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52 rows where experiment.library_layout = "PAIRED", technology = "smartseq" and tissue_curation_coarse = "Surface Structure"

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tissue_curation 3

devstage_curation_coarse 3

devstage_curation 3

tissue_curation_coarse 1

  • Surface Structure · 52 ✖

technology 1

  • smartseq · 52 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • PAIRED · 52 ✖
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
61390 61390 SRR12708451 SRX9187386 SRS7423761 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFN3 GSM4802478   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFN3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP GSM4802478 GSM4802478: MFN3; Danio rerio; RNA Seq GSM4802478   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802478 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFN3_R1_001.fastq.gz MFN3_R2_001.fastq.gz fastq fastq 14558703600.0 48529012.0 GSM4802478 r1 0:150 1:150 A:3871514784;C:3434394240;G:3331911824;T:3919968300;N:914452 150 150     3871514784 3434394240 3331911824 3919968300 914452 SRX9187386 SRS7423761 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.89707 0.89196 0.05724 0.05696 0.75396 0.75597 0.43181 0.41631 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61391 61391 SRR12708450 SRX9187385 SRS7423760 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFG3 GSM4802477   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFG3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802477 GSM4802477: MFG3; Danio rerio; RNA Seq GSM4802477   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802477 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFG3_R1_001.fastq.gz MFG3_R2_001.fastq.gz fastq fastq 10045323900.0 33484413.0 GSM4802477 r1 0:150 1:150 A:2619233046;C:2425417526;G:2312268655;T:2687771920;N:632753 150 150     2619233046 2425417526 2312268655 2687771920 632753 SRX9187385 SRS7423760 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90365 0.90046 0.06439 0.06489 0.75436 0.75641 0.54634 0.54693 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61394 61394 SRR12708447 SRX9187382 SRS7423757 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFN3 GSM4802474   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFN3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP GSM4802474 GSM4802474: XFN3; Danio rerio; RNA Seq GSM4802474   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802474 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFN3_R1_001.fastq.gz XFN3_R2_001.fastq.gz fastq fastq 11204873700.0 37349579.0 GSM4802474 r1 0:150 1:150 A:2943394483;C:2667470839;G:2579644073;T:3013655182;N:709123 150 150     2943394483 2667470839 2579644073 3013655182 709123 SRX9187382 SRS7423757 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90055 0.89407 0.05457 0.05489 0.74247 0.746 0.48492 0.48602 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61395 61395 SRR12708446 SRX9187381 SRS7423756 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFG3 GSM4802473   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFG3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802473 GSM4802473: XFG3; Danio rerio; RNA Seq GSM4802473   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802473 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFG3_R1_001.fastq.gz XFG3_R2_001.fastq.gz fastq fastq 11212083000.0 37373610.0 GSM4802473 r1 0:150 1:150 A:2979985262;C:2652925544;G:2513147966;T:3065318302;N:705926 150 150     2979985262 2652925544 2513147966 3065318302 705926 SRX9187381 SRS7423756 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.9056 0.89972 0.06159 0.06165 0.74194 0.74602 0.49523 0.44889 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61398 61398 SRR12708443 SRX9187378 SRS7423753 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFN2 GSM4802470   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFN2 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP GSM4802470 GSM4802470: MFN2; Danio rerio; RNA Seq GSM4802470   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802470 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFN2_R1_001.fastq.gz MFN2_R2_001.fastq.gz fastq fastq 9002969100.0 30009897.0 GSM4802470 r1 0:150 1:150 A:2383579322;C:2152753900;G:2013843514;T:2452228154;N:564210 150 150     2383579322 2152753900 2013843514 2452228154 564210 SRX9187378 SRS7423753 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.89613 0.89129 0.06896 0.06936 0.75235 0.75659 0.51059 0.50763 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61399 61399 SRR12708442 SRX9187377 SRS7423752 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFG2 GSM4802469   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFG2 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802469 GSM4802469: MFG2; Danio rerio; RNA Seq GSM4802469   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802469 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFG2_R1_001.fastq.gz MFG2_R2_001.fastq.gz fastq fastq 