|
| Status |
Public on Aug 11, 2017 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in tamoxifen-sensitive and tamoxifen-resistant human breast cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in LCC9 tamoxifen-resistant breast cancer cell lines relative to parental MCF-7 tamoxifen-sensitive cells
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| |
|
| Overall design |
Methods: MCF-7 and LCC9 cells were transfected, in three separate experiments, with pre-miR-29b-1, pre-miR-29a, or anti-miR-29a (which blocks both miR-29b-1 and miR-29a). RNA seq profiles were generated by deep sequencing, in triplicate, using Illumina Nextseq500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
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| |
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| Contributor(s) |
Muluhngwi P, Kalbfleisch TS, Rouchka EC, Klinge CM |
| Citation(s) |
28701793, 31263129, 34298743 |
| Submission date |
May 19, 2016 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
eric.rouchka@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
KY INBRE Bioinformatics Core
|
| Street address |
522 East Gray Street
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (18)
|
| GSM2159798 |
LCC9 cell line pre-miR-29b-1 transfected replicate 1 |
| GSM2159799 |
LCC9 cell line pre-miR-29b-1 transfected replicate 2 |
| GSM2159800 |
LCC9 cell line pre-miR-29b-1 transfected replicate 3 |
| GSM2159801 |
LCC9 cell line Anti-miR-29a transfected replicate 1 |
| GSM2159802 |
LCC9 cell line Anti-miR-29a transfected replicate 2 |
| GSM2159803 |
LCC9 cell line Anti-miR-29a transfected replicate 3 |
| GSM2159804 |
LCC9 cell line Pre-miR-29a transfected replicate 1 |
| GSM2159805 |
LCC9 cell line Pre-miR-29a transfected replicate 2 |
| GSM2159806 |
LCC9 cell line Pre-miR-29a transfected replicate 3 |
| GSM2159807 |
MCF-7 cell line pre-miR-29b-1 transfected replicate 1 |
| GSM2159808 |
MCF-7 cell line pre-miR-29b-1 transfected replicate 2 |
| GSM2159809 |
MCF-7 cell line pre-miR-29b-1 transfected replicate 3 |
| GSM2159810 |
MCF-7 cell line Anti-miR-29a transfected replicate 1 |
| GSM2159811 |
MCF-7 cell line Anti-miR-29a transfected replicate 2 |
| GSM2159812 |
MCF-7 cell line Anti-miR-29a transfected replicate 3 |
| GSM2159813 |
MCF-7 cell line Pre-miR-29a transfected replicate 1 |
| GSM2159814 |
MCF-7 cell line Pre-miR-29a transfected replicate 2 |
| GSM2159815 |
MCF-7 cell line Pre-miR-29a transfected replicate 3 |
|
| Relations |
| BioProject |
PRJNA322129 |
| SRA |
SRP075398 |
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