|
Status |
Public on Feb 13, 2018 |
Title |
Hela_SET9_KO_RNA-Seq |
Sample type |
SRA |
|
|
Source name |
HeLa
|
Organism |
Homo sapiens |
Characteristics |
cell line: Hela tag: SET9_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 |
SAMN06624498 |
SRA |
SRX2660371 |