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| Status |
Public on Jun 02, 2020 |
| Title |
AD20R2 |
| Sample type |
SRA |
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| Source name |
head
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| Organism |
Drosophila melanogaster |
| Characteristics |
age: day 20 after eclosion
genotype: hAPP transgenic
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Massive of fly heads of each group were collected and total RNAs were extracted with Trizol reagent, from which mRNAs were purified by poly-T oligo-attached magnetic beads.
Libraries were constructed for sequencing using a Superscript Double-Stranded cDNA Synthesis kit according to manufacturer's specifications.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Drosophila melanogaster whole genome dmel_r6.11 using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
The clean data were mapped to reference using Bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200, and fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using RSEM software.
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| Submission date |
Apr 15, 2019 |
| Last update date |
Jun 03, 2020 |
| Contact name |
Xianda Hu |
| E-mail(s) |
hellocean@hotmail.com
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| Organization name |
Beijing Tibetan Hospital, CTRC
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| Street address |
218 Anwaixiaoguanbeili St
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| City |
Beijing |
| ZIP/Postal code |
100029 |
| Country |
China |
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| Platform ID |
GPL23702 |
| Series (1) |
| GSE109489 |
Next generation sequencing based transcriptome comparison between wild-type Drosophila and an Alzheimer's disease model |
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| Relations |
| BioSample |
SAMN11419321 |
| SRA |
SRX5685991 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3722915_AD20R2.gene.fpkm.xls.gz |
1.4 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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