|
| Status |
Public on Dec 18, 2021 |
| Title |
D_CLIP_PC2_2_S20_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
drosophila whole fly total RNA CLIP, PC2/CMTR2 pulldown RNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole fly
target: PC2-bound RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
trizol extraction of RNA from wildtype flies followed by formaldehyde crosslinking to recombinant drosophila melanogaster CMTR1 or CMTR2, protein-bound RNA was proteinase K treated and Trizol-extracted.
Lexogen's quant-seq 3'FWD kit was used, using a random nonamer tagged partial p7 sequence (i.e. CACGACGCTCTTCCGATCTNNNNNNNNN) in place of the partial p7 sequence containing anchored oligoDT primer found in the manufacturer's protocol. The remainder of the protocol was performed as prescribed by Lexogen (Vienna). Size selection of libraries were carried out with PAGE.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
BCL2FASTQ --with-failed-reads --no-lane-splitting
bbduk for adapter trimming from read 2
STAR alignment of read 2
HTSEQCOUNT for gene counts
DESEQ2 for differential expression analysis
Genome_build: dmel:r6
Supplementary_files_format_and_content: .csv for read counts (matrix, normalised counts from DESEQ2 for both CLIP experiments), .tsv for differential expression output
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Dec 18, 2021 |
| Contact name |
Nathan Archer |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nottingham
|
| Department |
School of Veterinary Medicine and Sciences
|
| Lab |
ARCHER
|
| Street address |
Sutton Bonington
|
| City |
Loughborough |
| State/province |
East Midlands |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE138868 |
CLIP of mRNA capping enzyme CMTR2 in drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN13031769 |
| SRA |
SRX6992728 |
