|
| Status |
Public on Dec 31, 2019 |
| Title |
Muscle_8d_WT#2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: mTreg24 TCR-tg- (B6)
tissue: skeletal muscle
cell type: Whole tissue
age: 6-8 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1,000 cells were double-sorted by Moflo Astrios cel sorter into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts
|
| |
|
| Submission date |
Nov 14, 2019 |
| Last update date |
Dec 31, 2019 |
| 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) |
| GSE140419 |
Transcriptional characterization of tissue-Tregs and whole tissues of skeletal muscles in muscle Treg TCR transgenic mice. |
|
| Relations |
| BioSample |
SAMN13286665 |
| SRA |
SRX7141677 |
