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32 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "smartseq" and tissue_curation = "Skin"

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experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Skin · 32 ✖

technology 1

  • smartseq · 32 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 32 ✖

experiment.library_selection 1

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
51228 51228 SRR8591752 SRX5391965 SRS4379795 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   T cells 3 GSM3612324   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx T cells 3 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx GSM3612324 GSM3612324: T cells 3; Danio rerio; RNA Seq GSM3612324   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612324 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     T_cells_3_R2.fq.gz T_cells_3_R1.fq.gz fastq fastq 11144333100.0 37147777.0 GSM3612324 r1 0:150 1:150 A:3499952862;C:2003192621;G:2060397654;T:3580454183;N:335780 150 150     3499952862 2003192621 2060397654 3580454183 335780 SRX5391965 SRS4379795 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.7813 0.78015 0.18285 0.17813 0.83978 0.84051 0.5593 0.449 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51229 51229 SRR8591751 SRX5391964 SRS4379794 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   T cells 2 GSM3612323   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx T cells 2 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx GSM3612323 GSM3612323: T cells 2; Danio rerio; RNA Seq GSM3612323   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612323 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     T_cells_2_R2.fq.gz T_cells_2_R1.fq.gz fastq fastq 7919587200.0 26398624.0 GSM3612323 r1 0:150 1:150 A:2465301954;C:1441444830;G:1480576895;T:2531979045;N:284476 150 150     2465301954 1441444830 1480576895 2531979045 284476 SRX5391964 SRS4379794 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.78322 0.78133 0.14641 0.14616 0.8547 0.8537 0.46251 0.56483 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51230 51230 SRR8591750 SRX5391963 SRS4379793 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   T cells 1 GSM3612322   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx T cells 1 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx GSM3612322 GSM3612322: T cells 1; Danio rerio; RNA Seq GSM3612322   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612322 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     T_cells_1_R2.fq.gz T_cells_1_R1.fq.gz fastq fastq 10355072400.0 34516908.0 GSM3612322 r1 0:150 1:150 A:2939445450;C:2059218859;G:2124006194;T:3229931547;N:2470350 150 150     2939445450 2059218859 2124006194 3229931547 2470350 SRX5391963 SRS4379793 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.82838 0.8272 0.19005 0.18949 0.81128 0.81227 0.52045 0.51858 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51231 51231 SRR8591749 SRX5391962 SRS4379792 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   Neutrophils 3 GSM3612321   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP Neutrophils 3 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP GSM3612321 GSM3612321: Neutrophils 3; Danio rerio; RNA Seq GSM3612321   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612321 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     Neutrophils_3_R1.fq.gz Neutrophils_3_R2.fq.gz fastq fastq 8692700700.0 28975669.0 GSM3612321 r1 0:150 1:150 A:2652684352;C:1652069995;G:1735457120;T:2652129934;N:359299 150 150     2652684352 1652069995 1735457120 2652129934 359299 SRX5391962 SRS4379792 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.8145 0.81686 0.10965 0.10808 0.92713 0.92744 0.55607 0.57186 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51232 51232 SRR8591748 SRX5391961 SRS4379791 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   Neutrophils 2 GSM3612320   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP Neutrophils 2 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP GSM3612320 GSM3612320: Neutrophils 2; Danio rerio; RNA Seq GSM3612320   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612320 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     Neutrophils_2_R1.fq.gz Neutrophils_2_R2.fq.gz fastq fastq 7327680000.0 24425600.0 GSM3612320 r1 0:150 1:150 A:2187183417;C:1429377098;G:1474177623;T:2236324081;N:617781 150 150     2187183417 1429377098 1474177623 2236324081 617781 SRX5391961 SRS4379791 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.84825 0.84925 0.11406 0.11367 0.91244 0.91277 0.54443 0.52025 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51233 51233 SRR8591747 SRX5391960 SRS4379790 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   Neutrophils 1 GSM3612319   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP