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Series GSE81620 Query DataSets for GSE81620
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
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.
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
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
BioProject PRJNA322129
SRA SRP075398

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Supplementary file Size Download File type/resource
GSE81620_genes.fpkm_table.txt.gz 2.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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