 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 25, 2023 |
| Title |
Yng-55-T21 |
| Sample type |
SRA |
| |
|
| Source name |
satellite cells
|
| Organism |
Mus musculus |
| Characteristics |
age of donor/age of host: 5 weeks/ NA
tag: Tg(Pax7-EGFP)#Tajb
tissue: skeletal muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1000 GFP positive satellite cells from the donor mice were sorted by Fluorescence-Activated Cell Sorting (FACS) by gating for the GFP+/DAPI- cell population. These cells were sorted directly into the SMART-Seq (Takara) reaction buffer composed of lysis buffer, water and RNAse inhibitors, these cells act as the T0 time point.
Concurrently, 10,000-20,000 GFP positive cells were sorted from the same donor mouse and transplanted into the tibialis anterior of the host mouse. After 21 days, these cells were then reisolated by FACS directly into the SMART-Seq reaction buffer.
Sequencing ready libraries were generated using SMART-Seq HT kit (Takara, cat. #624456) and illumine adapters were added using Nextera XT (Illumina, cat. #FC-131-1024, FC-131-1001).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Kallisto was used to map reads to the mouse reference genome (mm10) and to quantifying abundances of transcripts using default settings
Transcript-level abundances were imported into R and collapsed into gene counts using the tximport package
To estimate the effects of the experimental conditions, we used DESeq2 to fit the following model gene-wise model: count~ time + age + time:age, where the variable time denotes the effect of engraftment, the variable age denotes the effect of aging, and the interaction variable time:age represents the reprogramming effect on genes in the aged niche.
For the purposes of ranking and visualization, we use the apeglm shrinkage approach.
Assembly: mm10
Supplementary files format and content: *_abundance.tsv: reports abundances as “estimated counts” (est_counts) and in Transcripts Per Million (TPM).
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/
|
| |
|
| Submission date |
Jul 14, 2022 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Vahab Soleimani |
| E-mail(s) |
vahab.soleimani@mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Human Genetics
|
| Street address |
3640 rue University
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A 0C7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE171997 |
RNA-Sequencing of young and aged satellite cells before and after transplantation into the young niche |
| GSE171998 |
Transcriptional reprogramming of skeletal muscle stem cells by the niche environment |
|
| Relations |
| BioSample |
SAMN29757883 |
| SRA |
SRX16246701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6339592_Yng-55-T21_NAJ1266A18-1_S4_abundance.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
