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| Status |
Public on Jul 15, 2015 |
| Title |
E2-siNCAPD3_GROseq |
| Sample type |
SRA |
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| Source name |
beast cancer cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
treatment: cells were transfected with siNCAPD3, after 1hr treatment with 100nM E2
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| 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.
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| Growth protocol |
MCF7 obtained from ATCC were cultured in ?-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
nascent RNA
cells were transfected with siNCAPD3, after 1hr treatment with 100nM E2, subjected to GRO-seq,
library strategy: GRO-seq
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| 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
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| Submission date |
Oct 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Qi Ma |
| E-mail(s) |
[email protected]
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| Organization name |
UCSD
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| Street address |
9500 Gilman Dr,
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| City |
San Diego |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE62228 |
Interphase condensins regulate ligand-depedent enhancer activation (GRO-seq) |
| GSE62229 |
Interphase condensins regulate ligand-depedent enhancer activation |
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| Relations |
| BioSample |
SAMN03103660 |
| SRA |
SRX730498 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1523198_Groseq-siNCAPD3-MCF7-E2-minusstrand.bigWig |
74.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM1523198_Groseq-siNCAPD3-MCF7-E2-plusstrand.bigWig |
79.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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