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Status |
Public on Dec 13, 2018 |
Title |
CBX8 KO rep 2 |
Sample type |
SRA |
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Source name |
T98G CBX8 KO cell line
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Organism |
Homo sapiens |
Characteristics |
genotype/variation: CBX8 KO
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Treatment protocol |
Doxycycline (1 ug/mL) for 72 hours
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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
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated using Trizol followed by RNA easy Oligo dT Library construction
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
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Description |
counts_matrix
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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
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Submission date |
Dec 12, 2018 |
Last update date |
Dec 14, 2018 |
Contact name |
Emily Dykhuizen |
Organization name |
Purdue University
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Department |
medicinal chemistry and molecular pharmacology
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Lab |
dykhuizen
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Street address |
201 S. University
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City |
West Lafayette |
State/province |
IN |
ZIP/Postal code |
47907 |
Country |
USA |
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Platform ID |
GPL23227 |
Series (1) |
GSE123689 |
CBX8 KO and WT re-expression RNA-seq |
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Relations |
BioSample |
SAMN10585400 |
SRA |
SRX5126516 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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