|
| Status |
Public on Mar 01, 2023 |
| Title |
HSC SYNCRIP-ADRA 3 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Bone Marrow Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone Marrow
cell type: Hematopoietic Stem Cell
genotype: Overexpressing SYNCRIP-HyperADAR fusion
time point: 48hr after transduction
cell type (sorted): GFP+ HSCs (Lin-, Sca1+, cKit+, CD150+ CD48-)
|
| Treatment protocol |
Cells were infected with virus expressing SYNCRIP-HyperADAR at 1:1 ratio (v/v) and sorted for GFP+ expression 48hrs post transduction.
|
| Growth protocol |
B6 mice were used to harvest bone marrow.HSC and MPP 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 is performed using the SMART-Seq v4 Ultra Low Input RNA Kit
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
HSC-SYNCRIPADAR-_vs_HSC-MIG-_HSC_snp_counts_dedupped_significance_fpkm.csv
|
| Data processing |
The paired-end RNA-seq reads to mouse (mm10) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Assembly: mm10
Supplementary files format and content: "HSC-SYNCRIPADAR-_vs_HSC-MIG-_HSC_snp_counts_dedupped_significance_fpkm.csv" and "MPP-SYNCRIPADAR-_vs_MPP-MIG-_MPP_snp_counts_dedupped_significance_fpkm.csv" files includes also difference frequency (editing frequency of a site in SYNCRIP_ADA sample subtracted to the average of editing frequency of the site in MIG sample), p value, adjusted p value, number of edit sites
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| |
|
| Submission date |
May 08, 2022 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Michael Kharas |
| E-mail(s) |
kharasm@mskcc.org
|
| 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) |
| GSE202464 |
HyperTRIBE uncovers SYNCRIP RNA binding activity in hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) |
|
| Relations |
| BioSample |
SAMN28155960 |
| SRA |
SRX15206393 |
