run_metadata: 53046
This data as json
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| 53046 | SRR9674331 | SRX6434717 | SRS5089276 | SRP214428 | PRJNA554249 | the role of SMN complex in tissue regeneration | GSE134187 | Transcriptome Analysis | we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants. | gemin4 hom 2 [miRNA seq] | GSM3938548 | source name:Homozygous gemin4 mutants repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos | gemin4 hom 2 [miRNA seq] | Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or "hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary" miRNA abundance is measured by RSEM "rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output" for mRNA Seq "rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance | Homozygous gemin4 mutants repeat 2 | Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols | strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos | GSM3938548 | GSM3938548: gemin4 hom 2 [miRNA seq]; Danio rerio; miRNA Seq | GSM3938548 | 1 | Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM3938548 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP214428 | mir_G4_2.fastq.gz | fastq | 6427925862.0 | 126037762.0 | GSM3938548 r1 | 0:51 | A:1491339645;C:1560095279;G:1804953332;T:1571434430;N:103176 | 51 | 1491339645 | 1560095279 | 1804953332 | 1571434430 | 103176 | SRX6434717 | SRS5089276 | SRA920248 | GEO | Burgess, NHGRI, NIH | 1 | 0.01032 | 0.00157 | 0.99504 | 0.70577 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | bulk | bulk | United States | 2019-07-12 | Larval | Larval | Whole Organism | All anatomical structures |