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Sample GSM5732674 Query DataSets for GSM5732674
Status Public on Jun 25, 2024
Title non-silencing scramble shRNA control replicate 2
Sample type SRA
 
Source name Immortalized non-FSHD human myoblast cell line WS234 (donor 15VBic)
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
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.
Growth protocol Cells were cultured in LHCN medium on 0.1% (w/v) gelatin coated plates at 37oC in 5% CO2 incubator.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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
 
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
Relations
BioSample SAMN24011080
SRA SRX13401709

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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