run_metadata: 34630
This data as json
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| 34630 | SRR32145161 | SRX27491068 | SRS23912866 | SRP560249 | PRJNA1216300 | Insulin like growth factor signalling regulates zebrafish lymphatic vessel development | GSE288160 | Transcriptome Analysis | RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet. | kat6a Replicate 1 | GSM8760183 | tissue:Chondrocyte|cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry|geo loc name:missing|collection date:missing | kat6a Replicate 1 | The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column | Chondrocyte | At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer | Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees. | cell type:Chondrocyte|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry | GSM8760183 | GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq | GSM8760183 r1 | GSM8760183 | 1 | At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP560249 | kat6a1_S1_L001_R1_001.fastq.gz | fastq | 1199414140.0 | 15781765.0 | GSM8760183 r1 | 0:76 | A:302128648;C:264050936;G:275501956;T:357525321;N:207279 | 76 | 302128648 | 264050936 | 275501956 | 357525321 | 207279 | SRX27491068 | SRS23912866 | SRA2062832 | Molecular Medicine and Pathology, University of Auckland | Molecular Medicine and Pathology, University of Auckland | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | New Zealand | 2025-01-27 | Larval | Larval | Bone or Cartilage | Skeletal Element |