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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 17, 2020 |
| Title |
Mettl3_KO2_30m_b2.r2 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
strain: C57BL/6
eu treatment time (min): 30
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| Treatment protocol |
Eight 6-cm plates of mESCs were seeded and controlled to afford the same amount of cells. After 48 h, 5-ethynyl Uridine (EU) was added to 0.5 mM at 60 min, 30 min, 20 min and 10 min before trypsinization collection.
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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 |
polyA RNA |
| Extraction protocol |
Total RNA was purified by Trizol and nascent RNA was captured by using Click-iT Nascent RNA Capture Kit (Invitrogen). Before constructing libraries ERCC RNA spike-in control (Ambion) was added to each sample (0.01 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) together with external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with ‘--rna-strandness R’ parameters. Annotation files (version M19, 2018-08-30, in gtf format for mouse) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.
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| Submission date |
Nov 18, 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 |
GPL21103 |
| Series (2) |
| GSE133582 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_nascentRNA] |
| GSE133600 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription |
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| Relations |
| BioSample |
SAMN13319880 |
| SRA |
SRX7175329 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4173972_Mettl3_KO2_30m_b2.r2_htseq.counts.txt.gz |
218.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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