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Series GSE82236 Query DataSets for GSE82236
Status Public on Aug 30, 2017
Title Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary We report the results of RNA-Seq and small RNA-Seq from a pair of HCA7-derived, KRAS wildtype CC and CC-CR cultured in 3D. A total of 361 genes showed more than a two-fold change in expression (false-discovery rate [FDR] - adjusted p<0.01) between CC-CR and CC; there were 141 transcripts upregulated and 220 transcripts downregulated in CC-CR compared to CC. Small RNA-Seq detected 7 miRNAs upregulated and 24 miRNAs downregulated in CC-CR cells compared to CC cells (fold change>2, FDR<0.01). Differential expression analysis revealed several novel candidates that may contribute to cetuximab resistance. The whole-transcriptome profilings using cetuximab resistance model from 3D culture provide novel candidates for cetuximab resistance and further functional studies might open the door to a novel understanding of how non-mutational mechanisms mediate cetuximab resistance.
Overall design mRNA and small-RNA profiles of cetuximab sensitive CC and resistant CC-CR from 3D culture were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 sequencer.
Contributor(s) Coffey R, Lu Y, Liu Q, Wang J
Citation(s) 29035371
Submission date Jun 03, 2016
Last update date May 15, 2019
Contact name Jing Wang
Organization name Vanderbilt University Medical Center
Street address 2220 Pierce Avenue
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (12)
GSM2186944 RNA-seq CC rep1
GSM2186945 RNA-seq CC rep2
GSM2186946 RNA-seq CC rep3
BioProject PRJNA324412
SRA SRP076105

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Supplementary file Size Download File type/resource
GSE82236_RNAseq_counts.txt.gz 439.9 Kb (ftp)(http) TXT
GSE82236_miRNA_counts.txt.gz 22.6 Kb (ftp)(http) TXT
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