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Sample GSM6132357 Query DataSets for GSM6132357
Status Public on Jun 13, 2022
Title AB678 OIP5-AS1:MIR-7 TSB 0h-1
Sample type SRA
 
Source name human myoblast
Organism Homo sapiens
Characteristics cell line: AB678
cell type: Human myoblast
cell status: Proliferating
treatment: transfected OIP5-AS1:MIR-7 TSB for 24h
Treatment protocol Human myoblasts were transfected with 50 nM TSB to block the interaction between OIP5-AS1 and miR-7 or with scrambled controls; 24 h later, the cells were replaced to frash growth medoium for 24h or induced to differentiate by replacement of the growth medium with differentiation medium for the indicated time points.
Growth protocol Human myoblasts were cultured in growth medium (equal volume mixture of Hamm's F10 media with 20% FBS and Promocell Skeletal Muscle Cell Growth Medium). Human myoblasts were induced to differentiate by growth to high density and replacement of the growth medium with differentiation medium (DMEM with 2% horse serum)
Extracted molecule total RNA
Extraction protocol Total RNA from cultured cells was isolated using the Direct-zolâ„¢ RNA MiniPrep kit (Zymo Research), which includes a digestion step using DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description transfected OIP5-AS1:MIR-7 TSB for 24h and further transfered into Proliferation medium for 24h human myoblast replicate-1
Data processing BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Assembly: hg19
Supplementary files format and content: text files containing counts
 
Submission date May 11, 2022
Last update date Jun 14, 2022
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL24676
Series (2)
GSE202752 LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis
GSE202793 LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis
Relations
BioSample SAMN28192759
SRA SRX15233790

Supplementary file Size Download File type/resource
GSM6132357_JhY3_4_7B_0hr_1_S4_geneCOUNT.txt.gz 218.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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