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| Status |
Public on May 12, 2021 |
| Title |
RNA-seq_MCF7-DR_1 |
| Sample type |
SRA |
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| Source name |
doxorubicin-resistant MCF7 (MCF7-DR)
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| Organism |
Homo sapiens |
| Characteristics |
treatment: treated with 1 μM doxorubicin hydrochloride
cell line: MCF7-DR
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| Treatment protocol |
The parental MCF7 cells were grown in a drug-free medium, resistant-derived cells were maintained in doxorubicin hydrochloride (MedChem Express, USA) at a concentration of 1 μM.
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| Growth protocol |
The MCF7 and doxorubicin-resistant MCF7 (MCF7-DR) cell lines originally obtained from the Cell Bank of the Type Culture Collection of the Chinese Academy of Sciences Committee (Shanghai, China), were kindly provided by the key laboratory of breast cancer in Shanghai, Fudan University. All cells were cultured in DMEM medium (KEL Biotech, China), supplemented with 2 mM L-Glutamine (Gibco, USA), 10% fetal bovine serum (KEL Biotech, China), 0.1 M sodium pyruvate (Gibco, USA), 50 units/mL penicillin and 50 µg/mL streptomycin (Sigma-Aldrich, USA). The MCF7 and MCF7-DR cells were grown in 10-cm culture dishes at 37 °C in a humidified 5% CO2 atmosphere, and the medium was renewed every 2-3 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was isolated from samples using TRIzol Reagent (Invitrogen, USA) and purified using RNeasy Mini Kit (QIAGEN, Germany). Agilent Bioanalyzer 2100 was used to assess RNA integrity.
The RNA‐seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's instructions. PE150 sequencing was performed on the Illumina HiSeq X Ten platform (Novogene Biotech, China). The ATAC-seq libraries were prepared using a total of 50,000 fresh cells were washed twice with 100 μl of cold PBS (KEL Biotech, China) and resuspended in 100 μl of lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 0.1% IGEPAL CA-630 (Sigma-Aldrich) and 3 mM MgCl2] for 10 min on ice to prepare the nuclei. Immediately after lysis, the suspension of nuclei was spun at 500 g at 4°C for 5 min to remove the supernatant. Nuclei were then incubated with the 50 μl of Tn5 transposition reaction mix (DIATRE Biotech, China) at 37 °C for 30 min. The stop buffer was then added directly into the reaction to end the tagmentation. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, Germany). PCR was performed to amplify the library for 12 cycles. Libraries were purified with Agencourt Ampure XP beads (Beckman, USA) to remove contaminating primer dimmers.
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| Library strategy |
RNA-Seq |
| Library source |
genomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads from RNA-seq experiments were aligned to genome build hg19 using STAR. All ATAC-Seq data sets were trimmed and aligned to genome build hg19 genome using Bowtie2.
Duplicate reads of RNA-seq and ATAC-seq data were removed with SAMtools.
The mRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff. MACS2 was used to identify regions of ATAC-seq peaks.
The top 10000 ATAC-seq peaks were used for known motif enrichment analysis, which were performed using HOMER (v4.9).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (bw) files were generated using deepTools.
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| Submission date |
May 10, 2021 |
| Last update date |
May 13, 2021 |
| Contact name |
Xuelong Wang |
| E-mail(s) |
wangxuelong100@126.com
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| Organization name |
Chinese Academy of Sciences
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| Street address |
No. 320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE174152 |
Integrated chromatin accessibility and transcriptome landscapes of doxorubicin-resistant breast cancer cells |
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| Relations |
| BioSample |
SAMN19092534 |
| SRA |
SRX10828153 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5287977_RNA-seq_MCF7-DR_1.bw |
33.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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