|
| Status |
Public on Mar 18, 2021 |
| Title |
DR-JF-Ott_KO3 |
| Sample type |
SRA |
| |
|
| Source name |
FACS-sorted myogenic progenitor cells from hindlimb skeletal muscle
|
| Organism |
Mus musculus |
| Characteristics |
genotype: NELF-BscKO (KO)
tissue: Skeletal muscle (hindlimbs)
cell type: Myogenic progenitor cells
treatment: Cardiotoxin
|
| Treatment protocol |
Skeletal muscle from the hindlimbs was damaged in vivo with cardiotoxin
|
| Growth protocol |
Hindlimb skeletal muscle was damaged with cardiotoxin, and provided a 48-hour in vivo recovery period. Skeletal muscle was isolated, mechanically and enzymatically digested, and myogenic progenitor cells FACS-sorted based on TdTomato expression (endogenous expression to all Pax7-expressing adult tissues), and Alpha-Integrin 7 expression. Purified myogenic progenitors immediately underwent RNA extraction. At all steps, myogenic progenitors were stored on ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a total RNA isolation kit (ThermoFisher cat. No. 12183020) on FACS-purified myogenic progenitor cells (TdT+, AI7+) at the specified timepoint
Total RNA (approx. 350 ng per sample) underwent rRNA depletion with a Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Illumina cat. No. MRZG12324). RNA library preparation proceeded with a KAPA stranded RNA-seq kit (roche 07962169001-KAPA KK8401). Fragmentation/1st strand / 2nd strand end-repair and A-tailing steps proceeded, followed with ligation to Illumina TruSeq LT Indexes (Illumina FC-121-2001 / FC-121-2002) followed by 8 cycles of PCR enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads aligned with STAR 2.6.0a
featureCounts -s2 v1.6.1 was used for summarization of counts
DESeq2 v1.26.0 was used for Differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tabluar format with DESeq2 output
|
| |
|
| Submission date |
Dec 07, 2020 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Jeffrey Dilworth |
| E-mail(s) |
fdilworth@wisc.edu
|
| Phone |
6082653758
|
| Organization name |
University of Wisconsin
|
| Street address |
1111 Highland Ave
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE150280 |
Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation |
| GSE162775 |
Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [RNAseq_48hrs] |
|
| Relations |
| BioSample |
SAMN17015509 |
| SRA |
SRX9641237 |
