|
| Status |
Public on Jul 25, 2023 |
| Title |
Female_SoaRSoaR_RNA-seq_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole pupa
|
| Organism |
Anopheles gambiae |
| Characteristics |
tissue: whole pupa
Sex: Female
genotype: SoaRSoaR
|
| Growth protocol |
A. gambiae pupae were maintained in standard insectary conditions (26–28°C, 75–80% humidity, and 12-/12-h light/dark cycle).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Trizol (Fisher Scientific, Cat. No.15-596-026) and the Direct-zol RNA MicroPrep Kit (Zymo Research, Cat. No. R2062).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (June 2020) (Document # 1000000124518 v00).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Female_SoaRSoaR_Rep3
counts_pupae_SOAR_RNA.tsv
|
| Data processing |
Reads were mapped to the ensembl AgamP4 genome, ERCCs and elements of the SOA-R and SOA-Ki cassettes (DsRed from SOA-R cassette, mTurquoise2 from SOA-KI cassette, SOA-HA-tag: element of SOA-KI cassette, integrated in front of the endogenous SOA locus), SV40 terminator (part of the SOA-R transgene) using the Ensembl AgamP4 annotation (release 48) together with lncRNA annotation from 10.1186/s12864-015-1507-3 and elements of SOA-KI and SOA-R cassettes. The mapping was performed with STAR (v. 2.7.3a) using the following parameters: outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Only uniquely mapped reads were used for downstream analysis
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v1.9) and DeepTools (v3.1.0)
Primary alignments were assigned to features using subread (v1.6.5) with the AgamP4 annotation (release 48) combined with lncRNA annotation 10.1186/s12864-015-1507-3 combined with the fragments of SOA-Ki and SOA-R cassettes as a reference.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Supplementary files format and content: tab-delimited text file with featureCounts count table output
|
| |
|
| Submission date |
May 25, 2023 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Frank Rühle |
| E-mail(s) |
f.ruehle@imb-mainz.de
|
| Organization name |
Institute of Molecular Biology (IMB)
|
| Department |
Bioinformatics Core Facility
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22033 |
| Series (2) |
| GSE210630 |
SOA confers X chromosome dosage compensation in Anopheles gambiae mosquitoes |
| GSE233473 |
The sex-specific factor SOA establishes X chromosome dosage compensation in Anopheles mosquitos [SOAR-RNA-seq] |
|
| Relations |
| BioSample |
SAMN35369585 |
| SRA |
SRX20519216 |
