run_metadata: 48009
This data as json
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| 48009 | SRR6910782 | SRX3858788 | SRS3106147 | SRP136723 | PRJNA447594 | RNAseq of regenerating yap mutant zebrafish hearts | GSE112452 | Transcriptome Analysis | A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed. | pubmed:30295714 | zebrafish heart yap sham 3 | GSM3070341 | tissue:7 xxx post injury sham yap mutant zebrafish heart replicate 3|injury type:Sham Injured|genotype:yap / | zebrafish heart yap sham 3 | Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. | 7 xxx post injury sham yap mutant zebrafish heart replicate 3 | Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury | RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. | Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. | injury type:Sham Injured|genotype:yap / | GSM3070341 | GSM3070341: zebrafish heart yap sham 3; Danio rerio; RNA Seq | GSM3070341 | 1 | RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. | GEO Accession:GSM3070341 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP136723 | 170715_I13_CL100028033_L1_HK500ZEBvisRAAFRACPEI-39_1.fq.gz | fastq | 951999850.0 | 19039997.0 | GSM3070341 r1 | 0:50 | A:264195948;C:210535284;G:216206679;T:260149711;N:912228 | 50 | 264195948 | 210535284 | 216206679 | 260149711 | 912228 | SRX3858788 | SRS3106147 | SRA675997 | GEO | Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin | 1 | 0.94079 | 0.07209 | 0.77506 | 0.57202 | 50 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2018-03-28 | Undetermined | Adult | Heart | Cardiovascular System |