:GFP negative cells from 5 dpf larvae\|drug:neomycin\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	cntl neo 1hr 1	Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.	GFP negative cells from 5 dpf larvae	For neomycin treatment 5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.	drug:neomycin\|time:1hr\|gfp status:negative\|genotype:TgsqET20\|experiment date:Mar2012	GSM1357159	GSM1357159: cntl neo 1hr 1; Danio rerio; RNA Seq	GSM1357159		1	Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized collected in a 2mL tube dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.	GEO Accession:GSM1357159	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP040561	loader:latf load	cntl_neo_1_1.fastq.gz	fastq	1687481850.0	33749637.0	GSM1357159 r1	0:50 1:0	A:448529802;C:398804686;G:391019451;T:449013498;N:114413	50	0		448529802	398804686	391019451	449013498	114413	SRX501278	SRS582350	SRA149178	GEO	Seidel, Genomics, Stowers Institute	1	0.93698	0.21557	0.66436	0.49756	50	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2014-03-25	Multi-stage	Multi-stage	Undetermined	Undetermined
63586	63586	SRR13951240	SRX10330055	SRS8449856	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT acrolein treated rep6	GSM5169491	source name:Zebrafish larvae WT acrolein treated larvae\|genotype:WT\|treatment:Acrolein\|tissue:Larvae	Zebrafish larvae WT acrolein treated rep6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT acrolein treated larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Acrolein\|tissue:Larvae	GSM5169491	GSM5169491: Zebrafish larvae WT acrolein treated rep6; Danio rerio; RNA Seq	GSM5169491		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169491	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAALRAAPEI-515_1.fq.gz V300079388_L3_HK500ZEBaopEAALRAAPEI-515_2.fq.gz	fastq fastq	4980022200.0	49800222.0	GSM5169491 r1	0:100 1:100	A:1333773139;C:1140685596;G:1152592074;T:1352971391;N:0	100	100		1333773139	1140685596	1152592074	1352971391	0	SRX10330055	SRS8449856	SRA1205863	GEO	ZMF, University Heidelberg	1	0.9486	0.11229	0.65967	0.47337	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63587	63587	SRR13951239	SRX10330054	SRS8449858	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT acrolein treated rep5	GSM5169490	source name:Zebrafish larvae WT acrolein treated larvae\|genotype:WT\|treatment:Acrolein\|tissue:Larvae	Zebrafish larvae WT acrolein treated rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT acrolein treated larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Acrolein\|tissue:Larvae	GSM5169490	GSM5169490: Zebrafish larvae WT acrolein treated rep5; Danio rerio; RNA Seq	GSM5169490		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169490	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_1.fq.gz V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_2.fq.gz	fastq fastq	4989256800.0	49892568.0	GSM5169490 r1	0:100 1:100	A:1333967860;C:1145275940;G:1156212626;T:1353800374;N:0	100	100		1333967860	1145275940	1156212626	1353800374	0	SRX10330054	SRS8449858	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94949	0.10728	0.65756	0.47006	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63588	63588	SRR13951238	SRX10330053	SRS8449857	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT acrolein treated rep4	GSM5169489	source name:Zebrafish larvae WT acrolein treated larvae\|genotype:WT\|treatment:Acrolein\|tissue:Larvae	Zebrafish larvae WT acrolein treated rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT acrolein treated larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Acrolein\|tissue:Larvae	GSM5169489	GSM5169489: Zebrafish larvae WT acrolein treated rep4; Danio rerio; RNA Seq	GSM5169489		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169489	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_1.fq.gz V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_2.fq.gz	fastq fastq	4991600600.0	49916006.0	GSM5169489 r1	0:100 1:100	A:1332160517;C:1148004219;G:1159807037;T:1351628827;N:0	100	100		1332160517	1148004219	1159807037	1351628827	0	SRX10330053	SRS8449857	SRA1205863	GEO	ZMF, University Heidelberg	1	0.95038	0.10485	0.65977	0.47668	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63589	63589	SRR13951237	SRX10330052	SRS8449855	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT acrolein treated rep3	GSM5169488	source name:Zebrafish larvae WT acrolein treated larvae\|genotype:WT\|treatment:Acrolein\|tissue:Larvae	Zebrafish larvae WT acrolein treated rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT acrolein treated larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Acrolein\|tissue:Larvae	GSM5169488	GSM5169488: Zebrafish larvae WT acrolein treated rep3; Danio