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| Status |
Public on Jun 01, 2020 |
| Title |
RNA-seq of siFEN1 MCF-7 cells treated with E2 - replicate 1 |
| Sample type |
SRA |
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| Source name |
MCF-7 siFEN1 E2 #1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
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| Treatment protocol |
Hormone treatments consisted of solvent Dimethylsulfoxide (DMSO) or 10nM of estradiol. Additionally cells were pretreated with 100nM of the FEN1 inhibitor prior to hormone treatment. For knockdown experiments 25nM of single or pooled duplexes of siRNA against FEN1 (Dharmacon MU-010344-01) or a non-targeting control pool (Dharmacon, D-001206-14-20) were transfected with Dharmafect according to manufactures protocol.
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| Growth protocol |
MCF-7were cultured in DMEM medium in the presence of 10% FBS and antibiotics (penicillin, streptavidin). For hormone deficient conditions, cells were deprived of hormone for 72 hours, by culturing in phenol-red-free DMEM containing 5% charcoal-treated serum, antibiotics and supplemented with L-glutamine, prior to hormone treatment.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequences were generated by theHiSeq 2500 High Output Mode, and aligned to the Human Reference Genome (assembly hg19, February 2009). Peak calling over input was performed using MACS peak caller (Zhang et al., 2008) version 1.3.7.1 and DFilter (Kumar et al., 2013), only considering peaks shared by both peak callers. RNA seq Read counts were mapped using Salmon v0.14.1 and Differential expression (DE) was performed using DESeq2 with an FDR (adjusted p-value) < 0.05. Median of ratios normalization was performed across all samples and differentially expressed genes were identified between E2 vs Vehicle and siFEN1 vs siControl conditions
Genome_build: Hg19
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| Submission date |
Mar 04, 2020 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Koen Flach |
| E-mail(s) |
koenflach@hotmail.com
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| Organization name |
NKI
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE95302 |
DNA structure-specific endonuclease FEN1 as a novel drug target in tamoxifen resistant breast cancer. |
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| Relations |
| BioSample |
SAMN14278899 |
| SRA |
SRX7846792 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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