run_metadata
20 rows where experiment.platform = "DNBSEQ" and tissue_curation = "Embryo Imprecise"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 30204 | 30204 | SRR27715729 | SRX23381950 | SRS20243484 | SRP485714 | PRJNA1068542 | The effects of HSP60 chaperone deficiency on zebrafish larvae | GSE254091 | Transcriptome Analysis | To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed. | pubmed:39147275 | Ko 3 | GSM8033238 | source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout|geo loc name:missing|collection date:missing | Ko 3 | Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample | embryo | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf. | tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout | GSM8033238 | GSM8033238: Ko 3; Danio rerio; RNA Seq | GSM8033238 r1 | GSM8033238 | 1 | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP485714 | 15_1.fq.gz 15_2.fq.gz | fastq fastq | 5020450600.0 | 25102253.0 | GSM8033238 r1 | 0:100 1:100 | A:1371660785;C:1125396855;G:1130384333;T:1393008627;N:0 | 100 | 100 | 1371660785 | 1125396855 | 1130384333 | 1393008627 | 0 | SRX23381950 | SRS20243484 | SRA1791378 | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | 2 | 0.9229 | 0.92453 | 0.12667 | 0.12674 | 0.65143 | 0.65232 | 0.48379 | 0.48431 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | Denmark | 2024-01-24 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||
| 30205 | 30205 | SRR27715730 | SRX23381949 | SRS20243483 | SRP485714 | PRJNA1068542 | The effects of HSP60 chaperone deficiency on zebrafish larvae | GSE254091 | Transcriptome Analysis | To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed. | pubmed:39147275 | control 3 | GSM8033237 | source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control|geo loc name:missing|collection date:missing | control 3 | Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample | embryo | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf. | tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control | GSM8033237 | GSM8033237: control 3; Danio rerio; RNA Seq | GSM8033237 r1 | GSM8033237 | 1 | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP485714 | 14_1.fq.gz 14_2.fq.gz | fastq fastq | 5020525200.0 | 25102626.0 | GSM8033237 r1 | 0:100 1:100 | A:1366975716;C:1129522599;G:1135845277;T:1388181608;N:0 | 100 | 100 | 1366975716 | 1129522599 | 1135845277 | 1388181608 | 0 | SRX23381949 | SRS20243483 | SRA1791378 | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | 2 | 0.92923 | 0.93091 | 0.11899 | 0.11908 | 0.65117 | 0.651 | 0.48861 | 0.48085 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | Denmark | 2024-01-24 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||
| 30206 | 30206 | SRR27715731 | SRX23381948 | SRS20243485 | SRP485714 | PRJNA1068542 | The effects of HSP60 chaperone deficiency on zebrafish larvae | GSE254091 | Transcriptome Analysis | To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed. | pubmed:39147275 | Ko 2 | GSM8033236 | source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout|geo loc name:missing|collection date:missing | Ko 2 | Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample | embryo | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf. | tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout | GSM8033236 | GSM8033236: Ko 2; Danio rerio; RNA Seq | GSM8033236 r1 | GSM8033236 | 1 | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP485714 | 13_1.fq.gz 13_2.fq.gz | fastq fastq | 5016980000.0 | 25084900.0 | GSM8033236 r1 | 0:100 1:100 | A:1362095542;C:1131485761;G:1140659655;T:1382739042;N:0 | 100 | 100 | 1362095542 | 1131485761 | 1140659655 | 1382739042 | 0 | SRX23381948 | SRS20243485 | SRA1791378 | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | 2 | 0.92867 | 0.92952 | 0.12009 | 0.11989 | 0.64989 | 0.65129 | 0.48735 | 0.48822 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | Denmark | 2024-01-24 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||