Neutrophils 1 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP GSM3612319 GSM3612319: Neutrophils 1; Danio rerio; RNA Seq GSM3612319   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612319 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     Neutrophils_1_R1.fq.gz Neutrophils_1_R2.fq.gz fastq fastq 12087825300.0 40292751.0 GSM3612319 r1 0:150 1:150 A:3327151170;C:2523891980;G:2588985485;T:3644916170;N:2880495 150 150     3327151170 2523891980 2588985485 3644916170 2880495 SRX5391960 SRS4379790 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.88642 0.88127 0.10539 0.10565 0.85151 0.85451 0.45008 0.4553 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51234 51234 SRR8591746 SRX5391959 SRS4379789 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   MLCs 4 GSM3612318   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP MLCs 4 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612318 GSM3612318: MLCs 4; Danio rerio; RNA Seq GSM3612318   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612318 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     MLCs_4_R2.fq.gz MLCs_4_R1.fq.gz fastq fastq 8636325300.0 28787751.0 GSM3612318 r1 0:150 1:150 A:2653500651;C:1647706630;G:1681001556;T:2652196955;N:1919508 150 150     2653500651 1647706630 1681001556 2652196955 1919508 SRX5391959 SRS4379789 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.82279 0.82455 0.10092 0.10051 0.87625 0.87411 0.64616 0.67509 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51235 51235 SRR8591745 SRX5391958 SRS4379788 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   MLCs 3 GSM3612317   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP MLCs 3 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612317 GSM3612317: MLCs 3; Danio rerio; RNA Seq GSM3612317   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612317 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     MLCs_3_R1.fq.gz MLCs_3_R2.fq.gz fastq fastq 9768968700.0 32563229.0 GSM3612317 r1 0:150 1:150 A:2993731360;C:1868928141;G:1920209904;T:2983932349;N:2166946 150 150     2993731360 1868928141 1920209904 2983932349 2166946 SRX5391958 SRS4379788 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.80623 0.80159 0.09971 0.09865 0.85754 0.85677 0.57368 0.57722 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51236 51236 SRR8591744 SRX5391957 SRS4379787 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   MLCs 2 GSM3612316   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP MLCs 2 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612316 GSM3612316: MLCs 2; Danio rerio; RNA Seq GSM3612316   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612316 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     MLCs_2_R2.fq.gz MLCs_2_R1.fq.gz fastq fastq 13514398200.0 45047994.0 GSM3612316 r1 0:150 1:150 A:3741759684;C:2708870921;G:2854612129;T:4207496675;N:1658791 150 150     3741759684 2708870921 2854612129 4207496675 1658791 SRX5391957 SRS4379787 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.85592 0.84009 0.10566 0.10231 0.85904 0.86689 0.46757 0.54817 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51237 51237 SRR8591743 SRX5391956 SRS4379786 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   MLCs 1 GSM3612315   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP MLCs 1 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612315 GSM3612315: MLCs 1; Danio rerio; RNA Seq GSM3612315   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612315 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     MLCs_1_R1.fq.gz MLCs_1_R2.fq.gz fastq fastq 6037864832.0 20003506.0 GSM3612315 r1 0:150.92 1:150.92 A:1818516368;C:1085016023;G:1139951931;T:1985307132;N:9073378 150 150     1818516368 1085016023 1139951931 1985307132 9073378 SRX5391956 SRS4379786 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.74163 0.65034 0.20675 0.17721 0.85285 0.87409 0.66103 0.66629 151 151 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51238 51238 SRR8591742 SRX5391955 SRS4379784 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   Keratinocytes 3 GSM3612314   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP Keratinocytes 3 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP GSM3612314 GSM3612314: Keratinocytes 3; Danio rerio; RNA Seq GSM3612314   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612314 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     Keratinocytes_3_R1.fq.gz Keratinocytes_3_R2.fq.gz fastq fastq 7155019200.0 23850064.0 GSM3612314 r1 0:150 1:150 A:2267290727;C:1304084105;G:1335196968;T:2248029844;N:417556 150 150     2267290727 1304084105 1335196968 2248029844 417556 SRX5391955 SRS4379784 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.77684 0.75758 0.12563 0.12043 0.87606 0.87618 0.63846 0.64712 