|
| Status |
Public on Dec 15, 2021 |
| Title |
63129: D. melanogaster macrophages_CG9005 mutant_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic macrophages
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: Embryonic macrophages from stage 17
cell type: Embryonic macrophages (hemocytes)
genotype: 3xMcherry-tagged macrophages
|
| Treatment protocol |
Dechorionated embryos were dissociated and Cherry-positive macrophages were sorted by FACS using the protocol from Attila Gyoergy et al., G3, 2018.
|
| Growth protocol |
Fly embryos of both genotypes were collected for stage 11 at 29°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from FACS-sorted mCherry-positive macrophages using Rneasy Plus Micro Kit (QIAGEN) and stored at -80C for quality control and RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina’s HiSeq2500, 50bp read length)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FACS-sorted labled macrophages
|
| Data processing |
Aligning the transcriptome sequence reads to the D. melanogaster reference genome (Ensembl BDGP6) with STAR version 2.5.1b using 2-pass alignment mode.
Counting the number of reads; the quality of the RNA-seq library was assessed by calculating the percentage of reads that are mapped to exonic and intronic regions of the genome, while using polyA selection for library preparation.
the reads were associated with known genes and the number of reads aligned within each gene was counted using HTSeq tool version 0.5.4p3.
the counts were normalised using the TMM normalisation method of the edgeR R/Bioconductor package ( (R version 3.4.4, Bioconductor version 3.6)
The data were log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalised counts are represented as TPM (Transcripts Per Kilobase Million) values.
Genome_build: the Drosophila melanogaster reference genome (Ensembl BDGP6)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for both wildtype and the mutant samples
|
| |
|
| Submission date |
Feb 19, 2021 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Daria Siekhaus |
| Organization name |
IST Austria
|
| Department |
Bertalanffy Building
|
| Street address |
Am Campus 1
|
| City |
Klosterneuburg |
| ZIP/Postal code |
3400 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE167132 |
A genetic program boosts mitochondrial function to power macrophage tissue invasion (RNA-seq, sorted macrophages) |
| GSE167134 |
A genetic program boosts mitochondrial function to power macrophage tissue invasion |
|
| Relations |
| BioSample |
SAMN18008886 |
| SRA |
SRX10135760 |
