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Sample GSM4105595 Query DataSets for GSM4105595
Status Public on Apr 30, 2023
Title BPE7 RNA-seq EpCAM high
Sample type SRA
 
Source name Effusion Patient 1 (BPE7) sorted EpCAM-high fraction
Organism Homo sapiens
Characteristics cell type: breast cancer cells
individual: Patient 1 (ER-)
treatment: no treatments
Treatment protocol For TWIST1 activation, cells were treated with (Z)-4-HydroxyTamoxifen at a final concentration of 20 nM for the indicated number of days.
Growth protocol Human mammary epithelial (HMLE) cells were cultured in Mammary Epithelial Cell Basal Medium containing 0.004 ml/ml BPE, 10 ng/ml EGF, 5 µg/ml hydrocortisone; HMLE-TWIST1-ER cells were propagated in medium containing Blasticidin S HCl at a final concentration of 10 µg/ml.
Extracted molecule total RNA
Extraction protocol ATAC-seq of HMLE-TWIST1-ER cells: 50000 cells were tagmented in 50 µl with 2.5 µl Tn5 according to Corces et al. 2017
RNA-seq of HMLE-TWIST1-ER cells: Total RNA was isolated using the miRNeasy Mini Kit (Qiagen).
RNA-seq of primary breast cancer cells: Total RNA was isolated using the Arcturus PicoPure RNA isolation kit.
ATAC-seq of HMLE-TWIST1-ER cells: Illumina Nextera DNA Library Preparation Kit (FC-121-1030) was used for library preparation. Libraries were selected for fragments less than 600 bp using AMPure XP beads for size selection.
RNA-seq of HMLE-TWIST1-ER cells: 1 μg of RNA was depleted for cytoplasmatic rRNAs, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix. A-tailing, adaptor ligation, and library enrichment were performed as described in the High Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina).
RNA-seq of primary breast cancer cells: Libraries were prepared from 1 μg of total RNA using a TruSeq Stranded Total RNA Kit with Ribo-Zero Human/Mouse/Rat (Illumina) according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Effusion Patient 1 (BPE7) sorted EpCAM-high fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx
Data processing ATAC-seq of HMLE-TWSIT1-ER cells: ATAC-seq reads were aligned to the human genome (hg38) using bowtie (Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -m1”
RNA-seq HMLE-TWIST1-ER cells: The STAR aligner (v 2.4.2a) with modified parameter settings (--twopassMode=Basic) is used for split-read alignment against the human genome assembly hg19 (GRCh37) and UCSC knownGene annotation (Dobin, A. et al. , 2013).
RNA-seq of primary breast cancer cells: RNA-sequencing reads were aligned to the human reference genome hg19 and quantified using the stranded option of STAR version 2.4.2a30.
Genome_build: ATAC-seq: hg38 RNA-seq: hg19 (GRCh37)
Supplementary_files_format_and_content: ATAC-seq of HMLE-TWIST1-ER cells: bigWig files were generated from homer tag directories using makeBigWig.pl.
RNA-seq of HMLE-TWIST1-ER cells: To quantify the number of reads mapping to annotated genes we use HTseq-count (v0.6.0) (Anders, S., Pyl, P. T. & Huber, W., 2015). FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values are calculated using custom scripts.
RNA-seq of primary breast cancer cells: The DESeq2 package was used to obtain normalized expression values as described (Raffel, S. et al., 2017).
 
Submission date Oct 02, 2019
Last update date Apr 30, 2023
Contact name Massimo Saini
E-mail(s) massimo.saini@unibas.ch
Phone 0762311275
Organization name University of Basel
Department Department of Biomedicine
Lab Nicola Aceto's Lab
Street address Mattenstrasse 28
City Basel
State/province Basel Canton
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL11154
Series (1)
GSE138329 Maintenance of epithelial traits and resistance to mesenchymal reprogramming promote proliferation in metastatic breast cancer
Relations
BioSample SAMN12898164
SRA SRX6938747

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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