| 30207 | 30207 | SRR27715732 | SRX23381947 | SRS20243482 | SRP485714 | PRJNA1068542 | The effects of HSP60 chaperone deficiency on zebrafish larvae | GSE254091 | Transcriptome Analysis | To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed. | pubmed:39147275 | control 2 | GSM8033235 | source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control|geo loc name:missing|collection date:missing | control 2 | Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample | embryo | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf. | tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control | GSM8033235 | GSM8033235: control 2; Danio rerio; RNA Seq | GSM8033235 r1 | GSM8033235 | 1 | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP485714 | 12_1.fq.gz 12_2.fq.gz | fastq fastq | 5014043600.0 | 25070218.0 | GSM8033235 r1 | 0:100 1:100 | A:1365729811;C:1126481057;G:1137205154;T:1384627578;N:0 | 100 | 100 | 1365729811 | 1126481057 | 1137205154 | 1384627578 | 0 | SRX23381947 | SRS20243482 | SRA1791378 | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | 2 | 0.92582 | 0.92658 | 0.11419 | 0.11406 | 0.65173 | 0.65257 | 0.48606 | 0.48533 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | Denmark | 2024-01-24 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||
| 30208 | 30208 | SRR27715733 | SRX23381946 | SRS20243480 | SRP485714 | PRJNA1068542 | The effects of HSP60 chaperone deficiency on zebrafish larvae | GSE254091 | Transcriptome Analysis | To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed. | pubmed:39147275 | Ko 1 | GSM8033234 | source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout|geo loc name:missing|collection date:missing | Ko 1 | Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample | embryo | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf. | tissue:embryo|cell line:5 dpf|genotype:hspd1 / |treatment:hspd1 knockout | GSM8033234 | GSM8033234: Ko 1; Danio rerio; RNA Seq | GSM8033234 r1 | GSM8033234 | 1 | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP485714 | 11_1.fq.gz 11_2.fq.gz | fastq fastq | 5245066800.0 | 26225334.0 | GSM8033234 r1 | 0:100 1:100 | A:1440549629;C:1168536590;G:1175698878;T:1460281703;N:0 | 100 | 100 | 1440549629 | 1168536590 | 1175698878 | 1460281703 | 0 | SRX23381946 | SRS20243480 | SRA1791378 | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | 2 | 0.92279 | 0.92105 | 0.13454 | 0.13464 | 0.65238 | 0.65291 | 0.47828 | 0.48217 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | Denmark | 2024-01-24 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||
| 30209 | 30209 | SRR27715734 | SRX23381945 | SRS20243481 | SRP485714 | PRJNA1068542 | The effects of HSP60 chaperone deficiency on zebrafish larvae | GSE254091 | Transcriptome Analysis | To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed. | pubmed:39147275 | control 1 | GSM8033233 | source name:embryo|tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control|geo loc name:missing|collection date:missing | control 1 | Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample | embryo | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf. | tissue:embryo|cell line:5 dpf|genotype:hspd1+/+|treatment:control | GSM8033233 | GSM8033233: control 1; Danio rerio; RNA Seq | GSM8033233 r1 | GSM8033233 | 1 | The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP485714 | 10_1.fq.gz 10_2.fq.gz | fastq fastq | 5460961000.0 | 27304805.0 | GSM8033233 r1 | 0:100 1:100 | A:1485370839;C:1228940953;G:1237868479;T:1508780729;N:0 | 100 | 100 | 1485370839 | 1228940953 | 1237868479 | 1508780729 | 0 | SRX23381945 | SRS20243481 | SRA1791378 | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital | 2 | 0.92598 | 0.92555 | 0.12074 | 0.12035 | 0.65731 | 0.6577 | 0.46497 | 0.47306 | 100 | 100 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | Denmark | 2024-01-24 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||
| 74329 | 74329 | SRR23635030 | SRX19518333 | SRS16905710 | SRP425040 | PRJNA939370 | The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq] | GSE226182 | Transcriptome Analysis | Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform. | parent bioproject:PRJNA939357 | pubmed:38427557 | KO replicate 2 bulk RNAseq | GSM7067524 | source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing | KO replicate 2 bulk RNAseq | Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample | embryo | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out | GSM7067524 | GSM7067524: KO replicate 2 bulk RNAseq; Danio rerio; RNA Seq | GSM7067524 r1 | GSM7067524 | 1 | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | DNBSEQ | DNBSEQ-G400 | SRP425040 | KO2.fastq.gz | fastq | 4188284200.0 | 41882842.0 | GSM7067524 r1 | 0:100 | A:1066992737;C:1011357361;G:1055554148;T:1041284278;N:13095676 | 100 | 1066992737 | 1011357361 | 1055554148 | 1041284278 | 13095676 | SRX19518333 | SRS16905710 | SRA1597336 | Yunnan University | Yunnan University | 1 | 0.88647 | 0.07541 | 0.7237 | 0.47069 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | bulk | bulk | China | 2023-02-27 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 74330 | 74330 | SRR23635031 | SRX19518332 | SRS16905709 | SRP425040 | PRJNA939370 | The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq] | GSE226182 | Transcriptome Analysis | Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform. | parent bioproject:PRJNA939357 | pubmed:38427557 | KO replicate 1 bulk RNAseq | GSM7067523 | source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing | KO replicate 1 bulk RNAseq | Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample | embryo | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out | GSM7067523 | GSM7067523: KO replicate 1 bulk RNAseq; Danio rerio; RNA Seq | GSM7067523 r1 | GSM7067523 | 1 | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | DNBSEQ | DNBSEQ-G400 | SRP425040 | KO1.fastq.gz | fastq | 4181083400.0 | 41810834.0 | GSM7067523 r1 | 0:100 | A:1077414361;C:996554293;G:1053357384;T:1040649776;N:13107586 | 100 | 1077414361 | 996554293 | 1053357384 | 1040649776 | 13107586 | SRX19518332 | SRS16905709 | SRA1597336 | Yunnan University | Yunnan University | 1 | 0.87685 | 0.07522 | 0.72699 | 0.48859 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | bulk | bulk | China | 2023-02-27 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 74331 | 74331 | SRR23635032 | SRX19518331 | SRS16905708 | SRP425040 | PRJNA939370 | The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq] | GSE226182 | Transcriptome Analysis | Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform. | parent bioproject:PRJNA939357 | pubmed:38427557 | WT replicate 2 bulk RNAseq | GSM7067522 | source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing | WT replicate 2 bulk RNAseq | Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample | embryo | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | tissue:embryo|age:48 hpf|genotype:wild type | GSM7067522 | GSM7067522: WT replicate 2 bulk RNAseq; Danio rerio; RNA Seq | GSM7067522 r1 | GSM7067522 | 1 | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | DNBSEQ | DNBSEQ-G400 | SRP425040 | WT2.fastq.gz | fastq | 1435167700.0 | 14351677.0 | GSM7067522 r1 | 0:100 | A:371412640;C:334204906;G:351277070;T:371684263;N:6588821 | 100 | 371412640 | 334204906 | 351277070 | 371684263 | 6588821 | SRX19518331 | SRS16905708 | SRA1597336 | Yunnan University | Yunnan University | 1 | 0.83841 | 0.15087 | 0.71417 | 0.50982 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | bulk | bulk | China | 2023-02-27 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 74332 | 74332 | SRR23635033 | SRX19518330 | SRS16905707 | SRP425040 | PRJNA939370 | The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq] | GSE226182 | Transcriptome Analysis | Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform. | parent bioproject:PRJNA939357 | pubmed:38427557 | WT replicate 1 bulk RNAseq | GSM7067521 | source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing | WT replicate 1 bulk RNAseq | Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample | embryo | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | tissue:embryo|age:48 hpf|genotype:wild type | GSM7067521 | GSM7067521: WT replicate 1 bulk RNAseq; Danio rerio; RNA Seq | GSM7067521 r1 | GSM7067521 | 1 | RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | DNBSEQ | DNBSEQ-G400 | SRP425040 | WT1.fastq.gz | fastq | 1961618800.0 | 19616188.0 | GSM7067521 r1 | 0:100 | A:518460045;C:447438337;G:477081234;T:509513188;N:9125996 | 100 | 518460045 | 447438337 | 477081234 | 509513188 | 9125996 | SRX19518330 | SRS16905707 | SRA1597336 | Yunnan University | Yunnan University | 1 | 0.81315 | 0.14097 | 0.72342 | 0.50905 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | bulk | bulk | China | 2023-02-27 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 