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19 rows where technology = "smartseq" and tissue_curation_coarse = "Respiratory System"

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  • Respiratory System · 19 ✖

tissue_curation 1

technology 1

  • smartseq · 19 ✖

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Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
60514 60514 SRR12340121 SRX8839908 SRS7103142 SRP273975 PRJNA649247 Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine GSE155287 Transcriptome Analysis In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   pubmed:33027664   sox17 gill DsRedx 3 GSM4698505   source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP sox17 gill DsRedx 3 Raw reads were first aligned to zebrafish reference genome danRer11 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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish gill   30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP GSM4698505 GSM4698505: sox17 gill DsRedx 3; Danio rerio; RNA Seq GSM4698505   1 30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing. GEO Accession:GSM4698505 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP273975     sox17_gill_DsRedx_3_R1.fq.gz sox17_gill_DsRedx_3_R2.fq.gz fastq fastq 6482204823.0 22206962.0 GSM4698505 r1 0:146.24 1:145.66 A:1892664132;C:1333446985;G:1270670352;T:1985394285;N:29069 146 145     1892664132 1333446985 1270670352 1985394285 29069 SRX8839908 SRS7103142 SRA1104756 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.79891 0.79555 0.23795 0.23516 0.886 0.88613 0.48969 0.48724 150 148 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-07-28 Adult Adult Gill Respiratory System
60515 60515 SRR12340120 SRX8839907 SRS7103140 SRP273975 PRJNA649247 Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine GSE155287 Transcriptome Analysis In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   pubmed:33027664   sox17 gill DsRedx 2 GSM4698504   source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP sox17 gill DsRedx 2 Raw reads were first aligned to zebrafish reference genome danRer11 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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish gill   30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP GSM4698504 GSM4698504: sox17 gill DsRedx 2; Danio rerio; RNA Seq GSM4698504   1 30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing. GEO Accession:GSM4698504 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP273975     sox17_gill_DsRedx_2_R1.fq.gz sox17_gill_DsRedx_2_R2.fq.gz fastq fastq 6871522969.0 23718551.0 GSM4698504 r1 0:145.07 1:144.64 A:1996597634;C:1433447769;G:1330303568;T:2111142421;N:31577 145 144     1996597634 1433447769 1330303568 2111142421 31577 SRX8839907 SRS7103140 SRA1104756 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.77789 0.77647 0.23871 0.23784 0.90319 0.90402 0.59462 0.59357 149 80 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-07-28 Adult Adult Gill Respiratory System
60516 60516 SRR12340119 SRX8839906 SRS7103139 SRP273975 PRJNA649247 Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine GSE155287 Transcriptome Analysis In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   pubmed:33027664   sox17 gill DsRedx 1 GSM4698503   source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP sox17 gill DsRedx 1 Raw reads were first aligned to zebrafish reference genome danRer11 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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish gill   30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP GSM4698503 GSM4698503: sox17 gill DsRedx 1; Danio rerio; RNA Seq GSM4698503   1 30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing. GEO Accession:GSM4698503 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP273975     sox17_gill_DsRedx_1_R1.fq.gz sox17_gill_DsRedx_1_R2.fq.gz fastq fastq 6640801871.0 23132663.0 GSM4698503 r1 0:143.42 1:143.65 A:1787496811;C:1555982056;G:1401318306;T:1895972742;N:31956 143 143     1787496811 1555982056 1401318306 1895972742 31956 SRX8839906 SRS7103139 SRA1104756 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.82205 0.82023 0.17657 0.17516 0.88799 0.88846 0.60101 0.5999 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-07-28 Adult Adult Gill Respiratory System
