run_metadata
980 rows where experiment.platform = "DNBSEQ" and tissue_curation_coarse = "All anatomical structures"
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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 | |||||||||||
| 64506 | 64506 | SRR17299063 | SRX13476323 | SRS11373166 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL58 | GSM5746868 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL58 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746868 | GSM5746868: Microwell seq datasets of Zebrafish 24hpf COL58; Danio rerio; RNA Seq | GSM5746868 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL58.bam | bam | 91823975304.0 | 527723996.0 | GSM5746868 r1 | 0:24 1:150 | A:27162173122;C:19911517883;G:21018214314;T:23663599459;N:68470526 | 24 | 150 | 27162173122 | 19911517883 | 21018214314 | 23663599459 | 68470526 | SRX13476323 | SRS11373166 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00273 | 0.74807 | 0.00242 | 0.067 | 0.99949 | 0.84889 | 0.32 | 0.62031 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64507 | 64507 | SRR17299062 | SRX13476322 | SRS11373165 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL57 | GSM5746867 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL57 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746867 | GSM5746867: Microwell seq datasets of Zebrafish 24hpf COL57; Danio rerio; RNA Seq | GSM5746867 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL57.bam | bam | 83668974276.0 | 480856174.0 | GSM5746867 r1 | 0:24 1:150 | A:24589284117;C:18203396283;G:19071978317;T:21739883658;N:64431901 | 24 | 150 | 24589284117 | 18203396283 | 19071978317 | 21739883658 | 64431901 | SRX13476322 | SRS11373165 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00288 | 0.75168 | 0.00269 | 0.07335 | 0.99969 | 0.84419 | 0.6 | 0.6312 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64508 | 64508 | SRR17299061 | SRX13476321 | SRS11373164 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL56 | GSM5746866 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL56 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746866 | GSM5746866: Microwell seq datasets of Zebrafish 24hpf COL56; Danio rerio; RNA Seq | GSM5746866 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL56.bam | bam | 86257073418.0 | 495730307.0 | GSM5746866 r1 | 0:24 1:150 | A:25447223471;C:18668491192;G:19647110520;T:22426583347;N:67664888 | 24 | 150 | 25447223471 | 18668491192 | 19647110520 | 22426583347 | 67664888 | SRX13476321 | SRS11373164 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00275 | 0.73434 | 0.00255 | 0.07548 | 0.99967 | 0.84325 | 0.4375 | 0.5398 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64509 | 64509 | SRR17299060 | SRX13476320 | SRS11373163 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL55 | GSM5746865 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL55 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746865 | GSM5746865: Microwell seq datasets of Zebrafish 24hpf COL55; Danio rerio; RNA Seq | GSM5746865 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL55.bam | bam | 90331122120.0 | 519144380.0 | GSM5746865 r1 | 0:24 1:150 | A:26895594483;C:19418243460;G:20453276913;T:23498626121;N:65381143 | 24 | 150 | 26895594483 | 19418243460 | 20453276913 | 23498626121 | 65381143 | SRX13476320 | SRS11373163 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00295 | 0.73613 | 0.00277 | 0.07262 | 0.99971 | 0.83926 | 0.66666 | 0.56101 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64510 | 64510 | SRR17299059 | SRX13476319 | SRS11373162 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL53 | GSM5746864 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL53 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746864 | GSM5746864: Microwell seq datasets of Zebrafish 24hpf COL53; Danio rerio; RNA Seq | GSM5746864 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL53.bam | bam | 89040837126.0 | 511728949.0 | GSM5746864 r1 | 0:24 1:150 | A:26403646377;C:19129690981;G:20273444200;T:23171059435;N:62996133 | 24 | 150 | 26403646377 | 19129690981 | 20273444200 | 23171059435 | 62996133 | SRX13476319 | SRS11373162 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00256 | 0.73401 | 0.00242 | 0.07541 | 0.99977 | 0.83731 | 0.36363 | 0.56119 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64511 | 64511 | SRR17299058 | SRX13476318 | SRS11373161 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL52 | GSM5746863 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL52 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746863 | GSM5746863: Microwell seq datasets of Zebrafish 24hpf COL52; Danio rerio; RNA Seq | GSM5746863 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL52.bam | bam | 92071528062.0 | 529146713.0 | GSM5746863 r1 | 0:24 1:150 | A:27250499787;C:19863195558;G:21006813218;T:23884436340;N:66583159 | 24 | 150 | 27250499787 | 19863195558 | 21006813218 | 23884436340 | 66583159 | SRX13476318 | SRS11373161 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00303 | 0.73044 | 0.00285 | 0.07319 | 0.99969 | 0.84118 | 0.6 | 0.55998 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64512 | 64512 | SRR17299057 | SRX13476317 | SRS11373160 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL51 | GSM5746862 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL51 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746862 | GSM5746862: Microwell seq datasets of Zebrafish 24hpf COL51; Danio rerio; RNA Seq | GSM5746862 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL51.bam | bam | 89393336592.0 | 513754808.0 | GSM5746862 r1 | 0:24 1:150 | A:26357157407;C:19229237017;G:20353675917;T:23391840285;N:61425966 | 24 | 150 | 26357157407 | 19229237017 | 20353675917 | 23391840285 | 61425966 | SRX13476317 | SRS11373160 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00318 | 0.74297 | 0.003 | 0.07874 | 0.99969 | 0.83481 | 0.6 | 0.58428 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64513 | 64513 | SRR17299056 | SRX13476316 | SRS11373159 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 24hpf COL50 | GSM5746861 | source name:Zebrafish 24hpf sample1|strain:AB|age:24 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 24hpf COL50 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 24hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:24 hours|tissue:whole organism | GSM5746861 | GSM5746861: Microwell seq datasets of Zebrafish 24hpf COL50; Danio rerio; RNA Seq | GSM5746861 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_24hpf_COL50.bam | bam | 93180912216.0 | 535522484.0 | GSM5746861 r1 | 0:24 1:150 | A:27511179288;C:19943495783;G:21163186103;T:24482014463;N:81036579 | 24 | 150 | 27511179288 | 19943495783 | 21163186103 | 24482014463 | 81036579 | SRX13476316 | SRS11373159 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00287 | 0.73081 | 0.00269 | 0.08165 | 0.99969 | 0.83469 | 0.53333 | 0.56313 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-21 | Pharyngula | Embryo | Whole Organism | All anatomical structures | |||||||||||
| 64514 | 64514 | SRR17137062 | SRX13321492 | SRS11229253 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL104 | GSM5718328 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL104 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718328 | GSM5718328: Microwell seq datasets of Zebrafish 72hpf COL104; Danio rerio; RNA Seq | GSM5718328 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL104.bam | 10X Genomics bam file | 90497447328.0 | 520100272.0 | GSM5718328 r1 | 0:24 1:150 | A:26568037621;C:19526761960;G:20762820842;T:23593883403;N:45943502 | 24 | 150 | 26568037621 | 19526761960 | 20762820842 | 23593883403 | 45943502 | SRX13321492 | SRS11229253 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00219 | 0.7651 | 0.00205 | 0.0914 | 0.99981 | 0.79953 | 0.5 | 0.51979 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64515 | 64515 | SRR17137061 | SRX13321491 | SRS11229252 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL103 | GSM5718327 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL103 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718327 | GSM5718327: Microwell seq datasets of Zebrafish 72hpf COL103; Danio rerio; RNA Seq | GSM5718327 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL103.bam | bam | 97437769842.0 | 559987183.0 | GSM5718327 r1 | 0:24 1:150 | A:28425257606;C:21026057575;G:22210354179;T:25724166722;N:51933760 | 24 | 150 | 28425257606 | 21026057575 | 22210354179 | 25724166722 | 51933760 | SRX13321491 | SRS11229252 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00232 | 0.76296 | 0.00214 | 0.09247 | 0.99975 | 0.7963 | 0.58333 | 0.50975 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64516 | 64516 | SRR17137060 | SRX13321490 | SRS11229251 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL102 | GSM5718326 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL102 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718326 | GSM5718326: Microwell seq datasets of Zebrafish 72hpf COL102; Danio rerio; RNA Seq | GSM5718326 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL102.bam | bam | 99647119878.0 | 572684597.0 | GSM5718326 r1 | 0:24 1:150 | A:29163675513;C:21410312143;G:22841561495;T:26179135838;N:52434889 | 24 | 150 | 29163675513 | 21410312143 | 22841561495 | 26179135838 | 52434889 | SRX13321490 | SRS11229251 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00211 | 0.75462 | 0.00197 | 0.08783 | 0.99979 | 0.79614 | 0.6 | 0.48777 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64517 | 64517 | SRR17137059 | SRX13321489 | SRS11229250 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL101 | GSM5718325 