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Sample GSM8275211 Query DataSets for GSM8275211
Status Public on Sep 29, 2024
Title gw null-2 -/- rep.2
Sample type SRA
 
Source name Whole body of first instar larvae
Organism Drosophila melanogaster
Characteristics tissue: Whole body of first instar larvae
genotype: gw null-2 -/-
Treatment protocol Fly culture and crosses were carried out at room temperature.
Extracted molecule total RNA
Extraction protocol First instar larvae were collected and extract total RNA by RNA basic kit (FastGene)
Total RNA libraries were prepared using the Strand-Specific mRNA Library Preparation method by BGI. mRNA was first purified using oligo dT-beads, fragmented, and then used to synthesize cDNA. The resulting double-stranded cDNA fragments underwent end-repair, followed by the addition of a single 'A' nucleotide to the 3' ends of the blunt fragments. Next, adaptors were ligated to the cDNAs, which were subsequently amplified by PCR.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Data processing Basecalling with Zebracall (version:1.0.11.83)
Raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke software developed by BGI. SOAPnuke software filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 100", steps of filtering: 1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), cut the adapter; 2. Filter read length: if the length of the sequencing read is less than 100 bp, discard the entire read; 3. Remove N: if the N content in the sequencing read accounts for 0.1% or more of the entire read, discard the entire read; 4. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing read account for 40.0% or more of the entire read, discard the entire read; 5. Obtain Clean reads: the output read quality value system is set to Phred+33.
Reads were mapped to Drosophila melanogaster BDGP6.28 genome using STAR (Version 2.7.0a)
Mapped reads were counted using featureCounts or RSEM
Assembly: Drosophila melanogaster BDGP6.28
Supplementary files format and content: Feature count text files contain two columns: 1. gene name, 2.read counts
Supplementary files format and content: RSEM count text files contain two columns: 1. transcript name, 2.read counts
 
Submission date May 17, 2024
Last update date Sep 29, 2024
Contact name Eriko Matsuura
E-mail(s) eriko.daichi.55@gmail.com
Organization name The University of Tokyo
Department IQB
Street address Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
 
Platform ID GPL32218
Series (1)
GSE267756 miRNA-mediated gene silencing in Drosophila larval development involves GW182-dependent and independent mechanisms
Relations
BioSample SAMN41436019
SRA SRX24591469

Supplementary file Size Download File type/resource
GSM8275211_featureCounts_homo2.tabular.gz 76.4 Kb (ftp)(http) TABULAR
GSM8275211_homo2.isoforms.results.gz 585.3 Kb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA

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