76526 | 76526 | SRR25007131 | SRX20762489 | SRS18050783 | SRP445520 | PRJNA986875 | Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish | GSE235668 | Transcriptome Analysis | Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target. | pubmed:38542412 | T3 1 | GSM7507240 | source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:36hpf|geo loc name:missing|collection date:missing | T3 1 | The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Embryos | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:Embryos|genotype:WT|developmental stage:36hpf | GSM7507240 | GSM7507240: T3 1; Danio rerio; RNA Seq | GSM7507240 r1 | GSM7507240 | 1 | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP445520 | T3_1.R1.fq.gz T3_1.R2.fq.gz | fastq fastq | 15316392300.0 | 51054641.0 | GSM7507240 r1 | 0:150 1:150 | A:3880671888;C:3784758050;G:3856071137;T:3794810224;N:81001 | 150 | 150 | 3880671888 | 3784758050 | 3856071137 | 3794810224 | 81001 | SRX20762489 | SRS18050783 | SRA1661372 | henan normal university | henan normal university | 2 | 0.41572 | 0.57842 | 0.09076 | 0.13329 | 0.79385 | 0.76142 | 0.43528 | 0.43567 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | bgi | bgi | unknown | rrna_depletion | trueseq | bulk | unknown | unknown | China | 2023-06-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 76527 | 76527 | SRR25007132 | SRX20762488 | SRS18050782 | SRP445520 | PRJNA986875 | Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish | GSE235668 | Transcriptome Analysis | Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target. | pubmed:38542412 | T1 1 | GSM7507236 | source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:10hpf|geo loc name:missing|collection date:missing | T1 1 | The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Embryos | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:Embryos|genotype:WT|developmental stage:10hpf | GSM7507236 | GSM7507236: T1 1; Danio rerio; RNA Seq | GSM7507236 r1 | GSM7507236 | 1 | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP445520 | T1_1.R1.fq.gz T1_1.R2.fq.gz | fastq fastq | 13484033700.0 | 44946779.0 | GSM7507236 r1 | 0:150 1:150 | A:3415746428;C:3329088326;G:3392039530;T:3347088129;N:71287 | 150 | 150 | 3415746428 | 3329088326 | 3392039530 | 3347088129 | 71287 | SRX20762488 | SRS18050782 | SRA1661372 | henan normal university | henan normal university | 2 | 0.40423 | 0.57514 | 0.07655 | 0.11873 | 0.80308 | 0.77092 | 0.46754 | 0.46803 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | bgi | bgi | unknown | rrna_depletion | trueseq | bulk | unknown | unknown | China | 2023-06-23 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 76528 | 76528 | SRR25007133 | SRX20762487 | SRS18050781 | SRP445520 | PRJNA986875 | Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish | GSE235668 | Transcriptome Analysis | Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target. | pubmed:38542412 | T1 2 | GSM7507237 | source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:10hpf|geo loc name:missing|collection date:missing | T1 2 | The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Embryos | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:Embryos|genotype:WT|developmental stage:10hpf | GSM7507237 | GSM7507237: T1 2; Danio rerio; RNA Seq | GSM7507237 r1 | GSM7507237 | 1 | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP445520 | T1_2.R1.fq.gz T1_2.R2.fq.gz | fastq fastq | 13733190600.0 | 45777302.0 | GSM7507237 r1 | 0:150 1:150 | A:3445382955;C:3412918499;G:3490188153;T:3384626806;N:74187 | 150 | 150 | 3445382955 | 3412918499 | 3490188153 | 3384626806 | 74187 | SRX20762487 | SRS18050781 | SRA1661372 | henan normal university | henan normal university | 2 | 0.43011 | 0.59623 | 0.08158 | 0.13068 | 0.80288 | 0.77544 | 0.47026 | 0.47364 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | bgi | bgi | unknown | rrna_depletion | trueseq | bulk | unknown | unknown | China | 2023-06-23 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 76529 | 76529 | SRR25007134 | SRX20762486 | SRS18050778 | SRP445520 | PRJNA986875 | Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish | GSE235668 | Transcriptome Analysis | Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target. | pubmed:38542412 | T2 1 | GSM7507238 | source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:24hpf|geo loc name:missing|collection date:missing | T2 1 | The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Embryos | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:Embryos|genotype:WT|developmental stage:24hpf | GSM7507238 | GSM7507238: T2 1; Danio rerio; RNA Seq | GSM7507238 r1 | GSM7507238 | 1 | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP445520 | T2_1.R2.fq.gz T2_1.R1.fq.gz | fastq fastq | 14649880200.0 | 48832934.0 | GSM7507238 r1 | 0:150 1:150 | A:3695224943;C:3636149584;G:3688479871;T:3629948859;N:76943 | 150 | 150 | 3695224943 | 3636149584 | 3688479871 | 3629948859 | 76943 | SRX20762486 | SRS18050778 | SRA1661372 | henan normal university | henan normal university | 2 | 0.43452 | 0.60496 | 0.08789 | 0.13132 | 0.7862 | 0.7528 | 0.44881 | 0.45341 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | bgi | bgi | unknown | rrna_depletion | trueseq | bulk | unknown | unknown | China | 2023-06-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 76530 | 76530 | SRR25007135 | SRX20762485 | SRS18050780 | SRP445520 | PRJNA986875 | Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish | GSE235668 | Transcriptome Analysis | Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target. | pubmed:38542412 | T2 2 | GSM7507239 | source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:24hpf|geo loc name:missing|collection date:missing | T2 2 | The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Embryos | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:Embryos|genotype:WT|developmental stage:24hpf | GSM7507239 | GSM7507239: T2 2; Danio rerio; RNA Seq | GSM7507239 r1 | GSM7507239 | 1 | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP445520 | T2_2.R1.fq.gz T2_2.R2.fq.gz | fastq fastq | 14696199900.0 | 48987333.0 | GSM7507239 r1 | 0:150 1:150 | A:3735683721;C:3615176348;G:3714335362;T:3630926317;N:78152 | 150 | 150 | 3735683721 | 3615176348 | 3714335362 | 3630926317 | 78152 | SRX20762485 | SRS18050780 | SRA1661372 | henan normal university | henan normal university | 2 | 0.42139 | 0.57658 | 0.08829 | 0.1292 | 0.78831 | 0.75617 | 0.44949 | 0.45776 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | bgi | bgi | unknown | rrna_depletion | trueseq | bulk | unknown | unknown | China | 2023-06-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 76531 | 76531 | SRR25007136 | SRX20762484 | SRS18050779 | SRP445520 | PRJNA986875 | Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish | GSE235668 | Transcriptome Analysis | Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target. | pubmed:38542412 | T3 2 | GSM7507241 | source name:Embryos|tissue:Embryos|genotype:WT|developmental stage:36hpf|geo loc name:missing|collection date:missing | T3 2 | The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Embryos | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:Embryos|genotype:WT|developmental stage:36hpf | GSM7507241 | GSM7507241: T3 2; Danio rerio; RNA Seq | GSM7507241 r1 | GSM7507241 | 1 | Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP445520 | T3_2.R2.fq.gz T3_2.R1.fq.gz | fastq fastq | 15346908000.0 | 51156360.0 | GSM7507241 r1 | 0:150 1:150 | A:3937027213;C:3752697817;G:3796118846;T:3860983131;N:80993 | 150 | 150 | 3937027213 | 3752697817 | 3796118846 | 3860983131 | 80993 | SRX20762484 | SRS18050779 | SRA1661372 | henan normal university | henan normal university | 2 | 0.4823 | 0.64213 | 0.10848 | 0.15245 | 0.77966 | 0.74752 | 0.43616 | 0.43697 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | rrna_depletion | trueseq | bulk | unknown | unknown | China | 2023-06-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 76532 | 76532 | SRR25081951 | SRX20835391 | SRS18112575 | SRP446710 | PRJNA987386 | Single nucleus chromatin landscapes during zebrafish early embryogenesis | PRJNA987386 | Other | Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis. | 6 hpf embryos | scRNA zf6hpf 2 | strain:AB/Wild type|isolate:scRNA zf6hpf 2|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | scRNA 6 hpf | scRNA 6 hpf rep2 oligo | scRNA 6 hpf rep2 oligo | scRNA seq of 6 hpf embryos | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP446710 | CNGB Experiment ID:CNX0591993 | DP8450003515BR_L01_5_1.fq.gz