11893039800.0 39643466.0 GSM4802469 r1 0:150 1:150 A:3160384920;C:2834257771;G:2698430613;T:3199226169;N:740327 150 150     3160384920 2834257771 2698430613 3199226169 740327 SRX9187377 SRS7423752 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90353 0.89813 0.06957 0.06993 0.75183 0.75607 0.46098 0.51543 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61402 61402 SRR12708439 SRX9187374 SRS7423749 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFN2 GSM4802466   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFN2 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP GSM4802466 GSM4802466: XFN2; Danio rerio; RNA Seq GSM4802466   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802466 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFN2_R1_001.fastq.gz XFN2_R2_001.fastq.gz fastq fastq 11313005400.0 37710018.0 GSM4802466 r1 0:150 1:150 A:2996096346;C:2703585714;G:2550898118;T:3061720444;N:704778 150 150     2996096346 2703585714 2550898118 3061720444 704778 SRX9187374 SRS7423749 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.88653 0.88127 0.06171 0.06088 0.74856 0.75252 0.51699 0.51503 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61403 61403 SRR12708438 SRX9187373 SRS7423748 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFG2 GSM4802465   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFG2 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802465 GSM4802465: XFG2; Danio rerio; RNA Seq GSM4802465   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802465 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFG2_R1_001.fastq.gz XFG2_R2_001.fastq.gz fastq fastq 11921269800.0 39737566.0 GSM4802465 r1 0:150 1:150 A:3191695537;C:2823855056;G:2636104989;T:3268877243;N:736975 150 150     3191695537 2823855056 2636104989 3268877243 736975 SRX9187373 SRS7423748 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.89811 0.89304 0.06734 0.0674 0.7391 0.74261 0.51932 0.45328 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61406 61406 SRR12708435 SRX9187370 SRS7423745 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFN1 GSM4802462   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFN1 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP GSM4802462 GSM4802462: MFN1; Danio rerio; RNA Seq GSM4802462   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802462 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFN1_R1_001.fastq.gz MFN1_R2_001.fastq.gz fastq fastq 12560283900.0 41867613.0 GSM4802462 r1 0:150 1:150 A:3295279231;C:3013386640;G:2898979550;T:3351847365;N:791114 150 150     3295279231 3013386640 2898979550 3351847365 791114 SRX9187370 SRS7423745 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.89681 0.89104 0.06566 0.06589 0.74272 0.74791 0.51645 0.51902 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61407 61407 SRR12708434 SRX9187369 SRS7423744 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFG1 GSM4802461   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFG1 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802461 GSM4802461: MFG1; Danio rerio; RNA Seq GSM4802461   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802461 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFG1_R1_001.fastq.gz MFG1_R2_001.fastq.gz fastq fastq 11317873500.0 37726245.0 GSM4802461 r1 0:150 1:150 A:2947830189;C:2733463243;G:2616872694;T:3018996791;N:710583 150 150     2947830189 2733463243 2616872694 3018996791 710583 SRX9187369 SRS7423744 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90788 0.90139 0.06383 0.06478 0.74268 0.74686 0.50725 0.50595 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61410 61410 SRR12708431 SRX9187366 SRS7423741 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFN1 GSM4802458   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFN1 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP GSM4802458 GSM4802458: XFN1; Danio rerio; RNA Seq GSM4802458   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802458 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFN1_R1_001.fastq.gz XFN1_R2_001.fastq.gz fastq fastq 11573931900.0 38579773.0 GSM4802458 r1 0:150 1:150 A:2999184334;C:2801583964;G:2672180906;T:3100254047;N:728649 150 150     2999184334 2801583964 2672180906 3100254047 728649 SRX9187366 SRS7423741 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.8962 0.88921 0.05791 0.05848 0.74097 0.7471 0.50594 0.5107 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61411 61411 SRR12708430 SRX9187365 SRS7423740 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFG1 GSM4802457   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFG1 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802457 GSM4802457: XFG1; Danio rerio; RNA Seq GSM4802457   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802457 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFG1_R1_001.fastq.gz XFG1_R2_001.fastq.gz fastq fastq 11738198700.0 39127329.0 GSM4802457 r1 0:150 1:150 A:3083667179;C:2816699592;G:2648683281;T:3188411465;N:737183 150 150     3083667179 2816699592 2648683281 3188411465 737183 SRX9187365 SRS7423740 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90455 0.89777 0.05668 0.05707 0.74631 0.75057 0.49373 0.48957 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
