|
| Status |
Public on Jan 17, 2020 |
| Title |
Mettl3_Control_30m_r2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
strain: C57BL/6
genotype: Mettl3_Control
eu treatment time (min): 30
|
| 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.
|
| 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.
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to mouse genome (mm10, version M19, 2018-08-30) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with default parameters. Annotation
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.
|
| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Jan 17, 2020 |
| Contact name |
Xiaoyang Dou |
| E-mail(s) |
[email protected]
|
| Organization name |
Center for Excellence in Molecular Cell Science, CAS
|
| Street address |
320 Yue Yang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN12172328 |
| SRA |
SRX6385230 |
