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Sample GSM2545496 Query DataSets for GSM2545496
Status Public on Feb 13, 2018
Title Hela_LSD1_KO_RNA-Seq
Sample type SRA
 
Source name HeLa
Organism Homo sapiens
Characteristics cell line: Hela
tag: LSD1_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 (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) 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
Relations
BioSample SAMN06624495
SRA SRX2660370

Supplementary file Size Download File type/resource
GSM2545496_Hela_LSD1_KO_RNA-Seq.minusStrand.bigWig 50.6 Mb (ftp)(http) BIGWIG
GSM2545496_Hela_LSD1_KO_RNA-Seq.plusStrand.bigWig 75.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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