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Sample GSM4275033 Query DataSets for GSM4275033
Status Public on Dec 16, 2021
Title 0.5-1h wt embryos RNA-seq replicate 2
Sample type SRA
 
Source name w1118 embryo
Organism Drosophila melanogaster
Characteristics background strain: w1118
genotype: wildtype
tissue: embryo
age: 0.5-1h
Extracted molecule polyA RNA
Extraction protocol Total RNAs were isolated from embryos at the indicated stages using TRIzol reagent (Thermo Fisher). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation kit (NEB) according to the user manual. The MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) . Briefly, 5 ug of fragmented mRNAs were incubated with 5 ug of anti m6A polyclonal antibody (millipore) in IP buffer (150 mM NaCl, 10 mM Tris–HCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4◦C for an additional 2 h. Beads with captured RNA fragments were then immediately washed 3 times with 500 μl of ice-cold IP buffer. Bound mRNAs were eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IP buffer and then extracted with Trizol reagent (Thermo Fisher).
To RNA-seq and RIP-seq, Illumina Truseq libraries were constructed according to the manufacturer’s instructions and sequenced using NovaSeq platform. with paired end read length of 150 bp. RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). MeRIP-Seq Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 0.5-1h_wt_embryos_FPKM.txt
Data processing For RNA-seq amd Fmr1 RIP-seq, the reads were mapped to the reference genome of Drosophila melanogaster (Release 6/dm6) with TopHat version 2.0.Differential expression analysis was carried out by cuffdiff.
For MeRIP (m6A)-seq, reads were processed using Cutadapt software with the parameter "cutadapt -m 20 -q 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCA -U 3", then the clean reads were aligned to the Drosophila genome (version dm6) using HISAT2. MACS2 software was used for m6A peak calling with the default options except for "-no modle".
Genome_build: dm6
Supplementary_files_format_and_content: bed file of the callpeak result. Txt files for the FPKM value of RNA-seq and FMR1 RIP-seq
 
Submission date Jan 16, 2020
Last update date Dec 16, 2021
Contact name Guoqiang Zhang
E-mail(s) gqzhang@ynu.edu.cn
Organization name INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES
Street address 1 Beichen West Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL25244
Series (1)
GSE143821 Dynamic FMR1 granule phase switch instructed by m6A modification contributes to maternal RNA decay
Relations
BioSample SAMN13874083
SRA SRX7573042

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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