 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 29, 2024 |
| Title |
gw null-2 -/- rep.1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole body of first instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Whole body of first instar larvae
genotype: gw null-2 -/-
|
| Treatment protocol |
Fly culture and crosses were carried out at room temperature.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
First instar larvae were collected and extract total RNA by RNA basic kit (FastGene)
Total RNA libraries were prepared using the Strand-Specific mRNA Library Preparation method by BGI. mRNA was first purified using oligo dT-beads, fragmented, and then used to synthesize cDNA. The resulting double-stranded cDNA fragments underwent end-repair, followed by the addition of a single 'A' nucleotide to the 3' ends of the blunt fragments. Next, adaptors were ligated to the cDNAs, which were subsequently amplified by PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Basecalling with Zebracall （version：1.0.11.83）
Raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke software developed by BGI. SOAPnuke software filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 100", steps of filtering: 1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), cut the adapter; 2. Filter read length: if the length of the sequencing read is less than 100 bp, discard the entire read; 3. Remove N: if the N content in the sequencing read accounts for 0.1% or more of the entire read, discard the entire read; 4. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing read account for 40.0% or more of the entire read, discard the entire read; 5. Obtain Clean reads: the output read quality value system is set to Phred+33.
Reads were mapped to Drosophila melanogaster BDGP6.28 genome using STAR (Version 2.7.0a)
Mapped reads were counted using featureCounts or RSEM
Assembly: Drosophila melanogaster BDGP6.28
Supplementary files format and content: Feature count text files contain two columns: 1. gene name, 2.read counts
Supplementary files format and content: RSEM count text files contain two columns: 1. transcript name, 2.read counts
|
| |
|
| Submission date |
May 17, 2024 |
| Last update date |
Sep 29, 2024 |
| Contact name |
Eriko Matsuura |
| E-mail(s) |
eriko.daichi.55@gmail.com
|
| Organization name |
The University of Tokyo
|
| Department |
IQB
|
| Street address |
Yayoi
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0032 |
| Country |
Japan |
| |
|
| Platform ID |
GPL32218 |
| Series (1) |
| GSE267756 |
miRNA-mediated gene silencing in Drosophila larval development involves GW182-dependent and independent mechanisms |
|
| Relations |
| BioSample |
SAMN41436020 |
| SRA |
SRX24591468 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8275210_featureCounts_homo1.tabular.gz |
76.5 Kb |
(ftp)(http) |
TABULAR |
| GSM8275210_homo1.isoforms.results.gz |
585.1 Kb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
