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Sample GSM4074024 Query DataSets for GSM4074024
Status Public on Jul 02, 2021
Title MDA_M6A_rep2 [m6A-seq]
Sample type SRA
 
Source name MDA-MB-231
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
treatment: None
antibody: m6A (Cat#202 011)
cell culture: DMEM + 10% FBS
Growth protocol Standard
Extracted molecule total RNA
Extraction protocol 250 ug RNA was phenol-chloroform extracted, rRNA depleted, and fragmented to ~100 nt. 1 ug fragmented RNA was saved as input and the rest was immunoprecipitated. RNA was precipitated and libraries were prepared with TruSeq Stranded Total RNA Preparation Kit according to manufacturer’s instructions.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description macs2_mda_filtered.bed
Data processing Library strategy: m6A-seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify m6A peaks using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs).
 
Submission date Sep 11, 2019
Last update date Jul 03, 2021
Contact name Gene Yeo
E-mail(s) geneyeo@ucsd.edu
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL20301
Series (1)
GSE137258 Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Relations
BioSample SAMN12727120
SRA SRX6830229

Supplementary file Size Download File type/resource
GSM4074024_M6A_IP_MDA_2_S20_L006_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.norm.neg.bw 71.8 Mb (ftp)(http) BW
GSM4074024_M6A_IP_MDA_2_S20_L006_R1_001.polyATrim.adapterTrim.rmRep.sorted.rg.norm.pos.bw 68.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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