|
| 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 |
