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GEO help: Mouse over screen elements for information. |
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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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