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51239 51239 SRR8591741 SRX5391954 SRS4379785 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   Keratinocytes 2 GSM3612313   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP Keratinocytes 2 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP GSM3612313 GSM3612313: Keratinocytes 2; Danio rerio; RNA Seq GSM3612313   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612313 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     Keratinocytes_2_R1.fq.gz Keratinocytes_2_R2.fq.gz fastq fastq 6456398100.0 21521327.0 GSM3612313 r1 0:150 1:150 A:2077468795;C:1142603883;G:1144675726;T:2084897858;N:6751838 150 150     2077468795 1142603883 1144675726 2084897858 6751838 SRX5391954 SRS4379785 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.74005 0.73114 0.1187 0.11653 0.8604 0.85985 0.56777 0.56778 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51240 51240 SRR8591740 SRX5391953 SRS4379783 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   Keratinocytes 1 GSM3612312   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP Keratinocytes 1 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP GSM3612312 GSM3612312: Keratinocytes 1; Danio rerio; RNA Seq GSM3612312   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612312 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     Keratinocytes_1_R2.fq.gz Keratinocytes_1_R1.fq.gz fastq fastq 13235365200.0 44117884.0 GSM3612312 r1 0:150 1:150 A:3733277705;C:2648363624;G:2742826351;T:4109351172;N:1546348 150 150     3733277705 2648363624 2742826351 4109351172 1546348 SRX5391953 SRS4379783 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.83183 0.82563 0.13916 0.13781 0.86048 0.86517 0.46753 0.45399 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51241 51241 SRR8591739 SRX5391952 SRS4379782 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   cLCs 4 GSM3612311   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP cLCs 4 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612311 GSM3612311: cLCs 4; Danio rerio; RNA Seq GSM3612311   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612311 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     cLCs_4_R1.fq.gz cLCs_4_R2.fq.gz fastq fastq 8713251600.0 29044172.0 GSM3612311 r1 0:150 1:150 A:2637859361;C:1663768374;G:1739990329;T:2671283369;N:350167 150 150     2637859361 1663768374 1739990329 2671283369 350167 SRX5391952 SRS4379782 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.82506 0.82564 0.14826 0.14636 0.92133 0.92194 0.64203 0.64155 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51242 51242 SRR8591738 SRX5391951 SRS4379781 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   cLCs 3 GSM3612310   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP cLCs 3 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612310 GSM3612310: cLCs 3; Danio rerio; RNA Seq GSM3612310   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612310 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     cLCs_3_R2.fq.gz cLCs_3_R1.fq.gz fastq fastq 8085762300.0 26952541.0 GSM3612310 r1 0:150 1:150 A:2358914181;C:1670033364;G:1711269394;T:2345255094;N:290267 150 150     2358914181 1670033364 1711269394 2345255094 290267 SRX5391951 SRS4379781 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.80361 0.80478 0.06011 0.06067 0.90666 0.90613 0.43542 0.42737 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51243 51243 SRR8591737 SRX5391950 SRS4379780 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   cLCs 2 GSM3612309   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP cLCs 2 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612309 GSM3612309: cLCs 2; Danio rerio; RNA Seq GSM3612309   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612309 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     cLCs_2_R2.fq.gz cLCs_2_R1.fq.gz fastq fastq 14035834800.0 46786116.0 GSM3612309 r1 0:150 1:150 A:3886956713;C:2808123594;G:3002545528;T:4337287271;N:921694 150 150     3886956713 2808123594 3002545528 4337287271 921694 SRX5391950 SRS4379780 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.80521 0.79346 0.13916 0.13314 0.88061 0.88872 0.5212 0.54523 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51244 51244 SRR8591736 SRX5391949 SRS4379779 SRP186291 PRJNA523219 Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs GSE126763 Transcriptome Analysis In order to have a comprehensive comparison of locally restricted mpeg1+ cells MLCs and cLCs we isolated locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls keratinocytes T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis including locally restricted mpeg1+ cells cLCs keratinocytes T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol library construction and whole transcriptome RNA sequencing were proformed by Novogene.   