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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 09, 2015 |
| Title |
METTL3 knockdown Mouse 3T3-L1 cell 2 |
| Sample type |
SRA |
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| Source name |
Mouse 3T3-L1 cell
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| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3-L1
treatment: METTL3 knockdown
tissue: Mouse embryo fibroblast 3T3-L1 pre-adipocytes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from transiently transfected cells with TRI® Reagent (Sigma). mRNA was extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen).
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
M3-knockdown2
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| Data processing |
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
m6A regions (m6A peaks) were identified by comparing the read abundance between m6A-Seq and RNA-seq samples of the same loci with a method applied in previous report (Meyer et al., 2012). Briefly, the entire mm10 genome was divided into 25 nt bins and the numbers of both m6A-Seq reads and RNA-Seq reads (used as control) mapped to each bin were counted by BEDTools’intersectBed and compared(Quinlan and Hall, 2010). Bins with statistically enriched m6A-Seq reads compared with the RNA-Seq reads (adjusted p-value <0.01, Fisher’s exact test together with Benjamini-Hocberg procedure) were identified and concatenated adjacently with BEDTools’ mergeBed (Quinlan and Hall, 2010).
Differentially expressed genes between control and FTO or METTL3 knockdown samples were determined using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: RPKM
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| Submission date |
Dec 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Bao-Fa Sun |
| E-mail(s) |
sunbf@big.ac.cn
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| Organization name |
Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)
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| Street address |
Da-Tun Road
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE53249 |
Transcriptomics analysis of gene expression in normal and FTO, METTL3 deficient Mouse embryo fibroblast 3T3-L1 pre-adipocytes |
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| Relations |
| BioSample |
SAMN02442444 |
| SRA |
SRX390709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1288563_mettl3-kd2-reads-number-rpkm.xls.gz |
969.7 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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