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL101 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718325 | GSM5718325: Microwell seq datasets of Zebrafish 72hpf COL101; Danio rerio; RNA Seq | GSM5718325 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL101.bam | bam | 103850532360.0 | 596842140.0 | GSM5718325 r1 | 0:24 1:150 | A:30253504994;C:22208170461;G:23486370057;T:27846281411;N:56205437 | 24 | 150 | 30253504994 | 22208170461 | 23486370057 | 27846281411 | 56205437 | SRX13321489 | SRS11229250 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00248 | 0.76955 | 0.00238 | 0.09242 | 0.99985 | 0.78549 | 0.0 | 0.48332 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64518 | 64518 | SRR17137058 | SRX13321488 | SRS11229249 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL100 | GSM5718324 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL100 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718324 | GSM5718324: Microwell seq datasets of Zebrafish 72hpf COL100; Danio rerio; RNA Seq | GSM5718324 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL100.bam | bam | 79732033224.0 | 458230076.0 | GSM5718324 r1 | 0:24 1:150 | A:23142121477;C:17273443279;G:18152994838;T:21124595570;N:38878060 | 24 | 150 | 23142121477 | 17273443279 | 18152994838 | 21124595570 | 38878060 | SRX13321488 | SRS11229249 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.0019 | 0.78954 | 0.00176 | 0.1 | 0.99977 | 0.79302 | 0.45454 | 0.53183 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64519 | 64519 | SRR17137057 | SRX13321487 | SRS11229248 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL99 | GSM5718323 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL99 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718323 | GSM5718323: Microwell seq datasets of Zebrafish 72hpf COL99; Danio rerio; RNA Seq | GSM5718323 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL99.bam | bam | 57905355774.0 | 332789401.0 | GSM5718323 r1 | 0:24 1:150 | A:16732054497;C:12484254815;G:13099812159;T:15561038953;N:28195350 | 24 | 150 | 16732054497 | 12484254815 | 13099812159 | 15561038953 | 28195350 | SRX13321487 | SRS11229248 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.0023 | 0.79516 | 0.00213 | 0.10777 | 0.99977 | 0.79413 | 0.5 | 0.52425 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64520 | 64520 | SRR17137056 | SRX13321486 | SRS11229247 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL98 | GSM5718322 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL98 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718322 | GSM5718322: Microwell seq datasets of Zebrafish 72hpf COL98; Danio rerio; RNA Seq | GSM5718322 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL98.bam | bam | 133922399388.0 | 769668962.0 | GSM5718322 r1 | 0:24 1:150 | A:39157671234;C:28685783001;G:30222645162;T:35787052837;N:69247154 | 24 | 150 | 39157671234 | 28685783001 | 30222645162 | 35787052837 | 69247154 | SRX13321486 | SRS11229247 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00205 | 0.77779 | 0.00189 | 0.10045 | 0.99977 | 0.7903 | 0.36363 | 0.52076 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64521 | 64521 | SRR17137055 | SRX13321485 | SRS11229246 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 72hpf COL97 | GSM5718321 | source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism | Microwell seq datasets of Zebrafish 72hpf COL97 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5718321 | GSM5718321: Microwell seq datasets of Zebrafish 72hpf COL97; Danio rerio; RNA Seq | GSM5718321 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL97.bam | bam | 102882979782.0 | 591281493.0 | GSM5718321 r1 | 0:24 1:150 | A:30066107926;C:21991309044;G:23041144876;T:27728508333;N:55909603 | 24 | 150 | 30066107926 | 21991309044 | 23041144876 | 27728508333 | 55909603 | SRX13321485 | SRS11229246 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00231 | 0.78387 | 0.00216 | 0.09479 | 0.99977 | 0.78638 | 0.63636 | 0.48401 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-12-05 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64522 | 64522 | SRR17075126 | SRX13263481 | SRS11185248 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL92 | GSM5709061 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL92 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709061 | GSM5709061: Micorwell seq datasets of Zebrafish 72hpf COL92; Danio rerio; RNA Seq | GSM5709061 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL92.bam | bam | 93305697882.0 | 536239643.0 | GSM5709061 r1 | 0:24 1:150 | A:27107741517;C:19830183542;G:20994123402;T:25327971257;N:45678164 | 24 | 150 | 27107741517 | 19830183542 | 20994123402 | 25327971257 | 45678164 | SRX13263481 | SRS11185248 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00194 | 0.78236 | 0.00179 | 0.10164 | 0.99975 | 0.78618 | 0.75 | 0.48898 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64523 | 64523 | SRR17075125 | SRX13263480 | SRS11185247 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL91 | GSM5709060 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL91 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709060 | GSM5709060: Micorwell seq datasets of Zebrafish 72hpf COL91; Danio rerio; RNA Seq | GSM5709060 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL91.bam | bam | 96227810904.0 | 553033396.0 | GSM5709060 r1 | 0:24 1:150 | A:27923073482;C:20564137902;G:21719882675;T:25970776374;N:49940471 | 24 | 150 | 27923073482 | 20564137902 | 21719882675 | 25970776374 | 49940471 | SRX13263480 | SRS11185247 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.0019 | 0.78115 | 0.00184 | 0.10758 | 0.99989 | 0.78725 | 0.4 | 0.49305 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64524 | 64524 | SRR17075124 | SRX13263479 | SRS11185246 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL90 | GSM5709059 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL90 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709059 | GSM5709059: Micorwell seq datasets of Zebrafish 72hpf COL90; Danio rerio; RNA Seq | GSM5709059 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL90.bam | bam | 101004540858.0 | 580485867.0 | GSM5709059 r1 | 0:24 1:150 | A:29424345909;C:21610893920;G:22734702528;T:27180463498;N:54135003 | 24 | 150 | 29424345909 | 21610893920 | 22734702528 | 27180463498 | 54135003 | SRX13263479 | SRS11185246 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00188 | 0.78353 | 0.00176 | 0.10575 | 0.99981 | 0.78699 | 0.55555 | 0.50829 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64525 | 64525 | SRR17075123 | SRX13263478 | SRS11185245 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL89 | GSM5709058 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL89 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709058 | GSM5709058: Micorwell seq datasets of Zebrafish 72hpf COL89; Danio rerio; RNA Seq | GSM5709058 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL89.bam | bam | 103228879080.0 | 593269420.0 | GSM5709058 r1 | 0:24 1:150 | A:30122538038;C:21933106979;G:23172314020;T:27949125385;N:51794658 | 24 | 150 | 30122538038 | 21933106979 | 23172314020 | 27949125385 | 51794658 | SRX13263478 | SRS11185245 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00229 | 0.78058 | 0.00208 | 0.11813 | 0.99967 | 0.78642 | 0.4375 | 0.51666 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64526 | 64526 | SRR17075130 | SRX13263477 | SRS11185244 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL96 | GSM5709065 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL96 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709065 | GSM5709065: Micorwell seq datasets of Zebrafish 72hpf COL96; Danio rerio; RNA Seq | GSM5709065 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL96.bam | bam | 72161390838.0 | 414720637.0 | GSM5709065 r1 | 0:24 1:150 | A:20858972054;C:15631755598;G:16378791674;T:19256108785;N:35762727 | 24 | 150 | 20858972054 | 15631755598 | 16378791674 | 19256108785 | 35762727 | SRX13263477 | SRS11185244 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.0024 | 0.78585 | 0.00221 | 0.10389 | 0.99971 | 0.79099 | 0.64285 | 0.51929 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64527 | 64527 | SRR17075129 | SRX13263476 | SRS11185243 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL95 | GSM5709064 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL95 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709064 | GSM5709064: Micorwell seq datasets of Zebrafish 72hpf COL95; Danio rerio; RNA Seq | GSM5709064 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL95.bam | bam | 116725350900.0 | 670835350.0 | GSM5709064 r1 | 0:24 1:150 | A:33766055210;C:25258192198;G:26422558801;T:31219012086;N:59532605 | 24 | 150 | 33766055210 | 25258192198 | 26422558801 | 31219012086 | 59532605 | SRX13263476 | SRS11185243 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00223 | 0.78242 | 0.00205 | 0.10222 | 0.99973 | 0.7948 | 0.76923 | 0.51107 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64528 | 64528 | SRR17075128 | SRX13263475 | SRS11185241 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL94 | GSM5709063 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL94 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709063 | GSM5709063: Micorwell seq datasets of Zebrafish 72hpf COL94; Danio rerio; RNA Seq | GSM5709063 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL94.bam | bam | 115204393758.0 | 662094217.0 | GSM5709063 r1 | 0:24 1:150 | A:33385976074;C:24728619684;G:25999313932;T:31027995525;N:62488543 | 24 | 150 | 33385976074 | 24728619684 | 25999313932 | 31027995525 | 62488543 | SRX13263475 | SRS11185241 