run_metadata: 44925
This data as json
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| 44925 | SRR6297667 | SRX3398646 | SRS2692826 | SRP125098 | PRJNA418729 | The CCCH type zinc finger transcription factor Zc3h8 protects hepatocytes from degeneration by repressing the inflammatory response in zebrafish. | GSE106985 | Transcriptome Analysis | Transcriptional profile of hepatocytes during the cq5 mutant liver degeneration middle stage 5.5 dpf and later stage 7.5 dpf. Overall design: Examination of gene expression at two different stages for mutant sample group and wild type control group. | D5.5WT | GSM2858887 | source name:Hepatocytes|strain:ABGO|tissue:liver|developmental stage:5.5 dpf | D5.5WT | Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.xls] tab delimited text file includes RPKMs for each Sample. [Table s1.xls] foldChange between developmental stages in each genotype cells. | Hepatocytes | Choose two different stages 5.5 and 7.5 dpf of zc3h8 / mutant and wild type group larves which hepatocytes were markerd by Tglfabp:Dendra2 NTR transgenic line and the zebrafish livers samples were respectively dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. | Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. | strain:ABGO|tissue:liver|developmental stage:5.5 dpf | GSM2858887 | GSM2858887: D5.5WT; Danio rerio; RNA Seq | GSM2858887 | 1 | Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. | GEO Accession:GSM2858887 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP125098 | D5_5WT1_R1.fq.gz D5_5WT1_R2.fq.gz | fastq fastq | 8603691600.0 | 43018458.0 | GSM2858887 r1 | 0:100 1:100 | A:2356107531;C:1974663463;G:1971836234;T:2292265726;N:8818646 | 100 | 100 | 2356107531 | 1974663463 | 1971836234 | 2292265726 | 8818646 | SRX3398646 | SRS2692826 | SRA631311 | GEO | Southwest university | 2 | 0.92814 | 0.92445 | 0.06252 | 0.06384 | 0.82873 | 0.82911 | 0.57879 | 0.57933 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | China | 2017-11-16 | Larval | Larval | Liver | Liver and Biliary System |