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Sample GSM2545498 Query DataSets for GSM2545498
Status Public on Feb 13, 2018
Title Hela_YY2_KO_RNA-Seq
Sample type SRA
Source name HeLa
Organism Homo sapiens
Characteristics cell line: Hela
tag: YY2_KO
Treatment protocol Cells grown to ~90% confluent were used for RNA-seq.
Growth protocol HeLa cells were cultured in MEM alpha medium supplemented with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from HeLa cells using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Data processing For computational analysis of RNA-seq data, sequencing reads were aligned to hg19 human genome using the “Tuxedo suite”: Bowtie2-Tophat
EdgeR ( was used to compute the differential expressed genes (P<0.001, dispersion 0.001).
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
The HOMER suite (Hypergeometric Optimization of Motif EnRichment) was used to generate the input of EdgeR and calling EdgeR
Submission date Mar 21, 2017
Last update date May 15, 2019
Contact name Wen Liu
Organization name Xiamen University
Department School of Pharmaceutical Sciences
Street address Xiang'an South Road, Xiang'an District
City Xiamen
State/province Fujian
ZIP/Postal code 361002
Country China
Platform ID GPL21290
Series (2)
GSE96877 Methylation of Transcription Factor YY2 Regulates its Transcriptional Activity and Cell Proliferation
GSE96878 Methylation of Transcription Factor YY2 Regulates its Transcriptional Activity and Cell Proliferation
BioSample SAMN06624497
SRA SRX2660372

Supplementary file Size Download File type/resource
GSM2545498_Hela_YY2_KO_RNA-Seq.minusStrand.bigWig 58.3 Mb (ftp)(http) BIGWIG
GSM2545498_Hela_YY2_KO_RNA-Seq.plusStrand.bigWig 92.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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