|
| Status |
Public on Dec 07, 2023 |
| Title |
Mettl3 cKO LSK SON rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse bone marrow
cell line: primary cells
cell type: hematopoietic stem and progenitor cell
genotype: SON overexpressing
|
| Treatment protocol |
Cells were infected with SON overexpressing lentivirus or empty vector 48hr post infection. GFP+ cells were sorted.
|
| Growth protocol |
WT and mettl3 cKO mice were used to harvest bone marrow. LSK (Lin-cKit+Sca1+) 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 |
Sorted cells were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.
After PicoGreen quantification and quality control by Agilent BioAnalyzer, library preparation was 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 |
| |
|
| Description |
KS_1_counts columns in the processed data files include its raw gene read counts, raw TE read counts, and alternative splicing event percentages.
|
| Data processing |
For the gene expression analysis, reads were aligned onto the Mouse reference genome (mm10) and the LENTI-SON construct by the tophat software.
For the transposable elements (Tes) expression analysis, adapters were trimmed by Cutadapt v4.1. Reads were aligned onto the Mouse reference genome (mm10) and the LENTI-SON construct by STAR v2.7.10b.
Precomputed RepeatMasker annotations v4.0.5 for all TEs were downloaded from RepeatMasker, which were then used to reconstruct full-length LTR copies with 'one code to find them all v1.0' with the default parameters.
The reconstructed TEs annotation and the mm10 basic genes annotation from GENCODE v25 were merged and was used as the reference database for gene quantification in HTSeq v2.0.2.
For the alternative splicing analysis, adapters were trimmed using Cutadapt v4.1. Reads were analyzed by VAST-TOOLS v2.5.1 with the database Mm2 using the default parameters.
Assembly: mm10
Supplementary files format and content: gene_expression.csv: Tab-delimited text file including the raw gene read counts for each sample.
Supplementary files format and content: te_expression.csv: Tab-delimited text file including the raw TE read counts for each sample.
Supplementary files format and content: as.csv: Tab-delimited text file including the alternative splicing event percentages for each sample.
|
| |
|
| Submission date |
May 04, 2023 |
| Last update date |
Dec 07, 2023 |
| Contact name |
Michael Kharas |
| E-mail(s) |
[email protected]
|
| Organization name |
Mamorial Sloan Kettering Cancer Center
|
| Department |
Molecular Pharmacology Program
|
| Lab |
Michael Kharas
|
| Street address |
417 68th street
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE231637 |
RNAseq identifies differentially expressed genes upon SON overexpression in WT and Mettl3 cKO LSK cells |
|
| Relations |
| BioSample |
SAMN34579193 |
| SRA |
SRX20213150 |
