run_metadata: 68125
This data as json
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| 68125 | SRR17606008 | SRX13774798 | SRS11654796 | SRP354915 | PRJNA796975 | Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish | GSE193630 | Transcriptome Analysis | In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury; | pubmed:35513710 | CEN WT Kidney RNAseq rep2 | GSM5815261 | source name:Kidney|strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation | CEN WT Kidney RNAseq rep2 | RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq | Kidney | animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction. | Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols. | Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study. | strain:EK|tissue:Kidney|genotype:Wild type|treatment:cardiomyocyte ablation | GSM5815261 | GSM5815261: CEN WT Kidney RNAseq rep2; Danio rerio; RNA Seq | GSM5815261 r1 | GSM5815261 | 1 | Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP354915 | CENWT2_1.fq.gz CENWT2_2.fq.gz | fastq fastq | 7219678800.0 | 72196788.0 | GSM5815261 r1 | 0:100 1:100 | A:1908750065;C:1680876268;G:1700533938;T:1929518529;N:0 | 100 | 100 | 1908750065 | 1680876268 | 1700533938 | 1929518529 | 0 | SRX13774798 | SRS11654796 | SRA1356624 | Cell biology, Duke University | Poss, Cell Biology, Duke University | 1 | 0.94561 | 0.06821 | 0.71792 | 0.54803 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2022-01-13 | Larval | Larval | Kidney | Renal System |