60517 60517 SRR12340118 SRX8839905 SRS7103141 SRP273975 PRJNA649247 Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine GSE155287 Transcriptome Analysis In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   pubmed:33027664   sox17 gill GFP 3 GSM4698502   source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP sox17 gill GFP 3 Raw reads were first aligned to zebrafish reference genome danRer11 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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish gill   30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP GSM4698502 GSM4698502: sox17 gill GFP 3; Danio rerio; RNA Seq GSM4698502   1 30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing. GEO Accession:GSM4698502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP273975     sox17_gill_GFP_3_R1.fq.gz sox17_gill_GFP_3_R2.fq.gz fastq fastq 5881408853.0 20262087.0 GSM4698502 r1 0:145.09 1:145.18 A:1611164278;C:1359776238;G:1263385328;T:1647055163;N:27846 145 145     1611164278 1359776238 1263385328 1647055163 27846 SRX8839905 SRS7103141 SRA1104756 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.85631 0.85552 0.14127 0.14135 0.88972 0.89065 0.53836 0.53645 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-07-28 Adult Adult Gill Respiratory System
60518 60518 SRR12340117 SRX8839904 SRS7103138 SRP273975 PRJNA649247 Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine GSE155287 Transcriptome Analysis In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   pubmed:33027664   sox17 gill GFP 2 GSM4698501   source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP sox17 gill GFP 2 Raw reads were first aligned to zebrafish reference genome danRer11 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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish gill   30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP GSM4698501 GSM4698501: sox17 gill GFP 2; Danio rerio; RNA Seq GSM4698501   1 30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing. GEO Accession:GSM4698501 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP273975     sox17_gill_GFP_2_R1.fq.gz sox17_gill_GFP_2_R2.fq.gz fastq fastq 6629269698.0 23040040.0 GSM4698501 r1 0:143.67 1:144.06 A:1792321281;C:1562626172;G:1410652523;T:1863639213;N:30509 143 144     1792321281 1562626172 1410652523 1863639213 30509 SRX8839904 SRS7103138 SRA1104756 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.87337 0.87168 0.16298 0.16158 0.86563 0.86582 0.57739 0.58009 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-07-28 Adult Adult Gill Respiratory System
60519 60519 SRR12340116 SRX8839903 SRS7103137 SRP273975 PRJNA649247 Deciphering Endoderm derived Macrophage like Metaphocytes in Zebrafish Gill and Intestine GSE155287 Transcriptome Analysis In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine we isolated endoderm derived GFP+ cells and remaining DsRedx+ cells hematopoiesis derived macrophages from the gill sox17 gill GFP sox17 gill DsRedx and intestine sox17 intestine GFP sox17 intestine DsRedx of 4 OHT treated Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP fish and performed RNA seq. Both T SNE analysis and feature gene comparison indicate that the endoderm derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm derived mpeg1+ cells as metaphocytes. Overall design: Different cell types form zebrafish gill and intestine including GFP labelled metaphocytes and DsRedx labelled macrophages were sorted by fluorescence activated cell sorting FACS. cDNA libraries were prepared according to standard Smart seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   pubmed:33027664   sox17 gill GFP 1 GSM4698500   source name:specific cells types in zebrafish gill|tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP sox17 gill GFP 1 Raw reads were first aligned to zebrafish reference genome danRer11 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: danRer11 Supplementary files format and content: comma separated values file including read counts and TPM values for each sample specific cells types in zebrafish gill   30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing.   tissue:gill|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP GSM4698500 GSM4698500: sox17 gill GFP 1; Danio rerio; RNA Seq GSM4698500   1 30 50 cells for each sample were sorted into lysis buffer 0.2% Triton X 100 solution by fluorescence activated cell sorting FACS for direct reverse transcription and cDNA amplification cDNA library was generated based on SMART seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair end sequencing. GEO Accession:GSM4698500 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP273975     sox17_gill_GFP_1_R1.fq.gz sox17_gill_GFP_1_R2.fq.gz fastq fastq 8550712115.0 29745129.0 GSM4698500 r1 0:143.49 1:143.98 A:2279816799;C:2045513877;G:1883280335;T:2342060508;N:40596 143 143     2279816799 2045513877 1883280335 2342060508 40596 SRX8839903 SRS7103137 SRA1104756 GEO Room 6319, Division of Life Science, Hong Kong University of Science and Technology 2 0.87481 0.87331 0.14783 0.14775 0.84824 0.84946 0.54943 0.47083 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   China 2020-07-28 Adult Adult Gill Respiratory System
