|
| Status |
Public on May 01, 2024 |
| Title |
AGI881_P1_B03, scRRBS (multi-omics) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse cell line single cell, IDHmutant mouse glioma cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse cell line single cell, IDHmutant mouse glioma cell
treatment (idhi): Yes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks. The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and 640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
The single-cell plates for the mouse glioma cells treaded by AG-881 or DMSO were profiled by the joint single-cell RRBS and whole transcriptome amplification (Smart-seq2) protocol. The library preparation and sequencing were performed as previously described (Chaligne et al, 2021). Single enzyme digestion (MspI) was used to enrich CpG dense regions in single-cell RRBS.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
scRRBS_mouse_multiomics_processed_CpG.tsv
|
| Data processing |
Analysis of single cell DNA methylation data was performed based on the methods detailed in Chaligne et al 2021. After demultiplexing, reads were mapped to the mm10 genome and cells with at least 25,000 CpG sites, 1 million reads and mapping efficiency greater than 30% were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: tsv
|
| |
|
| Submission date |
Mar 05, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Masashi Nomura |
| E-mail(s) |
masashin0914@hotmail.com
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Pathology
|
| Street address |
149 13th street
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE260933 |
Mutant IDH inhibitors induce lineage differentiation in IDH-mutant Oligodendroglioma II |
|
| Relations |
| BioSample |
SAMN40269502 |
| SRA |
SRX23842567 |
