|
| Status |
Public on Feb 08, 2019 |
| Title |
HTB.CtBP.1 |
| 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 |
SAMN10886804 |
| SRA |
SRX5349574 |