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00227 | 0.78471 | 0.00206 | 0.10458 | 0.99967 | 0.78591 | 0.4375 | 0.50275 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64529 | 64529 | SRR17075127 | SRX13263474 | SRS11185242 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL93 | GSM5709062 | source name:Zebrafish 72hpf sample2|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL93 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample2 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5709062 | GSM5709062: Micorwell seq datasets of Zebrafish 72hpf COL93; Danio rerio; RNA Seq | GSM5709062 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:GRCz11|intentional duplicate | Zebrafish_72hpf_COL93.bam | bam | 109890007632.0 | 631551768.0 | GSM5709062 r1 | 0:24 1:150 | A:31784495967;C:23590735781;G:24835459995;T:29625393694;N:53922195 | 24 | 150 | 31784495967 | 23590735781 | 24835459995 | 29625393694 | 53922195 | SRX13263474 | SRS11185242 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00221 | 0.77545 | 0.002 | 0.11238 | 0.99969 | 0.78879 | 0.4375 | 0.50979 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-30 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64530 | 64530 | SRR17010806 | SRX13200959 | SRS11127611 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL88 | GSM5699934 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL88 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699934 | GSM5699934: Micorwell seq datasets of Zebrafish 72hpf COL88; Danio rerio; RNA Seq | GSM5699934 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL88.bam | bam | 105325546890.0 | 605319235.0 | GSM5699934 r1 | 0:24 1:150 | A:30618141170;C:22639431941;G:23832910711;T:28175599693;N:59463375 | 24 | 150 | 30618141170 | 22639431941 | 23832910711 | 28175599693 | 59463375 | SRX13200959 | SRS11127611 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00204 | 0.77653 | 0.00184 | 0.1038 | 0.99969 | 0.78896 | 0.4 | 0.49664 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64531 | 64531 | SRR17010805 | SRX13200958 | SRS11127610 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL87 | GSM5699933 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL87 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699933 | GSM5699933: Micorwell seq datasets of Zebrafish 72hpf COL87; Danio rerio; RNA Seq | GSM5699933 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL87.bam | bam | 104410657848.0 | 600061252.0 | GSM5699933 r1 | 0:24 1:150 | A:30448105235;C:22372529466;G:23651054417;T:27884763811;N:54204919 | 24 | 150 | 30448105235 | 22372529466 | 23651054417 | 27884763811 | 54204919 | SRX13200958 | SRS11127610 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00239 | 0.76912 | 0.00221 | 0.11084 | 0.99971 | 0.78847 | 0.5 | 0.51741 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64532 | 64532 | SRR17010804 | SRX13200957 | SRS11127609 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL86 | GSM5699932 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL86 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699932 | GSM5699932: Micorwell seq datasets of Zebrafish 72hpf COL86; Danio rerio; RNA Seq | GSM5699932 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL86.bam | bam | 85539017526.0 | 491603549.0 | GSM5699932 r1 | 0:24 1:150 | A:24891444353;C:18382714837;G:19465935988;T:22755762595;N:43159753 | 24 | 150 | 24891444353 | 18382714837 | 19465935988 | 22755762595 | 43159753 | SRX13200957 | SRS11127609 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00186 | 0.7737 | 0.00168 | 0.10503 | 0.99973 | 0.78553 | 0.35714 | 0.52806 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64533 | 64533 | SRR17010803 | SRX13200956 | SRS11127608 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL85 | GSM5699931 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL85 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699931 | GSM5699931: Micorwell seq datasets of Zebrafish 72hpf COL85; Danio rerio; RNA Seq | GSM5699931 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL85.bam | bam | 96579499182.0 | 555054593.0 | GSM5699931 r1 | 0:24 1:150 | A:28258999810;C:20566647022;G:21776511096;T:25928948228;N:48393026 | 24 | 150 | 28258999810 | 20566647022 | 21776511096 | 25928948228 | 48393026 | SRX13200956 | SRS11127608 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00215 | 0.77075 | 0.00203 | 0.09684 | 0.99981 | 0.78348 | 0.44444 | 0.50291 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64534 | 64534 | SRR17010802 | SRX13200955 | SRS11127607 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL84 | GSM5699930 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL84 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699930 | GSM5699930: Micorwell seq datasets of Zebrafish 72hpf COL84; Danio rerio; RNA Seq | GSM5699930 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL84.bam | bam | 95402087292.0 | 548287858.0 | GSM5699930 r1 | 0:24 1:150 | A:27920812951;C:20371734068;G:21595614980;T:25463535654;N:50389639 | 24 | 150 | 27920812951 | 20371734068 | 21595614980 | 25463535654 | 50389639 | SRX13200955 | SRS11127607 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00199 | 0.76291 | 0.00186 | 0.09597 | 0.99981 | 0.79001 | 0.3 | 0.50069 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64535 | 64535 | SRR17010801 | SRX13200954 | SRS11127606 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL83 | GSM5699929 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL83 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699929 | GSM5699929: Micorwell seq datasets of Zebrafish 72hpf COL83; Danio rerio; RNA Seq | GSM5699929 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL83.bam | bam | 94589605254.0 | 543618421.0 | GSM5699929 r1 | 0:24 1:150 | A:27596905697;C:20243328527;G:21378738112;T:25321573995;N:49058923 | 24 | 150 | 27596905697 | 20243328527 | 21378738112 | 25321573995 | 49058923 | SRX13200954 | SRS11127606 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00216 | 0.77625 | 0.00202 | 0.09982 | 0.99979 | 0.78831 | 0.36363 | 0.51012 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64536 | 64536 | SRR17010800 | SRX13200953 | SRS11127605 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL82 | GSM5699928 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL82 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699928 | GSM5699928: Micorwell seq datasets of Zebrafish 72hpf COL82; Danio rerio; RNA Seq | GSM5699928 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL82.bam | bam | 89062661598.0 | 511854377.0 | GSM5699928 r1 | 0:24 1:150 | A:26102790989;C:19094974289;G:20282271482;T:23541508213;N:41116625 | 24 | 150 | 26102790989 | 19094974289 | 20282271482 | 23541508213 | 41116625 | SRX13200953 | SRS11127605 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00227 | 0.76728 | 0.00206 | 0.10248 | 0.99969 | 0.79196 | 0.29411 | 0.53203 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64537 | 64537 | SRR17010799 | SRX13200952 | SRS11127604 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Micorwell seq datasets of Zebrafish 72hpf COL81 | GSM5699927 | source name:Zebrafish 72hpf sample1|strain:AB|age:72 hours|tissue:whole organism | Micorwell seq datasets of Zebrafish 72hpf COL81 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 72hpf sample1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:72 hours|tissue:whole organism | GSM5699927 | GSM5699927: Micorwell seq datasets of Zebrafish 72hpf COL81; Danio rerio; RNA Seq | GSM5699927 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | assembly:Danio rerio reference genome GRCz11|intentional duplicate | Zebrafish_72hpf_COL81.bam | bam | 97306386444.0 | 559232106.0 | GSM5699927 r1 | 0:24 1:150 | A:28504741466;C:20782464199;G:21987624297;T:25985173510;N:46382972 | 24 | 150 | 28504741466 | 20782464199 | 21987624297 | 25985173510 | 46382972 | SRX13200952 | SRS11127604 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 2 | 0.00232 | 0.76473 | 0.00224 | 0.09727 | 0.99987 | 0.79153 | 0.66666 | 0.51198 | 24 | 150 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-11-22 | Larval | Larval | Whole Organism | All anatomical structures | |||||||||||
| 64538 | 64538 | SRR14915030 | SRX11229465 | SRS9283357 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL64 | GSM5400025 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL64 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400025 | GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq | GSM5400025 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL64_1_1.fq.gz Zebrafish_3m_COL64_1_2.fq.gz | fastq fastq | 3509355300.0 | 23395702.0 | GSM5400025 r1 | 0:150 1:150 | A:1033838372;C:621125453;G:637527732;T:1213662404;N:3201339 | 150 | 150 | 1033838372 | 621125453 | 637527732 | 1213662404 | 3201339 | SRX11229465 | SRS9283357 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.36321 | 0.02305 | 0.82554 | 0.50827 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64539 | 64539 | SRR14915031 | SRX11229465 | SRS9283357 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL64 | GSM5400025 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL64 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400025 | GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq | GSM5400025 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL64_2_1.fq.gz Zebrafish_3m_COL64_2_2.fq.gz | fastq fastq | 1665060900.0 | 11100406.0 | GSM5400025 r2 | 0:150 1:150 | A:462369470;C:317060096;G:327014453;T:557786784;N:830097 | 150 | 150 | 462369470 | 317060096 | 327014453 | 557786784 | 830097 | SRX11229465 | SRS9283357 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.13839 | 0.00808 | 0.91569 | 0.53255 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64540 | 64540 | SRR14915032 | SRX11229465 | SRS9283357 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL64 | GSM5400025 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL64 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400025 | GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq | GSM5400025 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL64_3_1.fq.gz Zebrafish_3m_COL64_3_2.fq.gz | fastq fastq | 2150244600.0 | 14334964.0 | GSM5400025 r3 | 0:150 1:150 | A:601841098;C:403651653;G:418726941;T:723163387;N:2861521 | 150 | 150 | 601841098 | 403651653 | 418726941 | 723163387 | 2861521 | SRX11229465 | SRS9283357 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.14947 | 0.00856 | 0.91563 | 0.52901 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64541 | 64541 | SRR14915033 | SRX11229465 | SRS9283357 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL64 | GSM5400025 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL64 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400025 | GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq | GSM5400025 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL64_4_1.fq.gz Zebrafish_3m_COL64_4_2.fq.gz | fastq fastq | 2197416600.0 | 14649444.0 | GSM5400025 r4 | 0:150 1:150 | A:623049639;C:408736499;G:423211202;T:740201304;N:2217956 | 150 | 150 | 623049639 | 408736499 | 423211202 | 740201304 | 2217956 | SRX11229465 | SRS9283357 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.31503 | 0.01599 | 0.86805 | 0.52639 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64542 | 64542 | SRR14915034 | SRX11229465 | SRS9283357 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL64 | GSM5400025 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL64 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400025 | GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq | GSM5400025 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL64_5_1.fq.gz Zebrafish_3m_COL64_5_2.fq.gz | fastq fastq | 15591467400.0 | 103943116.0 | GSM5400025 r5 | 0:150 1:150 | A:4293072963;C:3172864759;G:3328412245;T:4775949229;N:21168204 | 150 | 150 | 4293072963 | 3172864759 | 3328412245 | 4775949229 | 21168204 | SRX11229465 | SRS9283357 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.42792 | 0.02171 | 0.85798 | 0.53122 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64543 | 64543 | SRR14915035 | SRX11229465 | SRS9283357 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL64 | GSM5400025 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL64 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400025 | GSM5400025: Microwell seq datasets of Zebrafish 3m COL64; Danio rerio; RNA Seq | GSM5400025 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL64_6_1.fq.gz Zebrafish_3m_COL64_6_2.fq.gz | fastq fastq | 12549507270.0 | 144247210.0 | GSM5400025 r6 | 0:24 1:150 | A:4029002995;C:2554410310;G:2623555177;T:3319223578;N:23315210 | 24 | 150 | 4029002995 | 2554410310 | 2623555177 | 3319223578 | 23315210 | SRX11229465 | SRS9283357 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.38859 | 0.01815 | 0.85269 | 0.5308 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64544 | 64544 | SRR14915024 | SRX11229464 | SRS9283356 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL63 | GSM5400024 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL63 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400024 | GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq | GSM5400024 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL63_1_1.fq.gz Zebrafish_3m_COL63_1_2.fq.gz | fastq fastq | 2055042600.0 | 13700284.0 | GSM5400024 r1 | 0:150 1:150 | A:611481772;C:368434834;G:377372486;T:695791152;N:1962356 | 150 | 150 | 611481772 | 368434834 | 377372486 | 695791152 | 1962356 | SRX11229464 | SRS9283356 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.34483 | 0.02058 | 0.82974 | 0.52413 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64545 | 64545 | SRR14915025 | SRX11229464 | SRS9283356 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL63 | GSM5400024 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL63 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400024 | GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq | GSM5400024 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL63_2_1.fq.gz Zebrafish_3m_COL63_2_2.fq.gz | fastq fastq | 160975800.0 | 1073172.0 | GSM5400024 r2 | 0:150 1:150 | A:44979062;C:31715522;G:32816505;T:51394061;N:70650 | 150 | 150 | 44979062 | 31715522 | 32816505 | 51394061 | 70650 | SRX11229464 | SRS9283356 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.14018 | 0.00811 | 0.91565 | 0.53293 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64546 | 64546 | SRR14915026 | SRX11229464 | SRS9283356 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL63 | GSM5400024 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL63 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400024 | GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq | GSM5400024 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL63_3_1.fq.gz Zebrafish_3m_COL63_3_2.fq.gz | fastq fastq | 948599100.0 | 6323994.0 | GSM5400024 r3 | 0:150 1:150 | A:270719772;C:179859378;G:186167273;T:310493229;N:1359448 | 150 | 150 | 270719772 | 179859378 | 186167273 | 310493229 | 1359448 | SRX11229464 | SRS9283356 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.15861 | 0.00833 | 0.90536 | 0.53615 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64547 | 64547 | SRR14915027 | SRX11229464 | SRS9283356 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL63 | GSM5400024 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL63 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400024 | GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq | GSM5400024 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL63_4_1.fq.gz Zebrafish_3m_COL63_4_2.fq.gz | fastq fastq | 1296727200.0 | 8644848.0 | GSM5400024 r4 | 0:150 1:150 | A:373182160;C:244740194;G:252531468;T:424978804;N:1294574 | 150 | 150 | 373182160 | 244740194 | 252531468 | 424978804 | 1294574 | SRX11229464 | SRS9283356 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.30429 | 0.0152 | 0.86466 | 0.53074 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64548 | 64548 | SRR14915028 | SRX11229464 | SRS9283356 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL63 | GSM5400024 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL63 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400024 | GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq | GSM5400024 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL63_5_1.fq.gz Zebrafish_3m_COL63_5_2.fq.gz | fastq fastq | 7785040500.0 | 51900270.0 | GSM5400024 r5 | 0:150 1:150 | A:2174090918;C:1597924965;G:1665177229;T:2337394238;N:10453150 | 150 | 150 | 2174090918 | 1597924965 | 1665177229 | 2337394238 | 10453150 | SRX11229464 | SRS9283356 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.41787 | 0.01939 | 0.85403 | 0.5287 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64549 | 64549 | SRR14915029 | SRX11229464 | SRS9283356 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL63 | GSM5400024 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL63 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400024 | GSM5400024: Microwell seq datasets of Zebrafish 3m COL63; Danio rerio; RNA Seq | GSM5400024 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL63_6_1.fq.gz Zebrafish_3m_COL63_6_2.fq.gz | fastq fastq | 5937968196.0 | 68252508.0 | GSM5400024 r6 | 0:24 1:150 | A:1934581537;C:1211880492;G:1231715977;T:1548193534;N:11596656 | 24 | 150 | 1934581537 | 1211880492 | 1231715977 | 1548193534 | 11596656 | SRX11229464 | SRS9283356 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.37443 | 0.0171 | 0.85352 | 0.52813 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64550 | 64550 | SRR14915018 | SRX11229463 | SRS9283353 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL62 | GSM5400023 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL62 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400023 | GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq | GSM5400023 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL62_1_1.fq.gz Zebrafish_3m_COL62_1_2.fq.gz | fastq fastq | 1789905600.0 | 11932704.0 | GSM5400023 r1 | 0:150 1:150 | A:537842325;C:316956626;G:324348756;T:609120570;N:1637323 | 150 | 150 | 537842325 | 316956626 | 324348756 | 609120570 | 1637323 | SRX11229463 | SRS9283353 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.33127 | 0.02101 | 0.84187 | 0.5271 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64551 | 64551 | SRR14915019 | SRX11229463 | SRS9283353 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL62 | GSM5400023 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL62 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400023 | GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq | GSM5400023 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL62_2_1.fq.gz Zebrafish_3m_COL62_2_2.fq.gz | fastq fastq | 1289058300.0 | 8593722.0 | GSM5400023 r2 | 0:150 1:150 | A:365275974;C:247054954;G:250766392;T:425210421;N:750559 | 150 | 150 | 365275974 | 247054954 | 250766392 | 425210421 | 750559 | SRX11229463 | SRS9283353 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.11204 | 0.00628 | 0.92967 | 0.53143 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64552 | 64552 | SRR14915020 | SRX11229463 | SRS9283353 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL62 | GSM5400023 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL62 