run_metadata: 60509
This data as json
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| 60509 | SRR12340126 | SRX8839913 | SRS7103147 | 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 intestine DsRedx 2 | GSM4698510 | source name:specific cells types in zebrafish intestine|tissue:intestine|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP | sox17 intestine 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 intestine | 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:intestine|age:adult|genotype:Tgsox17:CreERT2;mpeg1:loxP DsRedx loxP GFP | GSM4698510 | GSM4698510: sox17 intestine DsRedx 2; Danio rerio; RNA Seq | GSM4698510 | 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:GSM4698510 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP273975 | sox17_intestine_DsRedx_2_R1.fq.gz sox17_intestine_DsRedx_2_R2.fq.gz | fastq fastq | 5763127951.0 | 19786561.0 | GSM4698510 r1 | 0:145.82 1:145.44 | A:1642307410;C:1243357808;G:1159617669;T:1717817199;N:27865 | 145 | 145 | 1642307410 | 1243357808 | 1159617669 | 1717817199 | 27865 | SRX8839913 | SRS7103147 | SRA1104756 | GEO | Room 6319, Division of Life Science, Hong Kong University of Science and Technology | 2 | 0.83861 | 0.8393 | 0.20669 | 0.20652 | 0.8647 | 0.8645 | 0.58971 | 0.59768 | 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 | Gut | Digestive System |