GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM6895410

Query DataSets for GSM6895410

Status

Public on Jan 13, 2023

Title

PWOFC-3

Sample type

SRA

Source name

Whole adult

Organism

Drosophila melanogaster

Characteristics

tissue: Whole adult
growth protocol: Feeding with yeast-glucose medium
treatment: Parkinson's Drosophila without FMT from control Drosophila
replicate: 3

Treatment protocol

adult Drosophila were cultured in a yeast-glucose based medium containing 250 μM rotenone (C23H22O6, dissolved in DMSO)

Growth protocol

Drosophila melanogaster w1118 was reared at 25℃ under 12 h light/12 h dark cycles on yeast-glucose medium (1 L water, 100 g yeast, 100 g glucose, 1.2% agar, 0.1% potassium sorbate)

Extracted molecule

polyA RNA

Extraction protocol

Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitaed by isopropyl alcohol.
After total RNAs of each samples were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmenta-tion buffer and reverse transcripted into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Berry Genomics.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

The whole Drosophila were collected after FMT experiments
dmel-count.txt

Data processing

All raw sequencing data were quality controlled by fastqc. Adapters, reads with more than 10% unknown nucleotide (N) content, and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data, The clean reads were mapped to the dm6 Drosophila reference genome using HISAT2.
For RNA-seq data, The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
For RNA-seq data, RNA differential expression analyses among groups were performed by DESeq2 (version 1.36.0). The genes/transcripts with the a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
Assembly: dm6
Supplementary files format and content: Tab-delimited text file (.txt) include raw read counts for the RNA-seq data of sterile samples

Submission date

Dec 26, 2022

Last update date

Jan 13, 2023

Contact name

Xiaoyun Wang

E-mail(s)

wang_xiaoyun@gibh.ac.cn

Organization name

Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

Department

Infection and Immunity