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400023 | GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq | GSM5400023 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL62_3_1.fq.gz Zebrafish_3m_COL62_3_2.fq.gz | fastq fastq | 1468221600.0 | 9788144.0 | GSM5400023 r3 | 0:150 1:150 | A:422901616;C:273721436;G:280933485;T:488734495;N:1930568 | 150 | 150 | 422901616 | 273721436 | 280933485 | 488734495 | 1930568 | SRX11229463 | SRS9283353 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.13434 | 0.00748 | 0.92383 | 0.53386 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64553 | 64553 | SRR14915021 | SRX11229463 | SRS9283353 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL62 | GSM5400023 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL62 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400023 | GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq | GSM5400023 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL62_4_1.fq.gz Zebrafish_3m_COL62_4_2.fq.gz | fastq fastq | 1551007800.0 | 10340052.0 | GSM5400023 r4 | 0:150 1:150 | A:450556375;C:286977972;G:294533181;T:517371969;N:1568303 | 150 | 150 | 450556375 | 286977972 | 294533181 | 517371969 | 1568303 | SRX11229463 | SRS9283353 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.27413 | 0.01353 | 0.88065 | 0.5239 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64554 | 64554 | SRR14915022 | SRX11229463 | SRS9283353 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL62 | GSM5400023 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL62 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400023 | GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq | GSM5400023 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL62_5_1.fq.gz Zebrafish_3m_COL62_5_2.fq.gz | fastq fastq | 8141951700.0 | 54279678.0 | GSM5400023 r5 | 0:150 1:150 | A:2279713850;C:1655964521;G:1727447219;T:2467915358;N:10910752 | 150 | 150 | 2279713850 | 1655964521 | 1727447219 | 2467915358 | 10910752 | SRX11229463 | SRS9283353 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.40205 | 0.02062 | 0.86571 | 0.53401 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64555 | 64555 | SRR14915023 | SRX11229463 | SRS9283353 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL62 | GSM5400023 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL62 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400023 | GSM5400023: Microwell seq datasets of Zebrafish 3m COL62; Danio rerio; RNA Seq | GSM5400023 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL62_6_1.fq.gz Zebrafish_3m_COL62_6_2.fq.gz | fastq fastq | 6366133998.0 | 73173954.0 | GSM5400023 r6 | 0:24 1:150 | A:2133593269;C:1284155615;G:1311954143;T:1624544767;N:11886204 | 24 | 150 | 2133593269 | 1284155615 | 1311954143 | 1624544767 | 11886204 | SRX11229463 | SRS9283353 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.3596 | 0.01726 | 0.86519 | 0.50248 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64556 | 64556 | SRR14915012 | SRX11229462 | SRS9283355 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL61 | GSM5400022 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL61 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400022 | GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq | GSM5400022 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL61_1_1.fq.gz Zebrafish_3m_COL61_1_2.fq.gz | fastq fastq | 4243314900.0 | 28288766.0 | GSM5400022 r1 | 0:150 1:150 | A:1245557842;C:757040428;G:775787197;T:1461026513;N:3902920 | 150 | 150 | 1245557842 | 757040428 | 775787197 | 1461026513 | 3902920 | SRX11229462 | SRS9283355 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.37049 | 0.02368 | 0.82613 | 0.52976 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64557 | 64557 | SRR14915013 | SRX11229462 | SRS9283355 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL61 | GSM5400022 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL61 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400022 | GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq | GSM5400022 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL61_2_1.fq.gz Zebrafish_3m_COL61_2_2.fq.gz | fastq fastq | 1240206900.0 | 8268046.0 | GSM5400022 r2 | 0:150 1:150 | A:342697940;C:238587916;G:245987086;T:412298823;N:635135 | 150 | 150 | 342697940 | 238587916 | 245987086 | 412298823 | 635135 | SRX11229462 | SRS9283355 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.13399 | 0.008 | 0.9181 | 0.52385 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64558 | 64558 | SRR14915014 | SRX11229462 | SRS9283355 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL61 | GSM5400022 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL61 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400022 | GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq | GSM5400022 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL61_3_1.fq.gz Zebrafish_3m_COL61_3_2.fq.gz | fastq fastq | 1347541200.0 | 8983608.0 | GSM5400022 r3 | 0:150 1:150 | A:378035707;C:253070106;G:262848999;T:451676944;N:1909444 | 150 | 150 | 378035707 | 253070106 | 262848999 | 451676944 | 1909444 | SRX11229462 | SRS9283355 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.16482 | 0.00934 | 0.90414 | 0.54039 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64559 | 64559 | SRR14915015 | SRX11229462 | SRS9283355 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL61 | GSM5400022 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL61 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400022 | GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq | GSM5400022 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL61_4_1.fq.gz Zebrafish_3m_COL61_4_2.fq.gz | fastq fastq | 2103237600.0 | 14021584.0 | GSM5400022 r4 | 0:150 1:150 | A:595972315;C:392671732;G:407063253;T:705390065;N:2140235 | 150 | 150 | 595972315 | 392671732 | 407063253 | 705390065 | 2140235 | SRX11229462 | SRS9283355 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.32134 | 0.01649 | 0.86316 | 0.49587 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64560 | 64560 | SRR14915016 | SRX11229462 | SRS9283355 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL61 | GSM5400022 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL61 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400022 | GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq | GSM5400022 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL61_5_1.fq.gz Zebrafish_3m_COL61_5_2.fq.gz | fastq fastq | 19534617300.0 | 130230782.0 | GSM5400022 r5 | 0:150 1:150 | A:5361819748;C:3997534297;G:4189722611;T:5957688281;N:27852363 | 150 | 150 | 5361819748 | 3997534297 | 4189722611 | 5957688281 | 27852363 | SRX11229462 | SRS9283355 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.43627 | 0.02217 | 0.85693 | 0.53022 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64561 | 64561 | SRR14915017 | SRX11229462 | SRS9283355 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL61 | GSM5400022 | source name:Zebrafish 3m sample3|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL61 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample3 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400022 | GSM5400022: Microwell seq datasets of Zebrafish 3m COL61; Danio rerio; RNA Seq | GSM5400022 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL61_6_1.fq.gz Zebrafish_3m_COL61_6_2.fq.gz | fastq fastq | 15060602538.0 | 173110374.0 | GSM5400022 r6 | 0:24 1:150 | A:4814003802;C:3077509029;G:3135215248;T:4005264504;N:28609955 | 24 | 150 | 4814003802 | 3077509029 | 3135215248 | 4005264504 | 28609955 | SRX11229462 | SRS9283355 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.39158 | 0.01982 | 0.85348 | 0.51089 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64562 | 64562 | SRR14915286 | SRX11229461 | SRS9283354 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL128 | GSM5400069 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL128 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400069 | GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq | GSM5400069 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL128_1_1.fq.gz Zebrafish_3m_COL128_1_2.fq.gz | fastq fastq | 3208770600.0 | 21391804.0 | GSM5400069 r1 | 0:150 1:150 | A:945845308;C:569438484;G:585368535;T:1105095075;N:3023198 | 150 | 150 | 945845308 | 569438484 | 585368535 | 1105095075 | 3023198 | SRX11229461 | SRS9283354 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.3414 | 0.02928 | 0.85021 | 0.51782 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64563 | 64563 | SRR14915287 | SRX11229461 | SRS9283354 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL128 | GSM5400069 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL128 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400069 | GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq | GSM5400069 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL128_2_1.fq.gz Zebrafish_3m_COL128_2_2.fq.gz | fastq fastq | 304801800.0 | 2032012.0 | GSM5400069 r2 | 0:150 1:150 | A:84325161;C:57825170;G:60519262;T:102006710;N:125497 | 150 | 150 | 84325161 | 57825170 | 60519262 | 102006710 | 125497 | SRX11229461 | SRS9283354 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.14941 | 0.01173 | 0.92151 | 0.54623 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64564 | 64564 | SRR14915288 | SRX11229461 | SRS9283354 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL128 | GSM5400069 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL128 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400069 | GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq | GSM5400069 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL128_3_1.fq.gz