pubmed:31006648   cLCs 1 GSM3612308   source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP cLCs 1 Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish epidermis   Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.   tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP GSM3612308 GSM3612308: cLCs 1; Danio rerio; RNA Seq GSM3612308   1 Different fluorescence labeled cell types from Tgkrt4:lyn GFP Tglck:DsRedx Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit. GEO Accession:GSM3612308 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP186291     cLCs_1_R1.fq.gz cLCs_1_R2.fq.gz fastq fastq 6917825858.0 22926042.0 GSM3612308 r1 0:150.87 1:150.87 A:2168007671;C:1152140252;G:1228288198;T:2358773829;N:10615908 150 150     2168007671 1152140252 1228288198 2358773829 10615908 SRX5391949 SRS4379779 SRA850414 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.6965 0.66301 0.20956 0.19509 0.8521 0.86218 0.6102 0.59061 151 151 B B biological fallback assumption illumina novaseq_era full_length random_priming nebnext sc single_cell_plate smartseq   China 2019-02-19 Adult Adult Skin Surface Structure
51261 51261 SRR8632324 SRX5431025 SRS4411020 SRP186864 PRJNA524286 The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation GSE127174 Transcriptome Analysis We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control   pubmed:31451657   Krt4+ GSM3629719   source name:keratinocytes|strain background:AB|gentoype/variation:wild type|tissue:keratinocytes Krt4+ Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts keratinocytes transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used. tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc.. zebrafish embryos were grown to 3 dpf in embryonic media strain background:AB|gentoype/variation:wild type|tissue:keratinocytes GSM3629719 GSM3629719: Krt4+; Danio rerio; RNA Seq GSM3629719   1 tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc.. GEO Accession:GSM3629719 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP186864     krt4.fastq.gz fastq 101078150.0 2021563.0 GSM3629719 r1 0:50 A:18002613;C:22778088;G:30701792;T:29589610;N:6047 50       18002613 22778088 30701792 29589610 6047 SRX5431025 SRS4411020 SRA852308 GEO Department of Biological Sciences, Purdue University 1 0.05911   0.00807   0.97461   0.77586   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq sc single_cell_plate smartseq   United States 2019-02-26 Larval Larval Skin Surface Structure
74790 74790 SRR24042941 SRX19844898 SRS17203996 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   mutant epidermis 7 GSM7135698   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant epidermis 7 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135698 GSM7135698: mutant epidermis 7; Danio rerio; RNA Seq GSM7135698 r1 GSM7135698 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py mut_epi_7_R1.fq.gz mut_epi_7_R2.fq.gz fastq fastq 5000082600.0 16666942.0 GSM7135698 r1 0:150 1:150 A:1356614389;C:1145976228;G:1015865485;T:1481123817;N:502681 150 150     1356614389 1145976228 1015865485 1481123817 502681 SRX19844898 SRS17203996 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.8389 0.84116 0.1854 0.18546 0.85543 0.85571 0.60232 0.62058 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74791 74791 SRR24042942 SRX19844897 SRS17203995 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   mutant epidermis 6 GSM7135697   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant epidermis 6 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135697 GSM7135697: mutant epidermis 6; Danio rerio; RNA Seq GSM7135697 r1 GSM7135697 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py mut_epi_6_R1.fq.gz mut_epi_6_R2.fq.gz fastq fastq 5150526900.0 17168423.0 GSM7135697 r1 0:150 1:150 A:1413867032;C:1148708171;G:1068645696;T:1518782074;N:523927 150 150     1413867032 1148708171 1068645696 1518782074 523927 SRX19844897 SRS17203995 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.85431 0.85836 0.20685 0.20717 0.86746 0.86645 0.546 0.5461 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74792 74792 SRR24042943 SRX19844896 SRS17203994 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   mutant epidermis 5 GSM7135696   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant epidermis 5 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135696 GSM7135696: mutant epidermis 5; Danio rerio; RNA Seq GSM7135696 r1 GSM7135696 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py mut_epi_5_R1.fq.gz mut_epi_5_R2.fq.gz fastq fastq 5444193600.0 18147312.0 GSM7135696 r1 0:150 1:150 A:1506955248;C:1203830842;G:1100776758;T:1632090095;N:540657 150 150     1506955248 1203830842 1100776758 1632090095 540657 SRX19844896 SRS17203994 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.84926 0.85327 0.24961 0.24986 0.86665 0.8658 0.59696 0.59563 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74793 