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Sample GSM3509503 Query DataSets for GSM3509503
Status Public on Dec 13, 2018
Title CBX8 KO rep 2
Sample type SRA
 
Source name T98G CBX8 KO cell line
Organism Homo sapiens
Characteristics genotype/variation: CBX8 KO
Treatment protocol Doxycycline (1 ug/mL) for 72 hours
Growth protocol Cells were plated 72 hrs prior to the experiment, cells were grown in Eagle's modified essential medium, 10% FBS, 1% sodium pyruvate, 1% penicillin/streptomycin, 1% glutamine, 1% non-essential amino acids, grown at 37 °C and 5% CO2
Extracted molecule total RNA
Extraction protocol RNA was isolated using Trizol followed by RNA easy
Oligo dT Library construction
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description counts_matrix
Data processing Reads were trimmed using trimmomatic on the Galaxy web interface. Parameters used: TruSeq3; headcrop, 8; sliding window with defaults; minlen, 30.
Paired end reads were aligned to the hg38 genome using HiSat2 defaults on the Galaxy web interface
Counts matrix was generated as reads per sythnetic transcript
Mean counts per million were generated from the replicates for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files for counts per transcript per replicate
 
Submission date Dec 12, 2018
Last update date Dec 14, 2018
Contact name Emily Dykhuizen
Organization name Purdue University
Department medicinal chemistry and molecular pharmacology
Lab dykhuizen
Street address 201 S. University
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platform ID GPL23227
Series (1)
GSE123689 CBX8 KO and WT re-expression RNA-seq
Relations
BioSample SAMN10585400
SRA SRX5126516

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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