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| Status |
Public on Aug 11, 2021 |
| Title |
LNCaP_m6A_rep2 |
| Sample type |
SRA |
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| Source name |
LNCaP
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| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
antibody: m6A
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| Growth protocol |
The human prostate epithelial cell line RWPE-1 (ATCC; CRL-11609) were cultured with Keratinoyte serum free medium supplemented with 0.05 mg/mL bovine pituitary extract (BPE), 5 ng/mL human recombinant epidermal growth factors (EGF), 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. The human prostate adenocarcinoma cell line LNCaP was cultured with RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37 °C. All cell lines were routinely tested for mycoplasma contamination.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara-Clontech, 634413), according to the manufacturer’s instructions.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
MeRIP-Seq
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| Data processing |
Library strategy: MeRIP-seq
Basecalls performed using Illuminal CASAVA software.
Cutadapt was used to remove the first 9 bases and N’s on both ends of reads. Reads with minimum of 25 bases were kept. Reads were aligned to human genome (hg19) using STAR. Duplicated reads were marked and removed by Picard. The bam files were transformed into bed12 format by bedtools, and then shifted to 200nt by a custom script and transformed back to bed6 format. Macs2 bdgopt sub-command was used to normalize each sample to a 10 million total reads.
MeTDiff was used to call m6A enriched peaks by combining both replicates with default parameters, and a custom script was used to merge all the peaks in LNCaP and RWPE to generate a reference peak set, on which the differential m6A enrichment analysis was based.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file
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| Submission date |
Apr 01, 2020 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Kexin Xu |
| Organization name |
UT Health Science Center at San Antonio
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| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
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| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE147885 |
N6-methyladenosine RNA methylome analyses in human prostate cell lines. |
| GSE147891 |
human prostate cell lines |
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| Relations |
| BioSample |
SAMN14517795 |
| SRA |
SRX8042019 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4447787_LNCaP_m6A_rep2.bw |
48.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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