74793 SRR24042944 SRX19844895 SRS17203993 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   mutant epidermis 4 GSM7135695   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant epidermis 4 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135695 GSM7135695: mutant epidermis 4; Danio rerio; RNA Seq GSM7135695 r1 GSM7135695 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py mut_epi_4_R1.fq.gz mut_epi_4_R2.fq.gz fastq fastq 5002087200.0 16673624.0 GSM7135695 r1 0:150 1:150 A:1390303577;C:1103953823;G:1001952998;T:1505374747;N:502055 150 150     1390303577 1103953823 1001952998 1505374747 502055 SRX19844895 SRS17203993 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.84071 0.84398 0.25782 0.25789 0.89045 0.89027 0.594 0.59396 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74794 74794 SRR24042945 SRX19844894 SRS17203992 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   mutant epidermis 3 GSM7135694   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant epidermis 3 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135694 GSM7135694: mutant epidermis 3; Danio rerio; RNA Seq GSM7135694 r1 GSM7135694 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py mut_epi_3_R1.fq.gz mut_epi_3_R2.fq.gz fastq fastq 5088778800.0 16962596.0 GSM7135694 r1 0:150 1:150 A:1423520633;C:1124312893;G:1051927427;T:1488506070;N:511777 150 150     1423520633 1124312893 1051927427 1488506070 511777 SRX19844894 SRS17203992 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.87032 0.87262 0.21802 0.21697 0.84478 0.84516 0.57085 0.56848 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74795 74795 SRR24042946 SRX19844893 SRS17203991 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   mutant epidermis 2 GSM7135693   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant epidermis 2 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135693 GSM7135693: mutant epidermis 2; Danio rerio; RNA Seq GSM7135693 r1 GSM7135693 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py mut_epi_2_R1.fq.gz mut_epi_2_R2.fq.gz fastq fastq 4328463900.0 14428213.0 GSM7135693 r1 0:150 1:150 A:1188821495;C:969906063;G:882155508;T:1287158594;N:422240 150 150     1188821495 969906063 882155508 1287158594 422240 SRX19844893 SRS17203991 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.85046 0.85261 0.24989 0.25021 0.89025 0.8897 0.55974 0.55601 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74796 74796 SRR24042947 SRX19844892 SRS17203990 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   mutant epidermis 1 GSM7135692   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant epidermis 1 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135692 GSM7135692: mutant epidermis 1; Danio rerio; RNA Seq GSM7135692 r1 GSM7135692 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py mut_epi_1_R1.fq.gz mut_epi_1_R2.fq.gz fastq fastq 4852088400.0 16173628.0 GSM7135692 r1 0:150 1:150 A:1355547120;C:1052947209;G:998601349;T:1444516092;N:476630 150 150     1355547120 1052947209 998601349 1444516092 476630 SRX19844892 SRS17203990 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.82126 0.82514 0.19738 0.19774 0.8521 0.85171 0.56371 0.58039 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74797 74797 SRR24042948 SRX19844891 SRS17203989 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   sibling epidermis 7 GSM7135691   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling epidermis 7 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135691 GSM7135691: sibling epidermis 7; Danio rerio; RNA Seq GSM7135691 r1 GSM7135691 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py sib_epi_7_R1.fq.gz sib_epi_7_R2.fq.gz fastq fastq 5331845400.0 17772818.0 GSM7135691 r1 0:150 1:150 A:1430690183;C:1254783660;G:1084303117;T:1561520361;N:548079 150 150     1430690183 1254783660 1084303117 1561520361 548079 SRX19844891 SRS17203989 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.85507 0.85819 0.17442 0.17439 0.8495 0.84991 0.59457 0.59698 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74798 74798 SRR24042949 SRX19844890 SRS17203987 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   sibling epidermis 6 GSM7135690   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling epidermis 6 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135690 GSM7135690: sibling epidermis 6; Danio rerio; RNA Seq GSM7135690 r1 GSM7135690 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py sib_epi_6_R1.fq.gz sib_epi_6_R2.fq.gz fastq fastq 5250903600.0 17503012.0 GSM7135690 r1 0:150 1:150 A:1422246673;C:1203178539;G:1084296067;T:1540644470;N:537851 150 150     1422246673 1203178539 1084296067 1540644470 537851 SRX19844890 SRS17203987 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.86662 0.86998 0.17496 0.17481 0.85697 0.85669 0.60671 0.60577 