74777 74777 SRR24042928 SRX19844911 SRS17204009 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 gill 8 GSM7135711   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 8 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135711 GSM7135711: mutant gill 8; Danio rerio; RNA Seq GSM7135711 r1 GSM7135711 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_gill_8_R1.fq.gz mut_gill_8_R2.fq.gz fastq fastq 4676495100.0 15588317.0 GSM7135711 r1 0:150 1:150 A:1307407255;C:1023522602;G:969790674;T:1375306960;N:467609 150 150     1307407255 1023522602 969790674 1375306960 467609 SRX19844911 SRS17204009 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.83959 0.8448 0.26782 0.26778 0.87125 0.87144 0.56023 0.56037 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 Gill Respiratory System
74778 74778 SRR24042929 SRX19844910 SRS17204008 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 gill 7 GSM7135710   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135710 GSM7135710: mutant gill 7; Danio rerio; RNA Seq GSM7135710 r1 GSM7135710 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_gill_7_R1.fq.gz mut_gill_7_R2.fq.gz fastq fastq 5888494500.0 19628315.0 GSM7135710 r1 0:150 1:150 A:1618640164;C:1326869398;G:1198422598;T:1743959857;N:602483 150 150     1618640164 1326869398 1198422598 1743959857 602483 SRX19844910 SRS17204008 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.84262 0.84414 0.2211 0.2217 0.85208 0.85275 0.54003 0.5392 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 Gill Respiratory System
74779 74779 SRR24042930 SRX19844909 SRS17204007 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 gill 6 GSM7135709   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135709 GSM7135709: mutant gill 6; Danio rerio; RNA Seq GSM7135709 r1 GSM7135709 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_gill_6_R1.fq.gz mut_gill_6_R2.fq.gz fastq fastq 5319891900.0 17732973.0 GSM7135709 r1 0:150 1:150 A:1487641547;C:1157753055;G:1092549232;T:1581414608;N:533458 150 150     1487641547 1157753055 1092549232 1581414608 533458 SRX19844909 SRS17204007 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.84896 0.85199 0.24621 0.24605 0.83378 0.83337 0.55455 0.55559 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 Gill Respiratory System
74780 74780 SRR24042931 SRX19844908 SRS17204006 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 gill 5 GSM7135708   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135708 GSM7135708: mutant gill 5; Danio rerio; RNA Seq GSM7135708 r1 GSM7135708 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_gill_5_R1.fq.gz mut_gill_5_R2.fq.gz fastq fastq 5529933300.0 18433111.0 GSM7135708 r1 0:150 1:150 A:1544115928;C:1211935586;G:1126417556;T:1646909383;N:554847 150 150     1544115928 1211935586 1126417556 1646909383 554847 SRX19844908 SRS17204006 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.85153 0.85305 0.23595 0.23538 0.83463 0.83522 0.55289 0.5526 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 Gill Respiratory System
74781 74781 SRR24042932 SRX19844907 SRS17204005 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 gill 4 GSM7135707   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135707 GSM7135707: mutant gill 4; Danio rerio; RNA Seq GSM7135707 r1 GSM7135707 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_gill_4_R1.fq.gz mut_gill_4_R2.fq.gz fastq fastq 5181547800.0 17271826.0 GSM7135707 r1 0:150 1:150 A:1461607714;C:1119875397;G:1036275299;T:1563269275;N:520115 150 150     1461607714 1119875397 1036275299 1563269275 520115 SRX19844907 SRS17204005 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.82652 0.82859 0.2619 0.26087 0.8508 0.851 0.5174 0.51758 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 Gill Respiratory System
74782 74782 SRR24042933 SRX19844906 SRS17204004 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 gill 3 GSM7135706   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135706 GSM7135706: mutant gill 3; Danio rerio; RNA Seq GSM7135706 r1 GSM7135706 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_gill_3_R1.fq.gz mut_gill_3_R2.fq.gz fastq fastq 5914269900.0 19714233.0 GSM7135706 r1 0:150 1:150 A:1744887146;C:1199785696;G:1139441688;T:1829560268;N:595102 150 150     1744887146 1199785696 1139441688 1829560268 595102 SRX19844906 SRS17204004 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.81829 0.82058 0.35062 0.34936 0.82822 0.82818 0.45594 0.45957 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 Gill Respiratory System
74783 74783 SRR24042934 SRX19844905 SRS17204003 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 gill 2 GSM7135705   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135705 GSM7135705: mutant gill 2; Danio rerio; RNA Seq GSM7135705 r1 GSM7135705 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_gill_2_R1.fq.gz mut_gill_2_R2.fq.gz fastq fastq 4408680900.0 14695603.0 GSM7135705 r1 0:150 1:150 A:1244600117;C:952046549;G:896094438;T:1315516801;N:422995 150 150     1244600117 952046549 896094438 1315516801 422995 SRX19844905 SRS17204003 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.84142 0.84219 0.24006 0.23884 0.84072 0.84017 0.54492 0.53976 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 Gill Respiratory System
