|
| Status |
Public on Mar 07, 2018 |
| Title |
e11a11_R47H_3 |
| Sample type |
SRA |
| |
|
| Source name |
e11a11_R47H_adult heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain information: elav-gal4,Repo-LexA/Y;LexAop2-TREM2-R47H,TYROBP/UAS-Aβ42
age: 1 week
tissue: Adult heads
rin: 6.9
|
| Treatment protocol |
Flies were quickly frozen in liquid nitrogen and heads were collected on dry ice.
|
| Growth protocol |
Flies were raised and maitained at 25°C under 12hr light/dak condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw sequencing reads were aligned to fly genome BDGP6 using star aligner (version 2.5.0b)
Following read alignment, featureCounts was used to quantify the gene expression at the gene level based on Ensembl gene model.
Genes with at least 5 reads in at least one sample were considered expressed and hence retained for further analysis, otherwise removed. Using limma's voom function, the gene level read counts data was normalized as counts per million (CPM) using trimmed mean of M-values normalization (TMM) method and subsequently log2 transformed.
The log2 CPM values were adjusted for RIN score using a linear regression.
Genome_build: BDGP6
Supplementary_files_format_and_content: log2 CPM
|
| |
|
| Submission date |
May 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bin Zhang |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
1470 Madison Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE99012 |
Molecular and Pathological Interactions among Aβ42, Tau, TREM2, and TYROBP in Drosophila Models |
|
| Relations |
| Reanalyzed by |
GSM3283416 |
| BioSample |
SAMN07137761 |
| SRA |
SRX2831428 |
