Metadata supporting data files in the published article: LncRNA RP11-19E11 is an E2F1 target required for proliferation and survival of basal breast cancer
Creators: name: Giro-Perafita A
name: L, Luo
name: Khodadadi-Jamayran A
name: Thompson M
name: Akgol Oksuz B
name: Tsirigos A
name: Dynlacht BD
name: Sánchez I
name: Esteva FJ
Publisher: name: figshare
Year: 2020
Subjects: subject: Cancer
subject: 111201 Cancer Cell Biology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 60404 Epigenetics (incl. Genome Methylation and Epigenomics)
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: 60408 Genomics
subject: Biomarkers
subject: 111202 Cancer Diagnosis
subject: 111204 Cancer Therapy (excl. Chemotherapy and Radiation Therapy)

description: Long non-coding RNAs (lncRNAs) play key roles in the regulation of breast cancer initiation and progression. This study identified the long non-coding RNA RP11-19E11.1 as an E2F1 target required for tumor cell proliferation and survival in basal breast cancer.<br> <b>Data access:</b> The raw RNA sequencing data (supporting figure 1) used during the study are publicly available in the NCBI Gene Expression Omnibus (GEO) repository: https://identifiers.org/geo:GSE73526 and https://identifiers.org/geo:GSE48213. The read count tables (supporting figures 1, 3 and 4) for all the sequencing samples (n=1162) in TCGA are publicly available at The National Cancer Institute’s (NCI) Genomic Data Commons (GDC) (https://portal.gdc.cancer.gov/). RNA sequencing datasets (supporting figures 3, 4, 5 and 6) generated during the current study are publicly available in the GEO repository: https://identifiers.org/geo:GSE138606. Additional datasets used (TCGA_patientID.xlsx) and generated (Viability_lncRNA.zip, qRT_PCR_lncRNA.zip, TNBC_CLASS.csv, GSEA_dataset_RNAseq.zip, AnexinV_RAW.zip, CellCycle_EDU_RAW.zip, Results_E2F_OE.pzfx and Chip_results.pzfx) during the study will be made available on request from the corresponding author, Prof Francisco J. Esteva, email: Francisco.Esteva@nyulangone.org.<br> <b>Study aims and methodology:</b> In the present study, the authors sought to identify clinically relevant lncRNAs deregulated specifically in basal breast cancer patients and then functionally evaluate a subset of these candidates in the oncogenic process <i>in vitro </i>and assess their value as prognostic markers.<br> All the experiments were performed on the following breast cancer cell lines: MDA-MB-231, Hs578T, MDA-MB-157, MDA-MB-468, MCF7, SkBr3, BT474, HCC2157, HCC38, HCC2157, BT549, HCC70, HCC1143 and T-47D. Normal breast MCF10A cells were also used.<br> The following techniques are described in detail in the published article: RNA interference, cell transfection, cell fractionation, chromatin precipitation, reverse transcription and quantitative real-time polymerase chain reaction (PCR), protein extraction and Western blotting, Fluorescence-activated cell sorting (FACS) analysis, Annexin-V staining, viability assays (after RNA interference and for drug sensitivity evaluation), Rapid amplification of cDNA ends (RACE) and Chromatin immunoprecipitation (ChiP). RNA sequencing processing of publicly available datasets, and processing of the publicly available TCGA data are described in detail in the published article. <b><br> </b><b>Datasets supporting the figures in the published article: </b>The dataset names, formats, their location and links to the datasets are provided in the file <b>Giro-Perafita et al.xlsx</b>.<br> <b> </b> <b>Software needed to access data: </b>The FlowJo datasets in the zipped files AnexinV_RAW.zip and CellCycle_EDU_RAW.zip, can be accessed using the FlowJo software.