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Status |
Public on Jun 25, 2024 |
Title |
non-silencing scramble shRNA control replicate 2 |
Sample type |
SRA |
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Source name |
Immortalized non-FSHD human myoblast cell line WS234 (donor 15VBic)
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Organism |
Homo sapiens |
Characteristics |
cell type: human myoblast cell line WS234 (donor 15VBic, female non-FSHD sample) treatment: non-silencing scramble shRNA control cell line: WS234
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Treatment protocol |
For preparing the lentivirus, HEK293T cells were transfected with the pMD2.G, psPAX2, and shRNA vector plasmids using polyethylenimine. Lentivirus-containing medium supernatant was centrifuged at 126086 x g for 2.5 hours at 4 oC using Optima L-100 XP ultracentrifuge, and the pellet was resuspended in LHCN medium. To transduce the cells, purified lentivirus was added to culture medium for 16 hours and fresh LHCN medium was replaced.
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Growth protocol |
Cells were cultured in LHCN medium on 0.1% (w/v) gelatin coated plates at 37oC in 5% CO2 incubator.
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Extracted molecule |
total RNA |
Extraction protocol |
5 days after SMCHD1 and non-silencing lentiviral transduction, RNA was collected using a PureLink RNA mini kit (Thermo Fisher Scientific #12183018A) according to the manufacturer’s protocol. rRNA depletionwas performed with a Ribo-Zero Magnetic Gold Kit (Illumina cat. No. MRZG12324). RNA library was prepared with a KAPA stranded RNA-seq kit (roche #07962169001).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
Reads are mapped to the hg38 genome using STAR. Counts were summarized using featureCounts function in Rsubread. DESeq2 was used to identify the differentially expressed genes. Genome_build: hg38 Supplementary_files_format_and_content: FeatureCount Table
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Submission date |
Dec 13, 2021 |
Last update date |
Jun 25, 2024 |
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 |
GPL20301 |
Series (2) |
GSE190828 |
SMCHD1 activates the expression of genes required for the expansion of human myoblasts (RNA-seq) |
GSE190830 |
SMCHD1 activates the expression of genes required for the expansion of human myoblasts |
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Relations |
BioSample |
SAMN24011080 |
SRA |
SRX13401709 |