|
| Status |
Public on Jan 12, 2020 |
| Title |
ph_RNAi_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ph RNAi ED from L3 wandering larvae (BL 64095 x VDRC50028)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: ph RNAi
develpmental stage: L3 wandering larvae
tissue: Eye Disc
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
About 150 ED were dissected from wandering larvae on ice and total RNA was extracted using TRIZOL reagent. Total RNA was purified using the RNeasy Mini Kit (Qiagen, 74104).
Poly-A RNAs were selected and libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
After initial quality checks using fastqc, reads were aligned to the dm6 version (dmel_r6.15 annotation) of the Drosophila genome using STAR with default parameters (v2.4.0i). Then, the reads were counted using htseq-count and the differential expression analysis was performed using the “DESeq2” R package (v1.22.1).
genome build: dm6
Ouput file of differential expression analysis using the DESeq2 R package. 8 Columns: FBgn (FlyBase Gene ID); Symbol; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj. bw files correpond to the merged (4 replicates) RPKM-normalized bigwig binary files (10bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.
|
| |
|
| Submission date |
Jul 10, 2019 |
| Last update date |
Jan 12, 2020 |
| Contact name |
Vincent Loubiere |
| E-mail(s) |
vincent.loubiere@imp.ac.at
|
| Phone |
+33663182164
|
| Organization name |
UMR9002; CNRS-UM
|
| Department |
Institute of Human Genetics
|
| Lab |
Chromatin and Cellular Biology
|
| Street address |
141 rue de la Cardonille
|
| City |
Montpellier |
| State/province |
FRANCE |
| ZIP/Postal code |
34090 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE126985 |
PRC1 facilitates stage-specific enhancer-promoter contacts during Drosophila development |
|
| Relations |
| BioSample |
SAMN12250159 |
| SRA |
SRX6428616 |
