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Status |
Public on Jan 13, 2023 |
Title |
PD-1 |
Sample type |
SRA |
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Source name |
Whole adult
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Organism |
Drosophila melanogaster |
Characteristics |
tissue: Whole adult growth protocol: Feeding with yeast-glucose medium treatment: Parkinson's Drosophila reared in based medium with rotenone replicate: 1
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Treatment protocol |
adult Drosophila were cultured in a yeast-glucose based medium containing 250 μM rotenone (C23H22O6, dissolved in DMSO)
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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)
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
The whole Drosophila were collected after rotenone treatment dmel-count.txt
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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
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Submission date |
Dec 26, 2022 |
Last update date |
Jan 13, 2023 |
Contact name |
Xiaoyun Wang |
E-mail(s) |
wang_xiaoyun@gibh.ac.cn
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Organization name |
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
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Department |
Infection and Immunity
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Street address |
190 Kaiyuan Avenue, Huangpu
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City |
Guangzhou |
State/province |
Guangdong |
ZIP/Postal code |
510530 |
Country |
China |
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Platform ID |
GPL25244 |
Series (1) |
GSE221760 |
The impact of gut microbiome on transcriptome in Parkinson's disease model revealed by fecal microbiota transplantation |
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Relations |
BioSample |
SAMN32409507 |
SRA |
SRX18851256 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
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