|
| Status |
Public on Mar 28, 2018 |
| Title |
RNAPII-1hour |
| Sample type |
SRA |
| |
|
| Source name |
Human Endothlial cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary Human Umbilical Vein Endothelial Cells
passage: P3-6
antibody: RNAPII, Millipore
agent: VEGF
time point: 1hour
|
| Treatment protocol |
50ng/ml VEGFa was used to treat serum-starved HUVEC cells. For modified RNA experiments, 0.5ug/ml modified RNA expressing GFP and ETS1 was used. For siRNA experiment, 10ng/ml siRNA was used.
|
| Growth protocol |
Primary HUVEC cells purchased from Lonza within 3-6 passages were grown in EBM2+1% FBS or EGM2 medium (Lonza)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChiP-seq: Chromatin DNA was extracted from sonicated nuclei and further selectively accumulated by ChiP-specific antibody. RNA-seq: total RNA were purified by Qiagen RNeasy column.
Illumina multiplex library protocol for ChiP-seq and mRNA seq of VEGF stimualtion is as described (Bing Zhang, et al. , 2013,Genome Res. 2013 Jun;23(6):917-27); Spike-in mRNA-seq protocol followed ScriptSeq v2 RNA-seq kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAPII ChIP-seq after VEGF stimulation for 1hour
|
| Data processing |
ChIP-seq reads were aligned to the hg19 human genome assembly using bowtie2 with the following configurations: -p 1
ChiP-seq Peaks were called using MACS with the following setting: -f BAM -g 2.45e9, and then peaks fall inside the blacklist of ChIP-seq regions were trimmed.
The reads density was calculated using Homer and displayed in tag heat map using JAVA Tree.
RNA-seq reads were aligned to the hg19 genome assembly using tophat2.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell, Cole, et al. , Nature protocols 7.3 (2012): 562-578. In short, cufflinks was used for transcript assembly supplying a set of gene model annotation from GENCODE 19, cuffmerge for assemblies merge, cuffdiff for differnetial analysis and CummeRbund for the following analysis.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm, peaks.bed
|
| |
|
| Submission date |
Jan 25, 2018 |
| Last update date |
Sep 25, 2018 |
| Contact name |
bing zhang |
| E-mail(s) |
bingzhang@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
Shanghai Center for Systems Biomedicine
|
| Lab |
Bing Zhang Lab
|
| Street address |
800 Dong Chuan Road
|
| City |
Minhang |
| State/province |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE109625 |
Dynamic and integrated transcriptional code orchestrates the angiogenic response [Seq] |
| GSE109626 |
Dynamic and integrated transcriptional code orchestrates the angiogenic response |
|
| Relations |
| BioSample |
SAMN08395202 |
| SRA |
SRX3599289 |