rerio; RNA Seq	GSM5169488		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169488	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_1.fq.gz V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_2.fq.gz	fastq fastq	4931029800.0	49310298.0	GSM5169488 r1	0:100 1:100	A:1313566945;C:1137259809;G:1149091650;T:1331111396;N:0	100	100		1313566945	1137259809	1149091650	1331111396	0	SRX10330052	SRS8449855	SRA1205863	GEO	ZMF, University Heidelberg	1	0.95011	0.10594	0.65711	0.48179	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63590	63590	SRR13951236	SRX10330051	SRS8449854	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT acrolein treated rep2	GSM5169487	source name:Zebrafish larvae WT acrolein treated larvae\|genotype:WT\|treatment:Acrolein\|tissue:Larvae	Zebrafish larvae WT acrolein treated rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT acrolein treated larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Acrolein\|tissue:Larvae	GSM5169487	GSM5169487: Zebrafish larvae WT acrolein treated rep2; Danio rerio; RNA Seq	GSM5169487		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169487	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_1.fq.gz V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_2.fq.gz	fastq fastq	4934978600.0	49349786.0	GSM5169487 r1	0:100 1:100	A:1318738318;C:1133208442;G:1143616038;T:1339415802;N:0	100	100		1318738318	1133208442	1143616038	1339415802	0	SRX10330051	SRS8449854	SRA1205863	GEO	ZMF, University Heidelberg	1	0.948	0.10568	0.65685	0.45325	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63591	63591	SRR13951235	SRX10330050	SRS8449851	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT acrolein treated rep1	GSM5169486	source name:Zebrafish larvae WT acrolein treated larvae\|genotype:WT\|treatment:Acrolein\|tissue:Larvae	Zebrafish larvae WT acrolein treated rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT acrolein treated larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Acrolein\|tissue:Larvae	GSM5169486	GSM5169486: Zebrafish larvae WT acrolein treated rep1; Danio rerio; RNA Seq	GSM5169486		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169486	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_1.fq.gz V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_2.fq.gz	fastq fastq	4916868000.0	49168680.0	GSM5169486 r1	0:100 1:100	A:1319311116;C:1122812867;G:1129767432;T:1344976585;N:0	100	100		1319311116	1122812867	1129767432	1344976585	0	SRX10330050	SRS8449851	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94789	0.10769	0.65537	0.47629	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63592	63592	SRR13951234	SRX10330049	SRS8449853	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT rep6	GSM5169485	source name:Zebrafish larvae WT larvae\|genotype:WT\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae WT rep6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Ctrl\|tissue:Larvae	GSM5169485	GSM5169485: Zebrafish larvae WT rep6; Danio rerio; RNA Seq	GSM5169485		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169485	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_1.fq.gz V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_2.fq.gz	fastq fastq	4918223600.0	49182236.0	GSM5169485 r1	0:100 1:100	A:1312501446;C:1129859893;G:1141743360;T:1334118901;N:0	100	100		1312501446	1129859893	1141743360	1334118901	0	SRX10330049	SRS8449853	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94736	0.10854	0.66095	0.46684	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63593	63593	SRR13951251	SRX10330048	SRS8449849	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT rep5	GSM5169484	source name:Zebrafish larvae WT larvae\|genotype:WT\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae WT rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Ctrl\|tissue:Larvae	GSM5169484	GSM5169484: Zebrafish larvae WT rep5; Danio rerio; RNA Seq	GSM5169484		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169484	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAAERAAPEI-505_1.fq.gz V300079388_L2_HK500ZEBaopEAAERAAPEI-505_2.fq.gz	fastq fastq	4921487400.0	49214874.0	GSM5169484 r1	0:100 1:100	A:1307773420;C:1137100007;G:1147334476;T:1329279497;N:0	100	100		1307773420	1137100007	1147334476	1329279497	0	SRX10330048	SRS8449849	SRA1205863	GEO	ZMF, University Heidelberg	1	0.9488	0.10243	0.65596	0.47526	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63594	63594	SRR13951250	SRX10330047	SRS8449847	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT rep4	GSM5169483	source name:Zebrafish larvae WT larvae\|genotype:WT\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae WT rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Ctrl\|tissue:Larvae	GSM5169483	