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Sample GSM4653987 Query DataSets for GSM4653987
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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