figure3a: miR34a asRNA stable over-expression cell lines.

In GranderLab/miR34a_asRNA_project: The miR34AasRNAproject package facilitates the transparency and reproducibility of the miR34a asRNA project and associated publication.

Description

RNA was extracted using the RNeasy mini kit (Qiagen) and subsequently treated with DNase (Ambion Turbo DNA-free, Life Technologies). 500ng RNA was used for cDNA synthesis using MuMLV (Life Technologies) and a 1:1 mix of oligo(dT) and random nanomers. QPCR was carried out using KAPA 2G SYBRGreen (Kapa Biosystems) using the Applied Biosystems 7900HT machine with the cycling conditions: 95 <c2><b0>C for 3 min, 95 <c2><b0>C for 3 s, 60 <c2><b0>C for 30 s. QPCR for miRNA expression analysis was performed according to the protocol for the TaqMan microRNA Assay kit (Life Technologies) with primer/probe sets purchased from the same company (TaqMan<c2><ae> MicroRNA Assay, hsa-miR-34a, human and Control miRNA Assay, RNU48, human) and the same cycling scheme as above. QPCR primers are shown below. Two experimental (technical) replicates were included in each QPCR run and delta ct was calculated for each sample using the mean of the gene of interest's technical replicates and the house keeping gene's technical replicates. delta-delta ct was calculated for each sample by subtracting the median dct value for the corresponding mock samples. Five independant experiments were performed in total. The Student's t-test was used to compare the mock vs miR34a asRNA overexpressing group's delta-delta ct values for both genes.

Format

A tibble with 120 rows and 7 variables:

'Biological Replicate'

Numeric; Indicates the biological replicate of the sample.

'Cell line'

Factor; Indicates the cell line the experiment was performed in.

'Genetic mod'

Factor; indicates the genetic modifications in the cell line.

gene

Character; indicates the gene that the Ct values correspond to.

Ct1

Numeric; The Ct value corresponding to the 1st technical triplicate.

Ct2

Numeric; The Ct value corresponding to the 2nd technical triplicate.

Ct3

Numeric; The Ct value corresponding to the 3rd technical triplicate.

...

Examples

getData('Figure 3a')

GranderLab/miR34a_asRNA_project documentation built on May 26, 2019, 7:26 a.m.