|
| Status |
Public on Aug 07, 2020 |
| Title |
A3Dmel_WD_male_msl2_227_R3 |
| Sample type |
SRA |
| |
|
| Source name |
Wing imaginal disc from third instar larva
|
| Organism |
Drosophila melanogaster |
| Characteristics |
gender: male
strain: Bloomington Drosophila Stock Center BDSC #5871
genotype/variation: msl-2 null mutant
|
| Treatment protocol |
3rd instar larval were collected, the gender separated by visual inspection of the genitals; then wing imaginal discs were dissected and transferred to TriZol reagent.
|
| Growth protocol |
Drosophila melanogaster were reared on a cornflour-molasses fruit fly medium [1l water, 12g agar-agar threads, 18g bakery yeast, 10g soya flour, 80g corn flour, 22g molasses, 80g malt extract, 2.4g 4-hydroxibenzoic acid methylester (Nipagin), 6.25ml propionic acid] at 25¡C, 70% relative humidity and 12 hr dark/12 hr light cycle.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were homogenized in TRIzol™ Reagent (Thermo Fisher 15596026) followed by RNA purification using a Direct-zol™ RNA MiniPrep kit (Zymo Research, R2050) according to the manufacturer's instruction.
TruSeq Stranded mRNA Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The mapping was performed to dm6 using STAR (2.6.1b) with default parameters, indexed using samtools (1.9) and QC done using deepTools (3.1.2), fastqc (0.11.7) and multiQC (1.6)
The bigwig file was prepared using deepTools bamCoverage (3.1.2), RPKM with bin size 25.
featureCounts (subread v1.6.1) using params: -p -B -C -Q 10 --primary.
For differential expression analysis we used DESeq2 (v1.18.1).
Genome_build: BDGP6
Supplementary_files_format_and_content: featureCounts count table output
|
| |
|
| Submission date |
Apr 15, 2019 |
| Last update date |
Aug 07, 2020 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
[email protected]
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23323 |
| Series (2) |
| GSE129796 |
Outcomes of MSL complex mutations on X chromosome dosage compensation by RNA-Seq |
| GSE129834 |
RNA nucleation by MSL2 induces selective compartmentalization of the X chromosome |
|
| Relations |
| BioSample |
SAMN11415991 |
| SRA |
SRX5681671 |
