|
| Status |
Public on Apr 01, 2022 |
| Title |
D1.DTR_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Tibialis anterior muscle
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tcrd-DTR
treatment_1: i.p. diptheria toxin
treatment_2: cardiotoxin-induced hindlimb skeletal muscle injury
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For MuSC and Vg6+ gdT cell samples, cells were isolated by enzymatic digestion of the indicated tissue and cells were purified by fluoresence activated cell sorting. 1000 cells were sorted in TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing. For whole muscle samples, tissue was homogenized in Trizol, and then RNA was isolated per the manufacterure protocl and cleaned up by ethanol precipitation. 2ng of purified RNA were added to TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the human reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts
|
| |
|
| Submission date |
Dec 09, 2021 |
| Last update date |
Apr 01, 2022 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
|
| Phone |
617-432-7747
|
| Organization name |
Harvard Medical School
|
| Department |
Microbiology and Immunobiology
|
| Lab |
CBDM
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE190588 |
IL-17A-producing gdT cells promote muscle regeneration in a microbiota-dependent manner |
|
| Relations |
| BioSample |
SAMN23828835 |
| SRA |
SRX13371901 |