Zebrafish_3m_COL128_3_2.fq.gz | fastq fastq | 1191613200.0 | 7944088.0 | GSM5400069 r3 | 0:150 1:150 | A:334533793;C:224286886;G:233943665;T:397197115;N:1651741 | 150 | 150 | 334533793 | 224286886 | 233943665 | 397197115 | 1651741 | SRX11229461 | SRS9283354 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.15569 | 0.0115 | 0.9207 | 0.54743 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64565 | 64565 | SRR14915289 | SRX11229461 | SRS9283354 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL128 | GSM5400069 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL128 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400069 | GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq | GSM5400069 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL128_4_1.fq.gz Zebrafish_3m_COL128_4_2.fq.gz | fastq fastq | 1766814000.0 | 11778760.0 | GSM5400069 r4 | 0:150 1:150 | A:500417014;C:333000747;G:344717291;T:586926285;N:1752663 | 150 | 150 | 500417014 | 333000747 | 344717291 | 586926285 | 1752663 | SRX11229461 | SRS9283354 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.29677 | 0.01992 | 0.88645 | 0.54665 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64566 | 64566 | SRR14915290 | SRX11229461 | SRS9283354 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL128 | GSM5400069 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL128 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400069 | GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq | GSM5400069 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL128_5_1.fq.gz Zebrafish_3m_COL128_5_2.fq.gz | fastq fastq | 15144379800.0 | 100962532.0 | GSM5400069 r5 | 0:150 1:150 | A:4075035270;C:3166217509;G:3409509586;T:4473533042;N:20084393 | 150 | 150 | 4075035270 | 3166217509 | 3409509586 | 4473533042 | 20084393 | SRX11229461 | SRS9283354 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.37107 | 0.02472 | 0.88509 | 0.54349 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64567 | 64567 | SRR14915291 | SRX11229461 | SRS9283354 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL128 | GSM5400069 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL128 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400069 | GSM5400069: Microwell seq datasets of Zebrafish 3m COL128; Danio rerio; RNA Seq | GSM5400069 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL128_6_1.fq.gz Zebrafish_3m_COL128_6_2.fq.gz | fastq fastq | 11721521832.0 | 134730136.0 | GSM5400069 r6 | 0:24 1:150 | A:3640769264;C:2518212610;G:2406793302;T:3133328455;N:22418201 | 24 | 150 | 3640769264 | 2518212610 | 2406793302 | 3133328455 | 22418201 | SRX11229461 | SRS9283354 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.34007 | 0.02128 | 0.88032 | 0.54961 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64568 | 64568 | SRR14915280 | SRX11229460 | SRS9289443 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL127 | GSM5400068 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL127 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400068 | GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq | GSM5400068 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL127_1_1.fq.gz Zebrafish_3m_COL127_1_2.fq.gz | fastq fastq | 2746310400.0 | 18308736.0 | GSM5400068 r1 | 0:150 1:150 | A:806781242;C:487253172;G:500916690;T:948772411;N:2586885 | 150 | 150 | 806781242 | 487253172 | 500916690 | 948772411 | 2586885 | SRX11229460 | SRS9289443 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.36116 | 0.03633 | 0.84587 | 0.53626 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64569 | 64569 | SRR14915281 | SRX11229460 | SRS9289443 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL127 | GSM5400068 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL127 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400068 | GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq | GSM5400068 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL127_2_1.fq.gz Zebrafish_3m_COL127_2_2.fq.gz | fastq fastq | 1701404100.0 | 11342694.0 | GSM5400068 r2 | 0:150 1:150 | A:469834000;C:332532377;G:339422396;T:558600197;N:1015130 | 150 | 150 | 469834000 | 332532377 | 339422396 | 558600197 | 1015130 | SRX11229460 | SRS9289443 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.1265 | 0.01237 | 0.93152 | 0.53316 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64570 | 64570 | SRR14915282 | SRX11229460 | SRS9289443 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL127 | GSM5400068 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL127 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400068 | GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq | GSM5400068 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL127_3_1.fq.gz Zebrafish_3m_COL127_3_2.fq.gz | fastq fastq | 1339582500.0 | 8930550.0 | GSM5400068 r3 | 0:150 1:150 | A:374492185;C:255730803;G:264255158;T:443331862;N:1772492 | 150 | 150 | 374492185 | 255730803 | 264255158 | 443331862 | 1772492 | SRX11229460 | SRS9289443 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.15302 | 0.01389 | 0.9236 | 0.52455 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64571 | 64571 | SRR14915283 | SRX11229460 | SRS9289443 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL127 | GSM5400068 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL127 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400068 | GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq | GSM5400068 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL127_4_1.fq.gz Zebrafish_3m_COL127_4_2.fq.gz | fastq fastq | 1367540100.0 | 9116934.0 | GSM5400068 r4 | 0:150 1:150 | A:387379474;C:258496197;G:266901212;T:453386759;N:1376458 | 150 | 150 | 387379474 | 258496197 | 266901212 | 453386759 | 1376458 | SRX11229460 | SRS9289443 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.32389 | 0.02782 | 0.87913 | 0.53804 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64572 | 64572 | SRR14915284 | SRX11229460 | SRS9289443 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL127 | GSM5400068 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL127 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400068 | GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq | GSM5400068 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL127_5_1.fq.gz Zebrafish_3m_COL127_5_2.fq.gz | fastq fastq | 10892960400.0 | 72619736.0 | GSM5400068 r5 | 0:150 1:150 | A:3010970636;C:2227858579;G:2327578951;T:3312264759;N:14287475 | 150 | 150 | 3010970636 | 2227858579 | 2327578951 | 3312264759 | 14287475 | SRX11229460 | SRS9289443 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.41723 | 0.03455 | 0.87345 | 0.53603 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64573 | 64573 | SRR14915285 | SRX11229460 | SRS9289443 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL127 | GSM5400068 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL127 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400068 | GSM5400068: Microwell seq datasets of Zebrafish 3m COL127; Danio rerio; RNA Seq | GSM5400068 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL127_6_1.fq.gz Zebrafish_3m_COL127_6_2.fq.gz | fastq fastq | 8590523028.0 | 98741644.0 | GSM5400068 r6 | 0:24 1:150 | A:2744332263;C:1751755618;G:1790836239;T:2287153559;N:16445349 | 24 | 150 | 2744332263 | 1751755618 | 1790836239 | 2287153559 | 16445349 | SRX11229460 | SRS9289443 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.37598 | 0.02831 | 0.87028 | 0.53692 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64574 | 64574 | SRR14915274 | SRX11229459 | SRS9283351 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL126 | GSM5400067 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL126 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400067 | GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq | GSM5400067 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL126_1_1.fq.gz Zebrafish_3m_COL126_1_2.fq.gz | fastq fastq | 3367480500.0 | 22449870.0 | GSM5400067 r1 | 0:150 1:150 | A:988357060;C:594065773;G:612600123;T:1169171017;N:3286527 | 150 | 150 | 988357060 | 594065773 | 612600123 | 1169171017 | 3286527 | SRX11229459 | SRS9283351 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.36442 | 0.03788 | 0.83707 | 0.53153 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64575 | 64575 | SRR14915275 | SRX11229459 | SRS9283351 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL126 | GSM5400067 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL126 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400067 | GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq | GSM5400067 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL126_2_1.fq.gz Zebrafish_3m_COL126_2_2.fq.gz | fastq fastq | 2217890100.0 | 14785934.0 | GSM5400067 r2 | 0:150 1:150 | A:611233800;C:426890176;G:440427980;T:738097977;N:1240167 | 150 | 150 | 611233800 | 426890176 | 440427980 | 738097977 | 1240167 | SRX11229459 | SRS9283351 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.13061 | 0.01274 | 0.92186 | 0.52329 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64576 | 64576 | SRR14915276 | SRX11229459 | SRS9283351 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL126 | GSM5400067 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL126 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400067 | GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq | GSM5400067 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL126_3_1.fq.gz Zebrafish_3m_COL126_3_2.fq.gz | fastq fastq | 2127274200.0 | 14181828.0 | GSM5400067 r3 | 0:150 1:150 | A:592506103;C:401844212;G:419018214;T:711110076;N:2795595 | 