|
| Status |
Public on May 31, 2021 |
| Title |
AG_mixed_R9_gMSL2_15h_A8 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Anopheles gambiae |
| Characteristics |
strain: vasa-Cas9 x msl-2gRNA
genotype/variation: msl-2 knock-out
developmental stage: 15h embryo
tissue: whole body
|
| Treatment protocol |
Non-fluorescent embryos were collected from over-night collections of msl-2.227/CyO-GFP D. melanogaster. For A. gambiae, vasa-Cas9 mothers were crossed with msl-2 gRNA or control gRNA fathers. Embryos were collected from egg dishes at indicated times after egg laying.
|
| 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 25C, 70% relative humidity and 12 hr dark/12 hr light cycle. A. gambiae mosquitoes were maintained in standard insectary conditions (28°, 75–80% humidity, 12-hr/12-hr light/dark 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 |
| |
|
| Description |
Parkour-ID 130_Keller_Akhtar
processed data file: RNAseq_AGAP_counts.txt
|
| Data processing |
For quality control, we used FastQC version: v0.11.3. For RNA-seq, paired-end reads were mapped with RNA STAR (Galaxy version 2.5.2b-0) to AgamP4_ensembl or dm6_ensembl with default parameters. The raw read counts per gene were obtained with featureCounts (1.4.6.p5) followed by differential expression analysis with DESeq2, R version 3.0.2.
Genome_build: BDGP6 (dm6, Release 6 plus ISO1 MT), AgamP4_ensembl
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited featureCounts count table output.
|
| |
|
| Submission date |
Jul 03, 2020 |
| Last update date |
May 31, 2021 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
| 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 |
GPL25232 |
| Series (2) |
| GSE153775 |
Two distinct mechanisms for X chromosome dosage compensation in Anopheles and Drosophila [RNA-seq] |
| GSE153780 |
Two distinct mechanisms for X chromosome dosage compensation in Anopheles and Drosophila |
|
| Relations |
| BioSample |
SAMN15443082 |
| SRA |
SRX8665040 |
