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Sample GSM2468916 Query DataSets for GSM2468916
Status Public on Apr 20, 2017
Title RNA-seq, 6-week-old WT mice, hippocampus, m6A-IP-2
Sample type SRA
Source name Hippocampus
Organism Mus musculus
Characteristics genotype: Wild-type
age: 6 weeks
treatment of rna sample: Poly(A) selection; m6A immunoprecipitation
biological replicate no.: 2
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from fresh hippocampi by using TRIzol Reagent (Invitrogen).
RNA-seq libraries were generated from 1 μg of total RNA from duplicated samples per condition. The input libraries for m6A-IP were generated from about 50 ng of poly(A)+ RNA fragments from duplicated samples per condition. The m6A-IP libraries were generated from all immunoprecipitated and eluted fragments of poly(A)+ RNA from duplicated samples per condition.The TruSeq LT RNA Library Preparation Kit v2 (Illumina) was used and the manufacturer’s protocol was followed. An Agilent 2100 BioAnalyzer and DNA1000 kit were used to quantify amplified cDNA and to control the quality of the libraries.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description Poly(A)+ RNA
Data processing For m6A-IP-seq, reads were first aligned to mouse genome (mm9) by Bowtie v2.2.3, using the local, sensitive and non-deterministic mode.
m6A peaks were identified by HOMER findPeaks, using the factor mode and additional settings (peak size = 100 nt; fragment length = 100 nt; maximum distance used to stitch peaks together = 50; fold change threshold = 3; local fold change = disabled; size of region to search for control tags = 1x peak size; p-value threshold = 0.0001; and false-discovery rate (FDR) threshold = 0.001).
High-confidence peaks found in both biological replicates were annotated by HOMER
The annotation of boundary genes were corrected using a Python script.
Tiled data files (TDF) for the Integrative Genomics Viewer (IGV) were generated by igvtools.
The genome-wide coverage data were normalized by 1,000,000/total read count, and were visualized by IGV.
In addition, reads from input samples were also aligned to mouse transcriptome annotations and genome assembly (mm9) using TopHat v2.0.13.
FPKM values were calculated by Cufflinks v2.2.1.
In addition, for RNA-seq, SR125 reads were first aligned to mouse transcriptome annotations and genome assembly (mm9) using TopHat v2.1.1.
FPKM values were calculated by Cufflinks v2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: For m6A-IP-seq, peak files with quantitative data and tag density files are included. In addition, for RNA-seq, gene expression values are in Cufflinks-normalized fpkm_tracking format.
Submission date Jan 26, 2017
Last update date May 15, 2019
Contact name Feiran Zhang
Organization name Emory University
Department Human Genetics
Lab Peng Jin
Street address 615 Michael St NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
Platform ID GPL21493
Series (1)
GSE94098 FTO regulates adult neurogenesis through modulating the dynamics of N6-methyladenosine
BioSample SAMN06273502
SRA SRX2518708

Supplementary file Size Download File type/resource
GSM2468916_RNASeq-mice-HPC-6week-m6AIP-2_homer_peaks.txt.gz 716.0 Kb (ftp)(http) TXT
GSM2468916_RNASeq-mice-HPC-6week-m6AIP-2_igv_track.tdf 57.5 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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