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Sample GSM4729633 Query DataSets for GSM4729633
Status Public on Aug 08, 2021
Title MCF7-YTHDC1-HaloTag WT E2 TT-Seq
Sample type SRA
 
Source name MCF7 cell
Organism Homo sapiens
Characteristics cell line: MCF7
cell type: human breast cancer cell line
treatment: E2 60 mins,Vehice
molecule subtype: nuclear RNA
Treatment protocol In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.EtOH were added to the cells for an hour. Cells were labeled in media for 15 min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.
Growth protocol MCF7 cells were incubated in DMEM media supplemented with 10% Fetal Bovine Serum (FBS, GenDEPOT) in 37°C CO2 incubator.
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Duffy et al., Mol Cell, 2015. M6A methylated RNA was immunoprecipitated by anti-m6A antibodies (202003, SYSY).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Data processing All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
MINT-Seq, TT-Seq, MeRIP-Seq,RNA-Seq, ChIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation. 
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
 
Submission date Aug 17, 2020
Last update date Aug 08, 2021
Contact name Ruoyu Wang
E-mail(s) ruoyu.wang@uth.tmc.edu
Organization name UTHealth McGovern Medical School
Street address 6431 Fannin St
City HOUSTON
State/province Texas
ZIP/Postal code 77054
Country USA
 
Platform ID GPL21697
Series (1)
GSE143441 N6-adenosine Methylation of Enhancer RNAs and YTHDC1 Facilitate Transcriptional Condensate Formation and 3D Chromatin Organization
Relations
BioSample SAMN15832991
SRA SRX8957549

Supplementary file Size Download File type/resource
GSM4729633_MCF7-YTHDC1-HaloTag-E2-WT-TT-Seq.neg.bigWig 103.3 Mb (ftp)(http) BIGWIG
GSM4729633_MCF7-YTHDC1-HaloTag-E2-WT-TT-Seq.pos.bigWig 108.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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