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Series GSE84114 Query DataSets for GSE84114
Status Public on Jan 20, 2017
Title Profiling in vivo Bone Lesion and ex vivo Bone-In-Culture Array Samples by Next-Generation Sequencing
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Based on RNA-seq, we performed transcriptomic profiling to examine the similarities or differences between BICA (bone-in-culture array) and IVBL (in vivo bone lesion). CIBERSORT analysis reveals that the major local cellular components are comparable between BICA and IVBL, but differ dramatically in orthotopic tumors. Principle component analysis of human RNAs indicated that the transcriptomic profiles of cancer cells in BICA are more closely mimicking IVBL, as compared to cancer cells in 2D and in orthotopic tumors. These results provide transcriptome-wide evidence supporting BICA as a platform to mimic bone microenvironment.
Overall design 2D culture cells, orthotopic tumors, BICA samples and bone lesions, all developed by MCF-7, are subject to NGS and then analyzed.
Contributor(s) Zhang X, Wang H, Tian L
Citation(s) 28429794
Submission date Jul 06, 2016
Last update date May 15, 2019
Contact name Hai Wang
Organization name Roswell Park Cancer Institute
Department Molecular and Cellular Biology
Lab Hai Wang
Street address Elm and Carlton Streets, MRC 328
City Buffalo
State/province NY
ZIP/Postal code 14263
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (17)
GSM2227407 MCF-7, rep1
GSM2227408 MCF-7, rep2
GSM2227409 MCF-7, rep3
BioProject PRJNA328044
SRA SRP078006

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Supplementary file Size Download File type/resource
GSE84114_BICA_RNAseq.Normalized.RData.gz 41.4 Mb (ftp)(http) RDATA
GSE84114_BICA_RNAseq.RData.gz 7.1 Mb (ftp)(http) RDATA
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Raw data are available in SRA
Processed data are available on Series record

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