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| Status |
Public on May 16, 2023 |
| Title |
LY2-n2_MeRIP |
| Sample type |
SRA |
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| Source name |
human breast cancer cell line LY2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: LY2
cell type: endocrine-resistant breast cancer
replicate number: Replicate 2
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| Growth protocol |
LY2 endocrine-resistant breast cancer cells, a gift from Robert Clarke (Georgetown, USA), were cultured in phenol red free MEM (51200_046, Gibco Sigma-Aldrich) supplemented with 10% charcoal dextran stripped (CDS), 2 mM l-glutamine and 10-8M 4-hydroxytamoxifen (4-OHT) (H7904, Sigma-Aldrich). Cells were incubated in a humidified incubator at 5% CO2 at 37°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was carried out using the RNeasy MIDI kit (74144, Qiagen) according to the manufacturer's instructions.
M6A IP library prep was performed by BGI (Hong Kong) using 200-350 μg of RNA and the Magna MeRIP™ m6A Kit (17-10499, Merck Millipore).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
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| Description |
2x100 paired-end sequence reads
LY2_MeRIP_peaks.narrowPeak
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| Data processing |
Library strategy: MeRIP-seq
Quality control checks were performed using FASTQC (v0.11.9) and MultiQC (v1.7). MCF7_rep3 fastq files were removed from further analysis after MCF7_rep3_2.fq.gz was reported as truncated.
MeRIP-seq reads were mapped GRCH38 human reference genome using Bowtie2. The SAM files from Bowtie were then sorted by coordinate and, using Picard Tools, they were converted to BAM file format.
Coverage files (bigWig) of the mapped reads were obtained running the genomecov tool from BEDTools software suite followed by the bedGraphToBigWig tool from the ucscGenomeBrowser/kent repository on GitHub.
For each individual cell line pooled narrowPeak files were obtained using the MACS2-callpeak tool from SevenBridges platform (https://www.sevenbridges.com/), with the default q-value (FDR) cutoff of 0.05.
Differential m6A methylation sites between cell lines (LY2-MCF7, T347-MCF7, MCF7-LY2) were predicted using the MeTDiff package (PEAK_CUTOFF_FDR = 0.05, DIFF_PEAK_CUTOFF_FDR = 0.05) with the IP/control (MeRIP/RNA) pairs as input.
Genome_build: Human reference genome NCBI build 38, GRCh38
Supplementary_files_format_and_content: Genome-wide read depth information in bigWig format.
Supplementary_files_format_and_content: Peaks of signal enrichment information based on pooled, normalized data.
Supplementary_files_format_and_content: Differential m6A methylation sites in Excel format.
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| Submission date |
Jun 10, 2021 |
| Last update date |
May 17, 2023 |
| Contact name |
Leonie Young |
| E-mail(s) |
lyoung@rcsi.com
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| Organization name |
RCSI
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| Department |
Surgery
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| Lab |
Endocrine Oncology Research Group
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| Street address |
31A York Street
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| City |
Dublin |
| State/province |
Dublin |
| ZIP/Postal code |
D02 HX03 |
| Country |
Ireland |
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| Platform ID |
GPL23227 |
| Series (2) |
| GSE176533 |
MeRIP-sequencing for dynamic epi-transcriptomic landscape mapping with disease progression in ER-positive breast cancer |
| GSE176535 |
Dynamic epi-transcriptomic landscape mapping with disease progression in ER-positive breast cancer |
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| Relations |
| BioSample |
SAMN19655282 |
| SRA |
SRX11110963 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5368777_MeRIP_LY2_rep_2.bw |
143.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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