|
| Status |
Public on Dec 08, 2020 |
| Title |
Parental_total_RNA_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
genotype: parental
|
| Growth protocol |
E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
Strand specific total RNA library preparation was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420S).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5) with parameter “-k 1” to keep only one locus when a read mapped to multiple genomic regions.
PCR duplicates were removed using samtools (v1.7) rmdup.
Strand specific reads were separated by samtools (v1.7) view with specific flags 99, 147, 83, 163.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files
|
| |
|
| Submission date |
Feb 07, 2019 |
| Last update date |
Dec 10, 2020 |
| Contact name |
Yang Shi |
| E-mail(s) |
yshi@hms.harvard.edu
|
| Organization name |
Fudan university
|
| Street address |
NO. 138, Yi-Xue-Yuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE126242 |
RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (total RNA-seq) |
| GSE126243 |
RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs |
|
| Relations |
| BioSample |
SAMN10884480 |
| SRA |
SRX5347798 |