64331 64331 SRR14551653 SRX10895137 SRS8987960 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   neuronal 72hpf Sample3 GSM5315776   tissue:Zebrafish embryo trunk|strain:AB* Tgnbt:dsred|age:72 hpf neuronal 72hpf Sample3 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Tgnbt:dsred|age:72 hpf GSM5315776 GSM5315776: neuronal 72hpf Sample3; Danio rerio; RNA Seq GSM5315776   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315776 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load neuronal72_Sample3_R1_001.fastq.gz neuronal72_Sample3_R2_001.fastq.gz fastq fastq 5811578187.0 19461304.0 GSM5315776 r1 0:149.33 1:149.29 A:1529597778;C:1363449364;G:1361318435;T:1556834579;N:378031 149 149     1529597778 1363449364 1361318435 1556834579 378031 SRX10895137 SRS8987960 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.86088 0.86196 0.09968 0.09909 0.76952 0.77553 0.47402 0.46267 149 149 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64332 64332 SRR14551652 SRX10895136 SRS8987961 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   neuronal 72hpf Sample2 GSM5315775   tissue:Zebrafish embryo trunk|strain:AB* Tgnbt:dsred|age:72 hpf neuronal 72hpf Sample2 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Tgnbt:dsred|age:72 hpf GSM5315775 GSM5315775: neuronal 72hpf Sample2; Danio rerio; RNA Seq GSM5315775   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315775 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load neuronal72_Sample2_R1_001.fastq.gz neuronal72_Sample2_R2_001.fastq.gz fastq fastq 5330377491.0 17862084.0 GSM5315775 r1 0:149.23 1:149.19 A:1408165778;C:1247044167;G:1242879903;T:1431943960;N:343683 149 149     1408165778 1247044167 1242879903 1431943960 343683 SRX10895136 SRS8987961 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.82586 0.83096 0.1393 0.14169 0.7907 0.79555 0.46473 0.48234 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64333 64333 SRR14551651 SRX10895135 SRS8987956 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   neuronal 72hpf Sample1 GSM5315774   tissue:Zebrafish embryo trunk|strain:AB* Tgnbt:dsred|age:72 hpf neuronal 72hpf Sample1 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Tgnbt:dsred|age:72 hpf GSM5315774 GSM5315774: neuronal 72hpf Sample1; Danio rerio; RNA Seq GSM5315774   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315774 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load neuronal72_Sample1_R1_001.fastq.gz neuronal72_Sample1_R2_001.fastq.gz fastq fastq 7122524050.0 23888399.0 GSM5315774 r1 0:149.11 1:149.05 A:1867527557;C:1687169064;G:1683673406;T:1883615223;N:538800 149 149     1867527557 1687169064 1683673406 1883615223 538800 SRX10895135 SRS8987956 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.88793 0.88809 0.12727 0.12826 0.7486 0.75635 0.42346 0.48977 149 149 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64334 64334 SRR14551650 SRX10895134 SRS8987957 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   OPC 72hpf Sample3 GSM5315773   tissue:Zebrafish embryo trunk|strain:AB* Tgolig2:dsred; Tgsox10:megfp|age:72 hpf OPC 72hpf Sample3 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Tgolig2:dsred;Tgsox10:megfp|age:72 hpf GSM5315773 GSM5315773: OPC 72hpf Sample3; Danio rerio; RNA Seq GSM5315773   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315773 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load OPC72_Sample3_R1_001.fastq.gz OPC72_Sample3_R2_001.fastq.gz fastq fastq 6630077092.0 22212439.0 GSM5315773 r1 0:149.27 1:149.22 A:1681054163;C:1589572166;G:1588126414;T:1770833666;N:490683 149 149     1681054163 1589572166 1588126414 1770833666 490683 SRX10895134 SRS8987957 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.69031 0.6945 0.1106 0.1101 0.85123 0.85389 0.45515 0.45517 149 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64335 64335 SRR14551649 SRX10895133 SRS8987958 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   OPC 72hpf Sample2 GSM5315772   tissue:Zebrafish embryo trunk|strain:AB* Tgolig2:dsred; Tgsox10:megfp|age:72 hpf OPC 72hpf Sample2 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Tgolig2:dsred;Tgsox10:megfp|age:72 hpf GSM5315772 GSM5315772: OPC 72hpf Sample2; Danio rerio; RNA Seq GSM5315772   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315772 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load OPC72_Sample2_R1_001.fastq.gz OPC72_Sample2_R2_001.fastq.gz fastq fastq 7703607275.0 25797864.0 GSM5315772 r1 0:149.33 1:149.29 A:2052466926;C:1756697559;G:1751055673;T:2142874669;N:512448 149 149     2052466926 1756697559 1751055673 2142874669 512448 SRX10895133 SRS8987958 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.78396 0.7872 0.15128 0.15083 0.80176 0.8043 0.47044 0.47071 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64336 64336 SRR14551648 SRX10895132 