|
| Status |
Public on Dec 07, 2023 |
| Title |
HSC APOBEC-YTH rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell line: bone marrow
cell type: primary cells
treatment: APOBEC-YTH OE
cell lineage: hematopoietic stem cells
|
| Treatment protocol |
Cells were infected with virus expressing APOBEC-YTH retrovirus or empty vector and sorted for GFP+ expression 48hrs post transduction.
Sorted cells were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform
|
| Growth protocol |
B6 mice were used to harvest bone marrow. HSC and MPP1-4 cells were FACS sorted and placed in SFEM media supplemented with cytokines (50 ng/ml SCF, 10 ng/ml IL-3, and 10 ng/ml IL-6, 10ng/ml TPO and 20 ng/ml FLT3L)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After PicoGreen quantification and quality control by Agilent BioAnalyzer, library preparation is performed using the SMART-Seq v4 Ultra Low Input RNA Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Alignment to mouse (mm10) genome using STAR aligner.
GATK workflow for calling variants in RNA-seq to identify all the mutations in each RNA-seq library.
We then restricted to the mutations within annotated mRNA transcripts, as well as restricting to C-to-T mutations in transcripts encoded by the forward strand and G-to-A mutations in transcripts encoded by the reverse strand. We also filtered out mutations found in the dbSNP database since they are most likely DNA-level mutations. We then combined the filtered sets of RNA editing events from all RNA-seq libraries of the same experiment and counted the number of reads containing reference (C/G) and alternative (T/A) alleles from each library at each site.
Gene expression levels from the bam files were quantified using featureCounts v2.0.3
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene read count values for each Sample
|
| |
|
| Submission date |
May 07, 2023 |
| Last update date |
Dec 07, 2023 |
| Contact name |
Michael G. Kharas |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Molecular Pharmacology Program
|
| Street address |
417 East 68th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE231862 |
DARTseq identifies m6A targets in mouse primary cells |
|
| Relations |
| BioSample |
SAMN34992392 |
| SRA |
SRX20248455 |