150 | 150 | 592506103 | 401844212 | 419018214 | 711110076 | 2795595 | SRX11229459 | SRS9283351 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.15085 | 0.01391 | 0.91912 | 0.50158 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64577 | 64577 | SRR14915277 | SRX11229459 | SRS9283351 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL126 | GSM5400067 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL126 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400067 | GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq | GSM5400067 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL126_4_1.fq.gz Zebrafish_3m_COL126_4_2.fq.gz | fastq fastq | 2170011000.0 | 14466740.0 | GSM5400067 r4 | 0:150 1:150 | A:612178252;C:405838172;G:422117791;T:727705097;N:2171688 | 150 | 150 | 612178252 | 405838172 | 422117791 | 727705097 | 2171688 | SRX11229459 | SRS9283351 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.31735 | 0.02846 | 0.87111 | 0.51932 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64578 | 64578 | SRR14915278 | SRX11229459 | SRS9283351 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL126 | GSM5400067 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL126 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400067 | GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq | GSM5400067 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL126_5_2.fq.gz Zebrafish_3m_COL126_5_1.fq.gz | fastq fastq | 12412172700.0 | 82747818.0 | GSM5400067 r5 | 0:150 1:150 | A:3428337367;C:2521025487;G:2650242372;T:3796533380;N:16034094 | 150 | 150 | 3428337367 | 2521025487 | 2650242372 | 3796533380 | 16034094 | SRX11229459 | SRS9283351 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.422 | 0.03542 | 0.8661 | 0.54056 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64579 | 64579 | SRR14915279 | SRX11229459 | SRS9283351 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL126 | GSM5400067 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL126 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400067 | GSM5400067: Microwell seq datasets of Zebrafish 3m COL126; Danio rerio; RNA Seq | GSM5400067 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL126_6_1.fq.gz Zebrafish_3m_COL126_6_2.fq.gz | fastq fastq | 10084544970.0 | 115914310.0 | GSM5400067 r6 | 0:24 1:150 | A:3246792678;C:2042678037;G:2092562882;T:2683662920;N:18848453 | 24 | 150 | 3246792678 | 2042678037 | 2092562882 | 2683662920 | 18848453 | SRX11229459 | SRS9283351 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.3807 | 0.03251 | 0.86726 | 0.53521 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64580 | 64580 | SRR14915268 | SRX11229458 | SRS9283350 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL125 | GSM5400066 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL125 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400066 | GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq | GSM5400066 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL125_1_1.fq.gz Zebrafish_3m_COL125_1_2.fq.gz | fastq fastq | 3535998000.0 | 23573320.0 | GSM5400066 r1 | 0:150 1:150 | A:1034469165;C:634010669;G:649729630;T:1214431364;N:3357172 | 150 | 150 | 1034469165 | 634010669 | 649729630 | 1214431364 | 3357172 | SRX11229458 | SRS9283350 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.34196 | 0.03294 | 0.84796 | 0.53906 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64581 | 64581 | SRR14915269 | SRX11229458 | SRS9283350 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL125 | GSM5400066 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL125 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400066 | GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq | GSM5400066 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL125_2_1.fq.gz Zebrafish_3m_COL125_2_2.fq.gz | fastq fastq | 2034814800.0 | 13565432.0 | GSM5400066 r2 | 0:150 1:150 | A:561299001;C:400914760;G:406578613;T:664823715;N:1198711 | 150 | 150 | 561299001 | 400914760 | 406578613 | 664823715 | 1198711 | SRX11229458 | SRS9283350 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.11368 | 0.01046 | 0.93576 | 0.5358 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64582 | 64582 | SRR14915270 | SRX11229458 | SRS9283350 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL125 | GSM5400066 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL125 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400066 | GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq | GSM5400066 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL125_3_1.fq.gz Zebrafish_3m_COL125_3_2.fq.gz | fastq fastq | 1715258700.0 | 11435058.0 | GSM5400066 r3 | 0:150 1:150 | A:478425920;C:330213303;G:338928699;T:565440723;N:2250055 | 150 | 150 | 478425920 | 330213303 | 338928699 | 565440723 | 2250055 | SRX11229458 | SRS9283350 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.13635 | 0.01121 | 0.93095 | 0.51679 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64583 | 64583 | SRR14915271 | SRX11229458 | SRS9283350 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL125 | GSM5400066 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL125 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400066 | GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq | GSM5400066 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL125_4_1.fq.gz Zebrafish_3m_COL125_4_2.fq.gz | fastq fastq | 1715104500.0 | 11434030.0 | GSM5400066 r4 | 0:150 1:150 | A:484886997;C:327078444;G:334782640;T:566633787;N:1722632 | 150 | 150 | 484886997 | 327078444 | 334782640 | 566633787 | 1722632 | SRX11229458 | SRS9283350 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.2998 | 0.02457 | 0.88629 | 0.5217 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64584 | 64584 | SRR14915272 | SRX11229458 | SRS9283350 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL125 | GSM5400066 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL125 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400066 | GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq | GSM5400066 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL125_5_2.fq.gz Zebrafish_3m_COL125_5_1.fq.gz | fastq fastq | 15018441600.0 | 100122944.0 | GSM5400066 r5 | 0:150 1:150 | A:4129076288;C:3096636754;G:3227410655;T:4544987986;N:20329917 | 150 | 150 | 4129076288 | 3096636754 | 3227410655 | 4544987986 | 20329917 | SRX11229458 | SRS9283350 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.39068 | 0.03076 | 0.87982 | 0.53718 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64585 | 64585 | SRR14915273 | SRX11229458 | SRS9283350 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL125 | GSM5400066 | source name:Zebrafish 3m sample6|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL125 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample6 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400066 | GSM5400066: Microwell seq datasets of Zebrafish 3m COL125; Danio rerio; RNA Seq | GSM5400066 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL125_6_2.fq.gz Zebrafish_3m_COL125_6_1.fq.gz | fastq fastq | 12189015984.0 | 140103632.0 | GSM5400066 r6 | 0:24 1:150 | A:3884770428;C:2485268235;G:2553035720;T:3242414970;N:23526631 | 24 | 150 | 3884770428 | 2485268235 | 2553035720 | 3242414970 | 23526631 | SRX11229458 | SRS9283350 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.35675 | 0.02764 | 0.87483 | 0.54135 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64586 | 64586 | SRR14915262 | SRX11229457 | SRS9283352 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL124 | GSM5400065 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL124 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400065 | GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq | GSM5400065 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL124_1_1.fq.gz Zebrafish_3m_COL124_1_2.fq.gz | fastq fastq | 3548358000.0 | 23655720.0 | GSM5400065 r1 | 0:150 1:150 | A:1045459196;C:629224836;G:647117553;T:1223292372;N:3264043 | 150 | 150 | 1045459196 | 629224836 | 647117553 | 1223292372 | 3264043 | SRX11229457 | SRS9283352 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.37097 | 0.02714 | 0.83451 | 0.53691 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64587 | 64587 | SRR14915263 | SRX11229457 | SRS9283352 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL124 | GSM5400065 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL124 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400065 | GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq | GSM5400065 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL124_2_1.fq.gz Zebrafish_3m_COL124_2_2.fq.gz | fastq fastq | 799052400.0 | 5327016.0 | GSM5400065 r2 | 0:150 1:150 | A:224388479;C:154147586;G:159607563;T:260469676;N:439096 | 150 | 150 | 224388479 | 154147586 | 159607563 | 260469676 | 439096 | SRX11229457 | SRS9283352 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.09953 | 0.00688 | 0.9361 | 0.51302 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64588 | 64588 | SRR14915264 | SRX11229457 | SRS9283352 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL124 | GSM5400065 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL124 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400065 | GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq | GSM5400065 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL124_3_1.fq.gz Zebrafish_3m_COL124_3_2.fq.gz | fastq fastq | 1789587900.0 | 11930586.0 | GSM5400065 r3 | 0:150 1:150 | A:504393249;C:331912683;G:346668689;T:603866933;N:2746346 | 150 | 150 | 504393249 | 331912683 | 346668689 | 603866933 | 2746346 | SRX11229457 | SRS9283352 