SRS8987959 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   OPC 72hpf Sample1 GSM5315771   tissue:Zebrafish embryo trunk|strain:AB* Tgolig2:dsred; Tgsox10:megfp|age:72 hpf OPC 72hpf Sample1 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Tgolig2:dsred;Tgsox10:megfp|age:72 hpf GSM5315771 GSM5315771: OPC 72hpf Sample1; Danio rerio; RNA Seq GSM5315771   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315771 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load OPC72_Sample1_R1_001.fastq.gz OPC72_Sample1_R2_001.fastq.gz fastq fastq 6819055600.0 22845167.0 GSM5315771 r1 0:149.27 1:149.22 A:1844296500;C:1523361309;G:1519052310;T:1931907615;N:437866 149 149     1844296500 1523361309 1519052310 1931907615 437866 SRX10895132 SRS8987959 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.83297 0.83417 0.1328 0.13254 0.78821 0.79318 0.46692 0.4635 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64337 64337 SRR14551647 SRX10895131 SRS8987955 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   SC 72hpf Sample3 GSM5315770   tissue:Zebrafish embryo trunk|strain:AB* Gtfoxd3:mCherry; Tgsox10:mEGFP|age:72 hpf SC 72hpf Sample3 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Gtfoxd3:mCherry;Tgsox10:mEGFP|age:72 hpf GSM5315770 GSM5315770: SC 72hpf Sample3; Danio rerio; RNA Seq GSM5315770   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315770 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load SC72_Sample3_R1_001.fastq.gz SC72_Sample3_R2_001.fastq.gz fastq fastq 5290486005.0 17724499.0 GSM5315770 r1 0:149.26 1:149.22 A:1416646219;C:1205875601;G:1205458968;T:1462077308;N:427909 149 149     1416646219 1205875601 1205458968 1462077308 427909 SRX10895131 SRS8987955 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.80356 0.80484 0.13757 0.13551 0.79017 0.79569 0.464 0.46891 149 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64338 64338 SRR14551646 SRX10895130 SRS8987954 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   SC 72hpf Sample2 GSM5315769   tissue:Zebrafish embryo trunk|strain:AB* Gtfoxd3:mCherry; Tgsox10:mEGFP|age:72 hpf SC 72hpf Sample2 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Gtfoxd3:mCherry;Tgsox10:mEGFP|age:72 hpf GSM5315769 GSM5315769: SC 72hpf Sample2; Danio rerio; RNA Seq GSM5315769   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315769 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load SC72_Sample2_R1_001.fastq.gz SC72_Sample2_R2_001.fastq.gz fastq fastq 5300704321.0 17740513.0 GSM5315769 r1 0:149.42 1:149.37 A:1270635814;C:1361971808;G:1357145534;T:1310555763;N:395402 149 149     1270635814 1361971808 1357145534 1310555763 395402 SRX10895130 SRS8987954 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.52849 0.53398 0.10216 0.10317 0.887 0.88956 0.49141 0.49821 150 148 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk Surface Structure
64339 64339 SRR14551645 SRX10895129 SRS8987953 SRP319894 PRJNA730034 Zebrafish Danio rerio Schwann cell oligodendrocyte lineage and neuron RNA sequencing GSE174486 Transcriptome Analysis RNA sequencing of cells collected from 72 hpf embryos: Schwann cells Gtfoxd3:mCherry;Tgsox10:mEGFP oligodendrocyte lineage cells Tgolig2:dsred;Tgsox10:megfp and neurons Tgnbt:dsred Overall design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells foxd3+/sox10+ double positive cells were collected from trunks of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos. For oligodendrocyte lineage cells olig2+/sox10+ double positive cells were collected from the trunks of Tgolig2:dsred;Tgsox10:megfp embryos. For neurons nbt+ cells were collected from the trunks of Tgnbt:dsred embryos. 3 replicates for each condition.   pubmed:33975920   SC 72hpf Sample1 GSM5315768   tissue:Zebrafish embryo trunk|strain:AB* Gtfoxd3:mCherry; Tgsox10:mEGFP|age:72 hpf SC 72hpf Sample1 For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations Zebrafish embryo trunk 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing. Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing Gtfoxd3:mCherry;Tgsox10:mEGFP for Schwann cells Tgolig2:dsred;Tgsox10:megfp for OPC and Tgnbt:dsred for neurons zebrafish embryos were raised in egg water at 28.5C to 72 hpf strain:AB* Gtfoxd3:mCherry;Tgsox10:mEGFP|age:72 hpf GSM5315768 GSM5315768: SC 72hpf Sample1; Danio rerio; RNA Seq GSM5315768   1 Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing GEO Accession:GSM5315768 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP319894   loader:latf load SC72_Sample1_R1_001.fastq.gz SC72_Sample1_R2_001.fastq.gz fastq fastq 5239512991.0 17546095.0 GSM5315768 r1 0:149.33 1:149.28 A:1298269567;C:1306015004;G:1299170862;T:1335241575;N:815983 149 149     1298269567 1306015004 1299170862 1335241575 815983 SRX10895129 SRS8987953 SRA1232603 GEO Kucenas Lab, Biology, University of Virginia 2 0.61524 0.62125 0.10182 0.10151 0.87393 0.87825 0.47941 0.47885 149 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2021-05-14 Larval Larval Trunk 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");;