|
| Status |
Public on Jun 30, 2021 |
| Title |
ProLib12 Pro-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEL
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: AF9 knockdown
sample type: ProLib12
|
| Treatment protocol |
RNAi experiments were performed as previously described (Yu et al. Science 2015)
|
| Growth protocol |
HEL, CCRF-CEM, THP1, MOLM-13, and iMA9 cells were grown in RPMI-1640 + 10% FBS.
SEM cells were grown in IMDM + 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP experiments and RNA extraction were performed as previously described (Yu et al. Science 2015) .
Pro-seq experiments were performed as previouly described (Kwak et al. Science 2013)
ChIP-seq and RNA-seq libraries were constructed as previously described (Yu et al. Science 2015) .
Pro-seq libraries were constructed as previouly described (Kwak et al. Science 2013)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ProLib12
|
| Data processing |
ChIP-seq and RNA-seq data were mapped to human genome using BWA.
Pro-seq data were mapped to human genome using Bowtie.
Bedgraph files of ChIP-seq data were generated using Homer.
For the calculation of percentage of CpG island-associated peaks, ChIP-seq peaks are called by ChIPseeqer (Giannopoulou and Elemento, 2011).
Average gene plots of Pro-seq data were generated using Homer.
Genome_build: hg19
Supplementary_files_format_and_content: peaks for ChIP-Seq, RPKM normalized data for RNA-Seq, peaks data for PRO-Seq
|
| |
|
| Submission date |
Jul 07, 2016 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Gang Wei |
| E-mail(s) |
gwei@fudan.edu.cn
|
| Phone |
+862151630626
|
| Organization name |
Fudan University
|
| Street address |
No 2005, Songhu Rd, Yangpu District
|
| City |
Shanghai |
| State/province |
Select a State or Province |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE84157 |
Major MLL fusion partners regulate promoter-proximal pausing and release of RNA polymerase II |
|
| Relations |
| BioSample |
SAMN05364442 |
| SRA |
SRX1902786 |