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.16702 | 0.01095 | 0.91569 | 0.53962 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64589 | 64589 | SRR14915265 | SRX11229457 | SRS9283352 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL124 | GSM5400065 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL124 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400065 | GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq | GSM5400065 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL124_4_1.fq.gz Zebrafish_3m_COL124_4_2.fq.gz | fastq fastq | 3069140100.0 | 20460934.0 | GSM5400065 r4 | 0:150 1:150 | A:874150840;C:568413182;G:589948834;T:1033550871;N:3076373 | 150 | 150 | 874150840 | 568413182 | 589948834 | 1033550871 | 3076373 | SRX11229457 | SRS9283352 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.31488 | 0.01869 | 0.87444 | 0.52778 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64590 | 64590 | SRR14915266 | SRX11229457 | SRS9283352 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL124 | GSM5400065 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL124 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400065 | GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq | GSM5400065 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL124_5_1.fq.gz Zebrafish_3m_COL124_5_2.fq.gz | fastq fastq | 15500682600.0 | 103337884.0 | GSM5400065 r5 | 0:150 1:150 | A:4271460153;C:3150814284;G:3316251816;T:4741035876;N:21120471 | 150 | 150 | 4271460153 | 3150814284 | 3316251816 | 4741035876 | 21120471 | SRX11229457 | SRS9283352 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.42634 | 0.02596 | 0.86789 | 0.53869 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64591 | 64591 | SRR14915267 | SRX11229457 | SRS9283352 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL124 | GSM5400065 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL124 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400065 | GSM5400065: Microwell seq datasets of Zebrafish 3m COL124; Danio rerio; RNA Seq | GSM5400065 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL124_6_1.fq.gz Zebrafish_3m_COL124_6_2.fq.gz | fastq fastq | 11909725626.0 | 136893398.0 | GSM5400065 r6 | 0:24 1:150 | A:3806418177;C:2424097718;G:2498410053;T:3158643077;N:22156601 | 24 | 150 | 3806418177 | 2424097718 | 2498410053 | 3158643077 | 22156601 | SRX11229457 | SRS9283352 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.39256 | 0.0232 | 0.85965 | 0.51961 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64592 | 64592 | SRR14915256 | SRX11229456 | SRS9283349 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL123 | GSM5400064 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL123 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400064 | GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq | GSM5400064 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL123_1_1.fq.gz Zebrafish_3m_COL123_1_2.fq.gz | fastq fastq | 3807078600.0 | 25380524.0 | GSM5400064 r1 | 0:150 1:150 | A:1122709493;C:680521766;G:695286045;T:1305023708;N:3537588 | 150 | 150 | 1122709493 | 680521766 | 695286045 | 1305023708 | 3537588 | SRX11229456 | SRS9283349 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.35742 | 0.02244 | 0.84433 | 0.53118 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64593 | 64593 | SRR14915257 | SRX11229456 | SRS9283349 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL123 | GSM5400064 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL123 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400064 | GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq | GSM5400064 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL123_2_1.fq.gz Zebrafish_3m_COL123_2_2.fq.gz | fastq fastq | 1538722800.0 | 10258152.0 | GSM5400064 r2 | 0:150 1:150 | A:429732126;C:296572020;G:302968410;T:508614732;N:835512 | 150 | 150 | 429732126 | 296572020 | 302968410 | 508614732 | 835512 | SRX11229456 | SRS9283349 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.13077 | 0.00804 | 0.92715 | 0.53507 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64594 | 64594 | SRR14915258 | SRX11229456 | SRS9283349 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL123 | GSM5400064 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL123 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400064 | GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq | GSM5400064 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL123_3_1.fq.gz Zebrafish_3m_COL123_3_2.fq.gz | fastq fastq | 2031065700.0 | 13540438.0 | GSM5400064 r3 | 0:150 1:150 | A:572071714;C:383932011;G:395219423;T:677149729;N:2692823 | 150 | 150 | 572071714 | 383932011 | 395219423 | 677149729 | 2692823 | SRX11229456 | SRS9283349 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.14905 | 0.00852 | 0.92598 | 0.53922 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64595 | 64595 | SRR14915259 | SRX11229456 | SRS9283349 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL123 | GSM5400064 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL123 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400064 | GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq | GSM5400064 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL123_4_1.fq.gz Zebrafish_3m_COL123_4_2.fq.gz | fastq fastq | 2227611000.0 | 14850740.0 | GSM5400064 r4 | 0:150 1:150 | A:634166526;C:418440499;G:429568047;T:743187782;N:2248146 | 150 | 150 | 634166526 | 418440499 | 429568047 | 743187782 | 2248146 | SRX11229456 | SRS9283349 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.30527 | 0.01591 | 0.8873 | 0.52617 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64596 | 64596 | SRR14915260 | SRX11229456 | SRS9283349 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL123 | GSM5400064 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL123 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400064 | GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq | GSM5400064 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL123_5_1.fq.gz Zebrafish_3m_COL123_5_2.fq.gz | fastq fastq | 17777963700.0 | 118519758.0 | GSM5400064 r5 | 0:150 1:150 | A:4902414982;C:3638996050;G:3803098479;T:5408950692;N:24503497 | 150 | 150 | 4902414982 | 3638996050 | 3803098479 | 5408950692 | 24503497 | SRX11229456 | SRS9283349 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.42515 | 0.0222 | 0.87592 | 0.53827 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64597 | 64597 | SRR14915261 | SRX11229456 | SRS9283349 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL123 | GSM5400064 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL123 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400064 | GSM5400064: Microwell seq datasets of Zebrafish 3m COL123; Danio rerio; RNA Seq | GSM5400064 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL123_6_1.fq.gz Zebrafish_3m_COL123_6_2.fq.gz | fastq fastq | 13923650172.0 | 160041956.0 | GSM5400064 r6 | 0:24 1:150 | A:4482285138;C:2834136946;G:2900635816;T:3680471572;N:26120700 | 24 | 150 | 4482285138 | 2834136946 | 2900635816 | 3680471572 | 26120700 | SRX11229456 | SRS9283349 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.38266 | 0.0197 | 0.87058 | 0.53906 | 24 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64598 | 64598 | SRR14915250 | SRX11229455 | SRS9283347 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL122 | GSM5400063 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL122 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400063 | GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq | GSM5400063 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL122_1_1.fq.gz Zebrafish_3m_COL122_1_2.fq.gz | fastq fastq | 3414690300.0 | 22764602.0 | GSM5400063 r1 | 0:150 1:150 | A:1009187609;C:606970670;G:622677920;T:1172654856;N:3199245 | 150 | 150 | 1009187609 | 606970670 | 622677920 | 1172654856 | 3199245 | SRX11229455 | SRS9283347 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.35805 | 0.02502 | 0.83887 | 0.54238 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | All anatomical structures | ||||||||||||||||||
| 64599 | 64599 | SRR14915251 | SRX11229455 | SRS9283347 | SRP324000 | PRJNA737474 | Construction the larval and adult zebrafish cell atlas at single cell resolution | GSE178150 | Transcriptome Analysis | Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate. | parent bioproject:PRJNA737471 | pubmed:36229673 | Microwell seq datasets of Zebrafish 3m COL122 | GSM5400063 | source name:Zebrafish 3m sample5|strain:AB|age:3 month 90 day|tissue:whole organism | Microwell seq datasets of Zebrafish 3m COL122 | Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 5 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 6 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns. | Zebrafish 3m sample5 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | strain:AB|age:3 month 90 day|tissue:whole organism | GSM5400063 | GSM5400063: Microwell seq datasets of Zebrafish 3m COL122; Danio rerio; RNA Seq | GSM5400063 | 1 | Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP324000 | Zebrafish_3m_COL122_2_1.fq.gz Zebrafish_3m_COL122_2_2.fq.gz | fastq fastq | 888162300.0 | 5921082.0 | GSM5400063 r2 | 0:150 1:150 | A:249596683;C:168975194;G:173081430;T:296037426;N:471567 | 150 | 150 | 249596683 | 168975194 | 173081430 | 296037426 | 471567 | SRX11229455 | SRS9283347 | SRA1244752 | GEO | Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine | 1 | 0.12808 | 0.008 | 0.92178 | 0.53589 | 150 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2021-06-25 | Adult | Adult | Whole Organism | 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");;