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| Status |
Public on Jan 17, 2020 |
| Title |
Mettl3_Control_Input_r2 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
strain: C57BL/6
m6a antibody: none
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| Growth protocol |
Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Non-ribosome RNA
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| Data processing |
Library strategy: MeRIP-seq
Illumina Casava software used for basecalling
Raw reads were trimmed with Trimmomatic-0.38 and aligned to mouse genome (mm10, version M19, 2018-08-30) and spike-in genomes including unmodified control RNA (Cypridina Luciferase) and m6A methylated control RNA (Gaussia Luciferase) (New England Biolabs) using HISAT (version 2.1.0) with default parameters.
Mapped reads were separated by strands with in-house script and m6A peaks on each strand were called using MACS (version 2) with parameter ‘--nomodel’ and ‘--keep-dup 5’ separately.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations together with peak summit, pvalue and qvalue reported by MACS2 for each sample.
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| Submission date |
Jul 01, 2019 |
| Last update date |
Jan 17, 2020 |
| Contact name |
Xiaoyang Dou |
| E-mail(s) |
[email protected]
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| Organization name |
Center for Excellence in Molecular Cell Science, CAS
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| Street address |
320 Yue Yang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE133599 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_m6ARIP] |
| GSE133600 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription |
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| Relations |
| BioSample |
SAMN12172709 |
| SRA |
SRX6385405 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not applicable for this record |
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