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| Status |
Public on Jan 03, 2020 |
| Title |
w1118-1 |
| Sample type |
SRA |
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| Source name |
wild type_ovary
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain background: w1118
age: 7-day-old
genotype/variation: wild type
tissue: ovary
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| Growth protocol |
Flies with the genotype: w1118 (control) and wh7, mei-p26 (experiments) cultured at 25 degree.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted by Trizol reagent (Invitrogen, USA) according to the instructions. RNA was quantified at by absorbance at 260 nm using a ND-1000 spectrophotometer (Nanodrop Techonology, USA) and quality was assessed using a Bioanalyzer 2100 (Agilent Technology, USA) with a RNA 6000 labchip kit (Agilent Technologies, USA)
Sample libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN) according to the manufacturer's protocols. Adaptors are ligated sequentially to the 3' and 5' ends of miRNAs. Subsequently, universal cDNA synthesis with UMI assignment, cDNA cleanup, library amplification and library cleanup are performed. Libraries were sequenced on an Illumina instrument (75-cycle single-end read, 75SE). Sequencing data was processed using the Illumina software BCL2FASTQ v2.20.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequencing data was processed using the Illumina software BCL2FASTQ v2.20.
The sequences generated went through a filtering process to obtain qualified reads. Trimmomatic (1) was implemented to clip the 3′ adaptor sequence, trim or remove the reads according to the quality score and discard trimmed reads shorter than 18 nucleotides.
Qualified reads after filtering low-quality data were analyzed using miRDeep2 (2) for aligning reads to the reference genome downloaded from UCSC.
Only reads that mapped perfectly to the genome five or less times were used for miRNA detection, since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs, and also identifies novel miRNAs.
Genome_build: BDGP5 (GCA_000001215.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jan 02, 2020 |
| Last update date |
Jan 03, 2020 |
| Contact name |
Hweijan Hsu |
| E-mail(s) |
[email protected]
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| Phone |
886-2-2787-1541
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| Organization name |
Academia Research
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| Department |
Institute of Cellular Biology
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| Lab |
Room 337
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| Street address |
no 128, Sec 2, Academia Rd. Nankang
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| City |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE142830 |
microRNA expression analysis in fly ovaries from wuho and mei-p26 mutants |
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| Relations |
| BioSample |
SAMN13708254 |
| SRA |
SRX7488422 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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