GSM5169483: Zebrafish larvae WT rep4; Danio rerio; RNA Seq	GSM5169483		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169483	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAADRAAPEI-504_1.fq.gz V300079388_L2_HK500ZEBaopEAADRAAPEI-504_2.fq.gz	fastq fastq	4902200200.0	49022002.0	GSM5169483 r1	0:100 1:100	A:1302490426;C:1131663107;G:1148042501;T:1320004166;N:0	100	100		1302490426	1131663107	1148042501	1320004166	0	SRX10330047	SRS8449847	SRA1205863	GEO	ZMF, University Heidelberg	1	0.9486	0.10416	0.66133	0.45959	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63595	63595	SRR13951249	SRX10330046	SRS8449846	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT rep3	GSM5169482	source name:Zebrafish larvae WT larvae\|genotype:WT\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae WT rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Ctrl\|tissue:Larvae	GSM5169482	GSM5169482: Zebrafish larvae WT rep3; Danio rerio; RNA Seq	GSM5169482		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169482	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAACRAAPEI-503_1.fq.gz V300079388_L2_HK500ZEBaopEAACRAAPEI-503_2.fq.gz	fastq fastq	4932506000.0	49325060.0	GSM5169482 r1	0:100 1:100	A:1314021251;C:1136250372;G:1148046464;T:1334187913;N:0	100	100		1314021251	1136250372	1148046464	1334187913	0	SRX10330046	SRS8449846	SRA1205863	GEO	ZMF, University Heidelberg	1	0.95001	0.10334	0.66003	0.474	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63596	63596	SRR13951248	SRX10330045	SRS8449848	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT rep2	GSM5169481	source name:Zebrafish larvae WT larvae\|genotype:WT\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae WT rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Ctrl\|tissue:Larvae	GSM5169481	GSM5169481: Zebrafish larvae WT rep2; Danio rerio; RNA Seq	GSM5169481		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169481	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAABRAAPEI-502_1.fq.gz V300079388_L2_HK500ZEBaopEAABRAAPEI-502_2.fq.gz	fastq fastq	4938494000.0	49384940.0	GSM5169481 r1	0:100 1:100	A:1313976068;C:1139517379;G:1153604159;T:1331396394;N:0	100	100		1313976068	1139517379	1153604159	1331396394	0	SRX10330045	SRS8449848	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94864	0.10252	0.65957	0.47642	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63597	63597	SRR13951247	SRX10330044	SRS8449845	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae WT rep1	GSM5169480	source name:Zebrafish larvae WT larvae\|genotype:WT\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae WT rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae WT larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:WT\|treatment:Ctrl\|tissue:Larvae	GSM5169480	GSM5169480: Zebrafish larvae WT rep1; Danio rerio; RNA Seq	GSM5169480		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169480	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L2_HK500ZEBaopEAAARAAPEI-501_1.fq.gz V300079388_L2_HK500ZEBaopEAAARAAPEI-501_2.fq.gz	fastq fastq	4920498800.0	49204988.0	GSM5169480 r1	0:100 1:100	A:1312070030;C:1133298664;G:1141858537;T:1333271569;N:0	100	100		1312070030	1133298664	1141858537	1333271569	0	SRX10330044	SRS8449845	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94865	0.10459	0.65965	0.46788	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63598	63598	SRR13951246	SRX10330043	SRS8449844	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae akr1a1a KO rep6	GSM5169479	source name:Zebrafish larvae akr1a1a KO larvae\|genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae akr1a1a KO rep6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae akr1a1a KO larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	GSM5169479	GSM5169479: Zebrafish larvae akr1a1a KO rep6; Danio rerio; RNA Seq	GSM5169479		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169479	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAARRAAPEI-521_1.fq.gz V300079388_L3_HK500ZEBaopEAARRAAPEI-521_2.fq.gz	fastq fastq	4983441000.0	49834410.0	GSM5169479 r1	0:100 1:100	A:1322739180;C:1153664354;G:1168919194;T:1338118272;N:0	100	100		1322739180	1153664354	1168919194	1338118272	0	SRX10330043	SRS8449844	SRA1205863	GEO	ZMF, University Heidelberg	1	0.9473	0.09632	0.66419	0.46649	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63599	63599	SRR13951245	SRX10330042	SRS8449843	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae akr1a1a KO rep5	GSM5169478	source name:Zebrafish larvae akr1a1a KO larvae\|genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae akr1a1a KO rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae akr1a1a KO larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	GSM5169478	GSM5169478: