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Sample GSM2091061 Query DataSets for GSM2091061
Status Public on Dec 07, 2016
Title Input1
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 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
BioSample SAMN04558425
SRA SRX1637682

Supplementary file Size Download File type/resource 10.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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