|
| Status |
Public on Dec 07, 2016 |
| Title |
Input2 |
| Sample type |
SRA |
| |
|
| Source name |
Input, S2R+ cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2R+ cells
cell type: embryonic cells
rip antibody: none
|
| Treatment protocol |
no treatment
|
| Growth protocol |
S2R+ cells were grown on standard conditions at room temperature
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent (Invitrogen). mRNA was purified by using two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen)
NEBNext Ultra directional Kit (NEB) was used omitting RNA fragmentation step for recovered m6A-RIP samples and following the manufacturer`s protocol for input samples.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
library strategy: MeRIP-Seq
|
| Data processing |
The samples were sequenced on two flowcells on the Illumina MiSeq (MiSeq Control Software Version 2.6.1.1). Readlength was 68 bp SR
Mapping was done using Star (v. 2.4.0h), secondary alignments were filtered. Mapping was done against BDGP6 (ensembl release 79).
After mapping peaks were called using MACS (v.1.4.1, parameters: "--nomodel --shiftsize 65 --to-small -w -S --keep-dup all --call-subpeaks --nolambda -g 90464385 ).
After peakcalling peaks were split into subpeaks using PeakSplitter (v.1.0).
Consensus peaks were obtained by intersecting subpeaks of both replicates ( using BEDTools (v.2.25.0)).
For each consensus peak the coverage was calculated as counts per million (CPM) for each of the samples and averaged for input and MeRIP samples. Foldchanges for MeRIP vs Input were calculated based on these.
Genome_build: BDGP6 Ensembl release 79
Supplementary_files_format_and_content: bigwig tracks
|
| |
|
| Submission date |
Mar 16, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
GPL16479 |
| Series (2) |
| GSE79296 |
m6A controls neurogenesis and sex determination in Drosophila via its nuclear reader protein YT521-B [MeRIP-Seq, S2R+ cells] |
| GSE79297 |
m6A controls neurogenesis and sex determination in Drosophila via its nuclear reader protein YT521-B |
|
| Relations |
| BioSample |
SAMN04558426 |
| SRA |
SRX1637683 |
