 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 15, 2015 |
| Title |
EtOH-siNCAPD3_GROseq |
| Sample type |
SRA |
| |
|
| Source name |
beast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
treatment: cells were transfected with siNCAPD3, after 1hr treatment with ethanol
|
| Treatment protocol |
Before experiment, the cells were changed to deficient MEM plus 5% charcoal treated phenol red free medium to culture for 3 days, followed by treatemnt of either 100nM 17-?-estrodial or ethanol for 1hr.
|
| Growth protocol |
MCF7 obtained from ATCC were cultured in ?-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MCF7 cells were subjected to nuclear run-on for 5minutes at 30 degree with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature; Li et al., 2013 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
nascent RNA
cells were transfected with siNCAPD3, after 1hr treatment with ethanol, subjected to GRO-seq,
library strategy: GRO-seq
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
|
| |
|
| Submission date |
Oct 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Qi Ma |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Dr,
|
| City |
San Diego |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE62228 |
Interphase condensins regulate ligand-depedent enhancer activation (GRO-seq) |
| GSE62229 |
Interphase condensins regulate ligand-depedent enhancer activation |
|
| Relations |
| BioSample |
SAMN03103659 |
| SRA |
SRX730497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1523197_Groseq-siNCAPD3-MCF7-EtoH-minusstrand.bigWig |
30.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM1523197_Groseq-siNCAPD3-MCF7-EtoH-plusstrand.bigWig |
32.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
