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| 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
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| 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.
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| Overall design |
2D culture cells, orthotopic tumors, BICA samples and bone lesions, all developed by MCF-7, are subject to NGS and then analyzed.
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| Contributor(s) |
Zhang X, Wang H, Tian L |
| Citation(s) |
28429794 |
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| Submission date |
Jul 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hai Wang |
| E-mail(s) |
hai.wang@roswellpark.org
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| Organization name |
Roswell Park Cancer Institute
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| Department |
Molecular and Cellular Biology
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| Lab |
Hai Wang
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| Street address |
Elm and Carlton Streets, MRC 328
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
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| Samples (17)
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| GSM2227410 |
MCF-7, rep4 |
| GSM2227411 |
Orth, rep1 |
| GSM2227412 |
Orth, rep2 |
| GSM2227413 |
Orth, rep3 |
| GSM2227414 |
BICA, rep1 |
| GSM2227415 |
BICA, rep2 |
| GSM2227416 |
BICA, rep3 |
| GSM2227417 |
BICA, rep4 |
| GSM2227418 |
BICA, rep5 |
| GSM2227419 |
BICA, rep6 |
| GSM2227420 |
IVBL, rep1 |
| GSM2227421 |
IVBL, rep2 |
| GSM2227422 |
IVBL, rep3 |
| GSM2227423 |
IVBL, rep4 |
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| Relations |
| BioProject |
PRJNA328044 |
| SRA |
SRP078006 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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