|
| Status |
Public on Sep 11, 2020 |
| Title |
Lola-O_1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 20-22 hours after egg laying
genotype: lola-O / Df(2R)ED2076
tissue: Embryo
|
| Growth protocol |
Flies were maintained on apple juice plates supplemented with fresh yeast. Embryos were collected for two hours at 25°C and subsequently developed for 20 hours, collected in Trizol and flash frozen in liquid nitrogen.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
100 lola-O mutant embryos were collected, flash frozen in liquid nitrogen, and RNA was isolated using Trizol reagent. 1 µg of Dnase I treated RNA was subjected to library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.
Librariesfor sequencing were prepared according to the NEBNext® Ultra™ Directional RNA Library Prep Kit protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Lola O knockout replicate 1
|
| Data processing |
The libraries were sequenced on NextSeq500 with 42 bp paired end
After sequencing reads were mapped using STAR (v. 2.5.2b) against ensembl release 87 (BDGP6).
Counts per gene were calculated using subread (1.5.1) with ensembl release 87 as a reference.
normalized bigwig tracks were created using samtools (v.1.3.1), bedtools (2.25.0) and kentUtils (v302).
Genome_build: BDGP6
Supplementary_files_format_and_content: counts per gene as tab separated file (tsv), read depth normalized bigwig tracks (bw)
|
| |
|
| Submission date |
Sep 11, 2017 |
| Last update date |
Sep 11, 2020 |
| Contact name |
Jean-Yves Roignant |
| Organization name |
Institute of molecular Biology
|
| Lab |
Roignant
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN07629755 |
| SRA |
SRX3176837 |
