|
| Status |
Public on Feb 11, 2023 |
| Title |
small_RNA_Kdm3 GLKD 3-5h progeny biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryo
genotype: Kdm3 GLKD progeny
treatment: none
|
| Growth protocol |
Flies were raised at 25°C on cornmeal medium. Embryos were collected on same medium plus fresh yeast.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 100 ul of embryos using TRIzol (Life Technologies). After DNase, RNA Anti 2S treatment for small RNA gel free protocol has been performed (Fasteris.com) Anti 2S treatment for small RNA gel free protocol
Libraries were prepared using QIAseq-miRNA kit.
Depletion of rRNA using QIAseq FastSelect –rRNA Fly Kit
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
A base calling pipeline proceeds to the demultiplexing prior to the generation of fast-q sequencefiles, i.e. by separating the libraries according to their indexes.
Genesupport/Fasteris developed an “in-lane” control spike in each lane of the flow-cell. These spiked control reads are mapped on the PhiX reference genome
The small RNA treatment uses the UMI-tools to detect the UMI sequence and remove bases that correspond to the standard illumina adapters.
The UMI-tools identifies the adapter and with the UMI sequence in each read. The UMIs and adapter sequence are trimmed from the read to produce “inserts”
We merged 18-30nt "inserts" for each library as a fastqsanger file (provided).
For library comparisons, read counts were normalized to one million reads
unique mapper reads were obtained using sR_Bowtie -m0 (Galaxy Version 2.1.1)
For alignments we used a cleaned version of r6.36 version of Drosophila melanogaster genome (dm6, Flybase) in which sequences corresponding to unmapped (chrU), Y chromosome (chrY) and mitochondrial chromosome (chrM) were removed (dm6_clean).
Assembly: dm6_clean
Supplementary files format and content: bigWig, DEseq2 result for biological triplicates as a tab-delimited text file
|
| |
|
| Submission date |
Feb 10, 2023 |
| Last update date |
Feb 11, 2023 |
| Contact name |
Antoine Boivin |
| E-mail(s) |
[email protected]
|
| Organization name |
Sorbonne Universite CNRS
|
| Department |
IBPS
|
| Lab |
LBD UMR7622
|
| Street address |
9 quai St Bernard
|
| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE203279 |
The histone demethylase KDM3 prevents auto-immune piRNAs production in Drosophila |
|
| Relations |
| BioSample |
SAMN33242348 |
| SRA |
SRX19331308 |