74784 74784 SRR24042935 SRX19844904 SRS17204002 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 gill 1 GSM7135704   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult mutant gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:mutant|Stage:adult GSM7135704 GSM7135704: mutant gill 1; Danio rerio; RNA Seq GSM7135704 r1 GSM7135704 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_gill_1_R1.fq.gz mut_gill_1_R2.fq.gz fastq fastq 5737020900.0 19123403.0 GSM7135704 r1 0:150 1:150 A:1628971228;C:1225892373;G:1171419964;T:1710176758;N:560577 150 150     1628971228 1225892373 1171419964 1710176758 560577 SRX19844904 SRS17204002 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.85749 0.85886 0.22848 0.22786 0.84751 0.8478 0.54349 0.54831 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 Gill Respiratory System
74785 74785 SRR24042936 SRX19844903 SRS17204001 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 gill 5 GSM7135703   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135703 GSM7135703: sibling gill 5; Danio rerio; RNA Seq GSM7135703 r1 GSM7135703 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_gill_5_R1.fq.gz sib_gill_5_R2.fq.gz fastq fastq 6562140600.0 21873802.0 GSM7135703 r1 0:150 1:150 A:1779900685;C:1529690989;G:1371763678;T:1880116831;N:668417 150 150     1779900685 1529690989 1371763678 1880116831 668417 SRX19844903 SRS17204001 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.88218 0.88445 0.15726 0.15686 0.80844 0.80856 0.477 0.47442 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 Gill Respiratory System
74786 74786 SRR24042937 SRX19844902 SRS17204000 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 gill 4 GSM7135702   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135702 GSM7135702: sibling gill 4; Danio rerio; RNA Seq GSM7135702 r1 GSM7135702 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_gill_4_R1.fq.gz sib_gill_4_R2.fq.gz fastq fastq 6257889900.0 20859633.0 GSM7135702 r1 0:150 1:150 A:1662270061;C:1479033481;G:1292962058;T:1822988793;N:635507 150 150     1662270061 1479033481 1292962058 1822988793 635507 SRX19844902 SRS17204000 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.87917 0.88287 0.17274 0.173 0.83287 0.8325 0.54714 0.55034 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 Gill Respiratory System
74787 74787 SRR24042938 SRX19844901 SRS17203999 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 gill 3 GSM7135701   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135701 GSM7135701: sibling gill 3; Danio rerio; RNA Seq GSM7135701 r1 GSM7135701 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_gill_3_R1.fq.gz sib_gill_3_R2.fq.gz fastq fastq 4697288100.0 15657627.0 GSM7135701 r1 0:150 1:150 A:1267251861;C:1084859605;G:951792210;T:1393022956;N:361468 150 150     1267251861 1084859605 951792210 1393022956 361468 SRX19844901 SRS17203999 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.87119 0.87101 0.22114 0.22034 0.84822 0.84638 0.56814 0.56703 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 Gill Respiratory System
74788 74788 SRR24042939 SRX19844900 SRS17203998 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 gill 2 GSM7135700   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135700 GSM7135700: sibling gill 2; Danio rerio; RNA Seq GSM7135700 r1 GSM7135700 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_gill_2_R1.fq.gz sib_gill_2_R2.fq.gz fastq fastq 4409361900.0 14697873.0 GSM7135700 r1 0:150 1:150 A:1190780563;C:1018286434;G:902403781;T:1297459939;N:431183 150 150     1190780563 1018286434 902403781 1297459939 431183 SRX19844900 SRS17203998 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.88022 0.88304 0.17039 0.17149 0.82793 0.82856 0.55968 0.56548 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 Gill Respiratory System
74789 74789 SRR24042940 SRX19844899 SRS17203997 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 gill 1 GSM7135699   source name:gill|tissue:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult sibling gill 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 gill   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:gill|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx cells|genotype:sibling|Stage:adult GSM7135699 GSM7135699: sibling gill 1; Danio rerio; RNA Seq GSM7135699 r1 GSM7135699 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_gill_1_R1.fq.gz sib_gill_1_R2.fq.gz fastq fastq 6054959100.0 20183197.0 GSM7135699 r1 0:150 1:150 A:1655928049;C:1376589574;G:1251684181;T:1770148028;N:609268 150 150     1655928049 1376589574 1251684181 1770148028 609268 SRX19844899 SRS17203997 SRA1614434 WEN lab, Life Science, Hong Kong University of Science and Technology WEN lab, Life Science, Hong Kong University of Science and Technology 2 0.88342 0.88635 0.14131 0.14119 0.83349 0.83343 0.57723 0.59252 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 Gill Respiratory System

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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");;