|
| Status |
Public on May 17, 2024 |
| Title |
3rG4 cl5 D7 RNA rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Day 7 differentiated mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129S1/CastEiJ x 129S1
cell type: Day 7 differentiated mouse embryonic stem cells
genotype: Xist 3'rG4 mutant
|
| Growth protocol |
Clonal TsixTST/+ mESC (TST) line was cultured as routine procedure. mESC were grown on inactivated feeders in high glucose D-MEM supplemented with 15% Hyclone FBS, 25 mM HEPES pH 7.2-7.5, 1x MEM non-essential amino acids, 1x Pen/Strep, 0.1 mM βME, and 500 U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein at 37°C with 5% CO2. EB differentiation was performed with growing feeder-depleted cells in the medium without LIF. Cells were kept in suspension until 3 days of differentiation and transferred to gelatinized plates on day 3 for further adherent growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRizol reagent.
oligo dT magnetic beads (NEB) were used for removing abundant rRNA from Xist 3’ rG4 deletion cells. 50 ng of rRNA depleted RNA was used for RNA-seq library preparation using NEBNext Ultra Directional RNA Library Prep Kit (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adaptor sequences were trimmed from the RNA-seq reads. Sequencing reads were allele-specifically aligned to 129S1/SvJm (mus) and CAST/Eih (cas) genomes using STAR aligner as previously described (Pinter et al., 2012).
Assembly: mm10
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
May 17, 2024 |
| Contact name |
yongwoo lee |
| E-mail(s) |
ylee@molbio.mgh.harvard.edu
|
| Phone |
6177552856
|
| Organization name |
MASSACHUSETTS GENERAL HOSPITAL
|
| Department |
Mol bio
|
| Lab |
Jeannie Lee Lab
|
| Street address |
185 Cambridge St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE219081 |
Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (RNA-Seq) |
| GSE219083 |
G-quadruplex folding in Xist RNA antagonizes PRC2 activity for step-wise regulation of X-chromosome inactivation |
|
| Relations |
| BioSample |
SAMN38690533 |
| SRA |
SRX22795392 |
