|
| Status |
Public on Feb 22, 2019 |
| Title |
S3 |
| Sample type |
SRA |
| |
|
| Source name |
saliva
|
| Organism |
Anopheles coluzzii |
| Characteristics |
strain: laboratory strain (Xag, 2R+, 2L+, 3R+, 3L+)
origin: originally collected in Cameroon
tissue: saliva from adult females
molecule subtype: small RNA
|
| Treatment protocol |
Adults 2-6 days post-emergence (dpe) were used for the experiments reported here. Saliva was collected in microcapillary tubes. Salivary glands were dissected in Phosphate Buffered Saline.
|
| Growth protocol |
A. coluzzii mosquitoes were reared under standard insectary conditions (28°C, 60%-70% humidity, 14:10 hours light:dark photoperiod).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Saliva was collected in microcapillary tubes. Salivary glands were dissected in Phosphate Buffered Saline.
Libraries were prepared at the EMBL Genomic Core facility using the Illumina TruSeq Small RNA Sample preparation kit.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
S3 cpm
|
| Data processing |
Raw reads were quality control checked by FastQC and then trimmed by cutadapt to remove 3’ adapters and discard reads shorter than 14 nucleotides.
Processed reads from each sample were mapped using Bowtie (-n 0 -l 18 -e 80) to the A. gambiae AgamP4 genome Assembly. Reads aligned to AgamP4 were then mapped (-n 0 -l 18 -e 80 – norc) to a collection of A. gambiae rRNA sequences obtained from VectorBase by the BioMart tool. After subtraction of ribosomal RNAs the remaining reads were mapped (-n 0 -l 18 -a --best --strata -e 80 --norc) to a list of miRNA precursors (known and predicted by MapMi and MiRDeep* software) and other non coding RNAs from A. gambiae (including tRNAs, snoRNAs, snRNAs, 7SL, 7SK and Rnase P) and finally to A. gambiae transcripts and repeats downloaded from VectorBase (-n 0 -l 18 -a --best --strata -e 80).
Raw read counts for each A. gambiae mature miRNA were computed from SAM files using a Python custom script. Reads with multiple highest score mappings were discarded. Expression values were calculated as count per millions (CPM) using the edgeR software. Reads mapping to precursor miRNAs were assigned to mature miRNAs based on their mapping position; an overhang of maximum 3 nucleotides for each side of the mature form was tolerated.
Genome_build: AgamP4
Supplementary_files_format_and_content: Tab-delimited text file including CPM values for each Sample.
|
| |
|
| Submission date |
Sep 29, 2018 |
| Last update date |
Feb 22, 2019 |
| Contact name |
Bruno Arca |
| E-mail(s) |
[email protected]
|
| Organization name |
Sapienza University
|
| Department |
Public Health and Infectious Diseases
|
| Street address |
P.le Aldo Moro 5
|
| City |
Rome |
| ZIP/Postal code |
00185 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18984 |
| Series (1) |
| GSE120658 |
MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions |
|
| Relations |
| BioSample |
SAMN10145502 |
| SRA |
SRX4777963 |