DP8450003515BR_L01_5_2.fq.gz | fastq fastq | 14588474300.0 | 291769486.0 | DP8450003515BR L01 5 1.fq.gz | 0:20 1:30 | A:3813233297;C:3660627848;G:3388591530;T:3724524333;N:1497292 | 20 | 30 | 3813233297 | 3660627848 | 3388591530 | 3724524333 | 1497292 | SRX20835391 | SRS18112575 | SRA1664681 | BGI Research, Shenzhen | BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen | 2 | 0.00464 | 0.0003 | 0.00396 | 0.00028 | 0.9978 | 0.99995 | 0.39694 | 0.5 | 20 | 30 | T | T | mates < 9% mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | China | 2023-06-30 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 76533 | 76533 | SRR25081952 | SRX20835390 | SRS18112575 | SRP446710 | PRJNA987386 | Single nucleus chromatin landscapes during zebrafish early embryogenesis | PRJNA987386 | Other | Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis. | 6 hpf embryos | scRNA zf6hpf 2 | strain:AB/Wild type|isolate:scRNA zf6hpf 2|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | scRNA 6 hpf | scRNA 6 hpf rep2 cDNA | scRNA 6 hpf rep2 cDNA | scRNA seq of 6 hpf embryos | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP446710 | CNGB Experiment ID:CNX0591991 | E100036348_L01_5_1.fq.gz E100036348_L01_5_2.fq.gz | fastq fastq | 55097250780.0 | 423825006.0 | E100036348 L01 5 1.fq.gz | 0:30 1:100 | A:16194629059;C:11467532715;G:12387290556;T:15046756280;N:1042170 | 30 | 100 | 16194629059 | 11467532715 | 12387290556 | 15046756280 | 1042170 | SRX20835390 | SRS18112575 | SRA1664681 | BGI Research, Shenzhen | BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen | 2 | 0.00035 | 0.58961 | 0.00033 | 0.06118 | 0.99993 | 0.82564 | 0.33333 | 0.62483 | 30 | 100 | T | B | mate1 technical by mapping diff | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | China | 2023-06-30 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 76534 | 76534 | SRR25081953 | SRX20835389 | SRS18112574 | SRP446710 | PRJNA987386 | Single nucleus chromatin landscapes during zebrafish early embryogenesis | PRJNA987386 | Other | Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis. | 6 hpf embryos | scRNA zf6hpf 1 | strain:AB/Wild type|isolate:scRNA zf6hpf 1|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | scRNA 6 hpf | scRNA 6 hpf rep1 oligo | scRNA 6 hpf rep1 oligo | scRNA seq of 6 hpf embryos | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP446710 | CNGB Experiment ID:CNX0591992 | DP8450003515BR_L01_4_2.fq.gz DP8450003515BR_L01_4_1.fq.gz | fastq fastq | 11338346750.0 | 226766935.0 | DP8450003515BR L01 4 1.fq.gz | 0:20 1:30 | A:2978703558;C:2824119061;G:2623216087;T:2911128054;N:1179990 | 20 | 30 | 2978703558 | 2824119061 | 2623216087 | 2911128054 | 1179990 | SRX20835389 | SRS18112574 | SRA1664681 | BGI Research, Shenzhen | BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen | 2 | 0.00475 | 0.00048 | 0.0041 | 0.00042 | 0.99799 | 0.99979 | 0.472 | 0.4 | 20 | 30 | T | T | mates < 9% mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | China | 2023-06-30 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 76535 | 76535 | SRR25081954 | SRX20835388 | SRS18112574 | SRP446710 | PRJNA987386 | Single nucleus chromatin landscapes during zebrafish early embryogenesis | PRJNA987386 | Other | Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis. | 6 hpf embryos | scRNA zf6hpf 1 | strain:AB/Wild type|isolate:scRNA zf6hpf 1|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal | scRNA 6 hpf | scRNA 6 hpf rep1 cDNA | scRNA 6 hpf rep1 cDNA | scRNA seq of 6 hpf embryos | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP446710 | CNGB Experiment ID:CNX0591990 | E100036348_L01_6_1.fq.gz E100036348_L01_6_2.fq.gz | fastq fastq | 28127062860.0 | 216362022.0 | E100036348 L01 6 1.fq.gz | 0:30 1:100 | A:8147068380;C:5889045118;G:6317467122;T:7772966880;N:515360 | 30 | 100 | 8147068380 | 5889045118 | 6317467122 | 7772966880 | 515360 | SRX20835388 | SRS18112574 | SRA1664681 | BGI Research, Shenzhen | BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen | 2 | 0.00014 | 0.82035 | 0.00012 | 0.07422 | 0.99995 | 0.81412 | 1.0 | 0.68234 | 30 | 100 | T | B | mate1 technical by mapping diff | bgi | bgi | unknown | cdna_unspecified | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | China | 2023-06-30 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;