Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer

Figure 1B_TEM

New Figure 1B_TEM

Figure 1B_image_57.tif

--Title: TEM image

-- Description: Raw data for TEM image 

Figure 1C and 1D

Figure 1C_NTA Capture MEV ExperimentReport

--Title: NTA Capture MEV Experiment Report

Figure 1D_NTA Capture SEV ExperimentReport

--Title: NTA Capture SEV ExperimentReport

-- Description: Raw data from hydrodynamic diameter distribution profiles of isolated large and small EVs measured by nanoparticle tracking analysis (NTA) with red vertical lines and blue numbers denote standard deviation and diameters at specific peaks, respectively.

Figure 1E qEV BCA and particle raw data

Figure 1E_qEV BCA and particle raw data.xlsx

-- Title: EV concentration determined by NTA, and protein levels determined by BCA assay of fractions acquired during separation on a qEV Original size exclusion chromatography (SEC) column.

-- Description:

Each row of the spreadsheet represents one sample. Column data are described below:

column A: qEV column fraction

column B: protein concentration (ug/20ul) measured by BCA

column C: protein concentration converted to (ng/20ul)

column D: protein concentration converted to (ng/ul)

column E: EV concentration (particle/ml) measured by Nanosight

column F: Total number of particles

column G: Particles mean measured by Nanosight

column H: Particles mode measured by Nanosight

Figure 1F_western blot raw_not_cropped.pptx

-- Title: Western blot raw images  

-- Description: antibodies recognising human HER2 (mouse monoclonal, anti-Neu, Santa Cruz, Cat # sc-33684, RRID:AB_627996), human EpCAM (rabbit monoclonal, AbCAM, Cat # ab223582, RRID:AB_2762366), Tubulin (    and human TSG101 (rabbit polyclonal, AbCAM, Cat # ab30871, RRID:AB_2208084). (Sigma).

Figure 2A and Figure S1

Figure 2A_RT-qPCR_rawdata.xlsx

-- Title: Raw data for RT-qPCR to examine the mRNA expression level of five protein-coding genes (EpCAM, BIRC5, YBX1, GAPDH, HPRT1) and three long non-coding RNAs (ZFAS1, HOTAIR, AGAP2-AS1) in BT-474 cells and their EVs.

-- Description:

For Figure 2A

Sheet 1: Each row of the spreadsheet represents Ct value from one sample (duplicate samples). Column data are described below:

column A: sample =  gene name

column B,C,D: Ct values for qRT-PCR from BT474 cells

column E,F,G: Ct values for qRT-PCR from BT474 EVs

For Figure S1

Sheet 2: Each row of the spreadsheet represents expression normalised to GAPDH for Figure S1.

Row 3: sample = gene name.

Column data are described below:

Row 5,6,7: Relative gene expression normalised to GAPDH

Figure 2B and C_meta_analysis_rawdata.xlsx

-- Title: DeSeq2 normalised log2 (x+1) expression values of 10 genes in 8,867 tumours and 6,874 normal tissues downloaded on 31st March 2020 from the UCSC Xena portal using the address https://toil.xenahubs.net/download/TCGA-GTEx-TARGET-gene-exp-counts.deseq2-normalized.log2.gz

-- Description: Each row of the spreadsheet represents one sample. The first 4 columns contain sample annotations and the subsequent 10 columns hold the actual gene expression values. Column data are described below:

column A: sample =  sample ID

column B: cat2 = organ/tissue classification

column C: X_study = non-cancer (GTEX) or cancer (TCGA) classification

column D: catN2a = specific organ or cancer type categorisation including the total number of samples within each category

columns E – N: expression values of genes that are designated as official HGNC symbols

-- Title: 201209_EVpaperScript.R

-- Description: The R script containing the code for all the above computations and visualisations for Figure 2B and C.

Funding provided by: Breast Cancer Foundation New Zealand
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001559
Award Number: Belinda Scott Science Fellowship

Funding provided by: Breast Cancer Foundation New Zealand
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001559
Award Number: Technology and Innovation Grant

Funding provided by: Cancer Research Trust New Zealand
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001552
Award Number: John Gavin Postdoctoral Fellowship (GOT-1717-JGPDF)