Zebrafish larvae akr1a1a KO rep5; Danio rerio; RNA Seq	GSM5169478		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169478	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_1.fq.gz V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_2.fq.gz	fastq fastq	4979727600.0	49797276.0	GSM5169478 r1	0:100 1:100	A:1324141918;C:1150666829;G:1165518713;T:1339400140;N:0	100	100		1324141918	1150666829	1165518713	1339400140	0	SRX10330042	SRS8449843	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94914	0.09649	0.66377	0.47093	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63600	63600	SRR13951244	SRX10330041	SRS8449852	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae akr1a1a KO rep4	GSM5169477	source name:Zebrafish larvae akr1a1a KO larvae\|genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae akr1a1a KO rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae akr1a1a KO larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	GSM5169477	GSM5169477: Zebrafish larvae akr1a1a KO rep4; Danio rerio; RNA Seq	GSM5169477		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169477	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_1.fq.gz V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_2.fq.gz	fastq fastq	4978998800.0	49789988.0	GSM5169477 r1	0:100 1:100	A:1333355936;C:1140285632;G:1151126213;T:1354231019;N:0	100	100		1333355936	1140285632	1151126213	1354231019	0	SRX10330041	SRS8449852	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94594	0.10032	0.66194	0.48009	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63601	63601	SRR13951243	SRX10330040	SRS8449842	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae akr1a1a KO rep3	GSM5169476	source name:Zebrafish larvae akr1a1a KO larvae\|genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae akr1a1a KO rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae akr1a1a KO larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	GSM5169476	GSM5169476: Zebrafish larvae akr1a1a KO rep3; Danio rerio; RNA Seq	GSM5169476		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169476	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAAORAAPEI-518_1.fq.gz V300079388_L3_HK500ZEBaopEAAORAAPEI-518_2.fq.gz	fastq fastq	4978639200.0	49786392.0	GSM5169476 r1	0:100 1:100	A:1331238273;C:1143633964;G:1152228372;T:1351538591;N:0	100	100		1331238273	1143633964	1152228372	1351538591	0	SRX10330040	SRS8449842	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94616	0.1007	0.66054	0.46712	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63602	63602	SRR13951242	SRX10330039	SRS8449850	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae akr1a1a KO rep2	GSM5169475	source name:Zebrafish larvae akr1a1a KO larvae\|genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae akr1a1a KO rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae akr1a1a KO larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	GSM5169475	GSM5169475: Zebrafish larvae akr1a1a KO rep2; Danio rerio; RNA Seq	GSM5169475		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169475	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAANRAAPEI-517_1.fq.gz V300079388_L3_HK500ZEBaopEAANRAAPEI-517_2.fq.gz	fastq fastq	4967553600.0	49675536.0	GSM5169475 r1	0:100 1:100	A:1324408005;C:1143569026;G:1158003192;T:1341573377;N:0	100	100		1324408005	1143569026	1158003192	1341573377	0	SRX10330039	SRS8449850	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94688	0.09559	0.66158	0.4794	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined
63603	63603	SRR13951241	SRX10330038	SRS8449841	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf	pubmed:34278746;pubmed:36711148	Zebrafish larvae akr1a1a KO rep1	GSM5169474	source name:Zebrafish larvae akr1a1a KO larvae\|genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae akr1a1a KO rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae akr1a1a KO larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	GSM5169474	GSM5169474: Zebrafish larvae akr1a1a KO rep1; Danio rerio; RNA Seq	GSM5169474		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169474	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP310389		V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_1.fq.gz V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_2.fq.gz	fastq fastq	4967500800.0	49675008.0	GSM5169474 r1	0:100 1:100	A:1323753410;C:1144795675;G:1158403216;T:1340548499;N:0	100	100		1323753410	1144795675	1158403216	1340548499	0	SRX10330038	SRS8449841	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94765	0.09715	0.66018	0.4542	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined

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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");;