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Status |
Public on Apr 30, 2023 |
Title |
M1-TAMd1_ATAC-seq |
Sample type |
SRA |
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Source name |
HMLE-TWIST1-ER cells, EMT-sensitive, clone 1
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Organism |
Homo sapiens |
Characteristics |
cell type: mammary epithelial cells resistance: EMT-sensitive treatment: untreated
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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.
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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.
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Extracted molecule |
genomic DNA |
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.
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 1500 |
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Description |
HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; untreated
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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).
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Submission date |
Oct 02, 2019 |
Last update date |
Apr 30, 2023 |
Contact name |
Massimo Saini |
E-mail(s) |
massimo.saini@unibas.ch
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Phone |
0762311275
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Organization name |
University of Basel
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Department |
Department of Biomedicine
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Lab |
Nicola Aceto's Lab
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Street address |
Mattenstrasse 28
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City |
Basel |
State/province |
Basel Canton |
ZIP/Postal code |
4058 |
Country |
Switzerland |
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Platform ID |
GPL18460 |
Series (1) |
GSE138329 |
Maintenance of epithelial traits and resistance to mesenchymal reprogramming promote proliferation in metastatic breast cancer |
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Relations |
BioSample |
SAMN12898119 |
SRA |
SRX6938732 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4105548_GS546_M1-TAMd1_m1.ucsc.bigWig |
180.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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