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Sample GSM2752793 Query DataSets for GSM2752793
Status Public on Aug 25, 2017
Title UI_Carcass_2
Sample type RNA
 
Source name mosquito female carcass; 18h post normal blood meal; replicate 2
Organism Anopheles gambiae
Characteristics Sex: female
tissue: Carcass
condition: 18h post blood meal
Treatment protocol Three-day-old virgin A. gambiae females were fed with either uninfected human blood, P. falciparum-infected blood or 10% sucrose solution. All mosquito groups were kept at 26°C and 80% humidity. At 18 h post feeding, female mosquitoes were dissected on ice to collect head, midgut, ovaries and the abdominal carcass. The latter includes the fat body as well as the cuticle. Per time point and sample, tissues of 15 female mosquitoes were pooled in cold PBS. After sample collection, the PBS was removed and 500 µl TRIzol added to the tissue samples. The tissues were homogenized using steal beads in a Qiagen tissue lyser (8 min of 50 rpm at 4°C) and kept at -80°C until further usage. The experiment was performed in four biological replicates.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. Briefly, after phase separation by centrifugation total RNA was purified by silica membrane, eluted with water and stored at -80°C. The total RNA yield was measured by NanoDropND-1000 Spectrophotometer. The integrity of total RNA was assessed with a 2100 Bioanalyzer and a RNA 6000 Nano LabChip kit. Furthermore, the ratio of miRNA fraction to small RNAs from isolated total RNA was monitored by use of the Agilent Small RNA kit.
Label Cy3
Label protocol An amount of 100 ng total RNA was processed with the miRNA Complete Labeling and Hyb Kit according the supplier’s recommendations. In brief, samples were dephosphorylated with calf intestine alkaline phosphatase and further denatured with DMSO. The sample RNA functioned as acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3’, 5’-cytidine bisphosphate having a single Cy3 label attached to the 3’ phosphate of the nucleotide (Cy3-pCp).
 
Hybridization protocol Labeling reactions were column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.
Scan protocol After scanning at 5 µm resolution with a G2565CA high-resolution laser microarray scanner features were extracted with an image analysis tool version A.11.5.1.1 using the default protocol
Data processing Microarray data were analysed using the R limma package. All arrays were corrected for background using the normexp function and normalized by quantile normalization. Next, the data of all replicated spots on the array were pooled using the avereps function, which resulted in an elist containing log2 relative expression values
 
Submission date Aug 24, 2017
Last update date Jan 23, 2018
Contact name Lena Lampe
Organization name Max-Planck-Institute for Infection Biology
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 13357
Country Germany
 
Platform ID GPL23950
Series (1)
GSE103034 miRNA expression in Anopheles gambiae tissues

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
miRNABrightCorner30 12.3480732
Blank 4.068322137
A_38_P00037508 4.571092761
Mosq_P00000098 4.519829635
A_38_P00030835 4.4916079
A_38_P00021383 4.437342251
A_38_P00020817 6.264597692
A_38_P00015017 4.456439965
miRFill 4.827447974
A_38_P00031135 4.44274794
A_38_P00031360 4.536006907
A_38_P00030877 4.400019766
A_38_P00021593 4.508102123
A_38_P00030655 4.537537171
A_38_P00031051 4.512230813
A_38_P00002680 4.534713739
A_38_P00020075 4.372056182
A_38_P00030733 4.442871295
A_38_P00001033 4.647852482
A_38_P00030686 4.426921235

Total number of rows: 3812

Table truncated, full table size 99 Kbytes.




Supplementary file Size Download File type/resource
GSM2752793_UI_Carcass_2.txt.gz 7.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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