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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 20, 2017 |
| Title |
RNA-seq, 6-week-old WT mice, hippocampus, m6A-IP-2 |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Mus musculus |
| Characteristics |
genotype: Wild-type
age: 6 weeks
treatment of rna sample: Poly(A) selection; m6A immunoprecipitation
biological replicate no.: 2
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Poly(A)+ RNA
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| 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 annotatePeaks.pl.
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.
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| Submission date |
Jan 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Feiran Zhang |
| Organization name |
Emory University
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| Department |
Human Genetics
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| Lab |
Peng Jin
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| Street address |
615 Michael St NE
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE94098 |
FTO regulates adult neurogenesis through modulating the dynamics of N6-methyladenosine |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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