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74799 74799 SRR24042950 SRX19844889 SRS17203988 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   sibling epidermis 5 GSM7135689   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling epidermis 5 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135689 GSM7135689: sibling epidermis 5; Danio rerio; RNA Seq GSM7135689 r1 GSM7135689 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py sib_epi_5_R1.fq.gz sib_epi_5_R2.fq.gz fastq fastq 5357108100.0 17857027.0 GSM7135689 r1 0:150 1:150 A:1442683833;C:1246002420;G:1107335060;T:1560544984;N:541803 150 150     1442683833 1246002420 1107335060 1560544984 541803 SRX19844889 SRS17203988 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.88017 0.88379 0.15935 0.1591 0.83822 0.83784 0.5992 0.59047 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74800 74800 SRR24042951 SRX19844888 SRS17203986 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   sibling epidermis 4 GSM7135688   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling epidermis 4 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135688 GSM7135688: sibling epidermis 4; Danio rerio; RNA Seq GSM7135688 r1 GSM7135688 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py sib_epi_4_R1.fq.gz sib_epi_4_R2.fq.gz fastq fastq 4729031400.0 15763438.0 GSM7135688 r1 0:150 1:150 A:1269897945;C:1106204392;G:980800578;T:1371651398;N:477087 150 150     1269897945 1106204392 980800578 1371651398 477087 SRX19844888 SRS17203986 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.89554 0.89737 0.15933 0.1589 0.84173 0.84181 0.57695 0.58999 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74801 74801 SRR24042952 SRX19844887 SRS17203985 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   sibling epidermis 3 GSM7135687   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling epidermis 3 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135687 GSM7135687: sibling epidermis 3; Danio rerio; RNA Seq GSM7135687 r1 GSM7135687 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py sib_epi_3_R1.fq.gz sib_epi_3_R2.fq.gz fastq fastq 5540201400.0 18467338.0 GSM7135687 r1 0:150 1:150 A:1505221042;C:1289954851;G:1159697425;T:1584759074;N:569008 150 150     1505221042 1289954851 1159697425 1584759074 569008 SRX19844887 SRS17203985 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.88805 0.89059 0.13525 0.1353 0.84084 0.84155 0.58614 0.58632 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74802 74802 SRR24042953 SRX19844886 SRS17203984 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   sibling epidermis 2 GSM7135686   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling epidermis 2 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135686 GSM7135686: sibling epidermis 2; Danio rerio; RNA Seq GSM7135686 r1 GSM7135686 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py sib_epi_2_R1.fq.gz sib_epi_2_R2.fq.gz fastq fastq 3922961700.0 13076539.0 GSM7135686 r1 0:150 1:150 A:1059915956;C:914101921;G:808452034;T:1140105054;N:386735 150 150     1059915956 914101921 808452034 1140105054 386735 SRX19844886 SRS17203984 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.88232 0.88475 0.19744 0.1966 0.83489 0.8342 0.45587 0.45386 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure
74803 74803 SRR24042954 SRX19844885 SRS17203983 SRP430475 PRJNA951376 Spic is required for the differentiation of metaphocyte progenitor cells GSE228732 Transcriptome Analysis Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings parent bioproject:PRJNA951389 pubmed:37148242   sibling epidermis 1 GSM7135685   source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling epidermis 1 Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample epidermis   The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135685 GSM7135685: sibling epidermis 1; Danio rerio; RNA Seq GSM7135685 r1 GSM7135685 1 The EGFP+DsRedx progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071 Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217 Roche for 23 cycles and purified with the Ampure XP beads A63881 Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501 Vazyme.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP430475   loader:fastq load.py sib_epi_1_R1.fq.gz sib_epi_1_R2.fq.gz fastq fastq 4876464000.0 16254880.0 GSM7135685 r1 0:150 1:150 A:1349569338;C:1090614080;G:1014099843;T:1421695200;N:485539 150 150     1349569338 1090614080 1014099843 1421695200 485539 SRX19844885 SRS17203983 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.88374 0.88675 0.17619 0.17572 0.83889 0.83883 0.42946 0.57922 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown sc single_cell_plate smartseq   China 2023-04-02 Adult Adult Skin Surface Structure

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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");;