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Sample GSM4073997 Query DataSets for GSM4073997
Status Public on Jul 02, 2021
Title LM2_SMINPUT_rep2 [eCLIP-seq]
Sample type SRA
 
Source name MDA-MB-231-LM2
Organism Homo sapiens
Characteristics cell line: MDA-MB-231-LM2
treatment: None
cell culture: DMEM + 10% FBS
Growth protocol Standard
Extracted molecule total RNA
Extraction protocol 20M cells were UV-crosslinked, lysed and sonicated. RNA was fragmented and protein-RNA complexes were immunoprecipitated with a YTHDF2 antibody. Inputs (2% of lysate) were saved and run alongside IP samples. IP samples were stringently washed, and for all samples the RNA was dephosphorylated, followed by on-bead ligation of barcoded RNA adapters to the 3’ end. RNA-protein complexes were run on standard protein gels and transferred to nitrocellulose membranes where the RNA in the region 65 kDa – 140kDa was excised off the membrane and proteinase K treated. RNA was then reverse transcribed followed by treatment with ExoSAP-IT to remove excess oligonucleotides. Samples were cleaned up with Dynabeads MyOne Silane and subject to qPCR to determine the appropriate number of PCR cycles.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description LM2_1-LM2_2.idr.final.bed
Data processing Library strategy: eCLIP-seq
Raw sequencing reads were trimmed for adapter sequences and barcode 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 eCLIP peaks.
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 SAMN12727086
SRA SRX6830202

Supplementary file Size Download File type/resource
GSM4073997_YTHDF2.LM2_INPUT_2.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.neg.bw 24.4 Mb (ftp)(http) BW
GSM4073997_YTHDF2.LM2_INPUT_2.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.pos.bw 25.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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