NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3595393 Query DataSets for GSM3595393
Status Public on Feb 08, 2019
Title HTB.CtBP.2
Sample type SRA
 
Source name HTB17_wild type CtBP
Organism Homo sapiens
Characteristics cell line: HTB17
cell type: glioblastoma cell line
genotype/variation: wild type CtBP
Growth protocol HTB17 cells overexpressing wt CtBP1 or R342W were grown in 150 mm dishes in DMEM supplemented with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol The cells were washed with PBS and RNA was isolated using TRIzol reagent (Invitrogen).
Ribosomal RNA was depleted from total RNA and libraries were constructed using the Eukaryotic RiboMinus and Ion Total RNA-seq v2 kits (Life Technologies, Thermofisher) according to the manufacturer’s directions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description CtBP.ave
Data processing Sequencing was performed on an Ion Torrent Proton.
Reads were aligned to the hg19 human genome sequence using the TMAP aligner map4 algorithm. Soft-clipping at both 5’ and 3’ ends of the reads was permitted during alignment with a minimum seed length of 20 nt.
The nucleotide coverage for all non-redundant exons was calculated and normalized to total exon coverage using custom scripts in R. Expression values are total normalized nucleotide exon coverage per gene.
Fold changes in gene expression, p values and q values were calculated using custom R scripts and Microsoft Excel. Expressed genes were defined as those with at least 900 nucleotides of average normalized coverage in at least one of the four groups or a p value less than or equal to 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet of average nucleotide exon coverage per expressed gene in each group with fold change in expression and statistics
 
Submission date Feb 07, 2019
Last update date Feb 12, 2019
Contact name Govindaswamy Chinnadurai
E-mail(s) g.chinnadurai@health.slu.edu
Organization name Saint Louis University
Department Molecular Microbiology and Immunology
Street address 1100 South Grand Blvd
City St. Louis
State/province MO
ZIP/Postal code 63104
Country USA
 
Platform ID GPL17303
Series (1)
GSE126253 A pathogenic CtBP1 missense mutation causes altered cofactor binding and transcriptional activity
Relations
BioSample SAMN10886803
SRA SRX5349575

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap