|
| Status |
Public on Apr 06, 2023 |
| Title |
MCF7△ESR1, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
cell line: MCF7
cell type: cancer
genotype: cancer
treatment: n/a
|
| Treatment protocol |
for all HCR samples
|
| Growth protocol |
all cancer cells were grown to 70-80% confluence in DMEM (Gibco) supplemented with 10% FBS (Hyclone) in 100 mm dishes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation from these cancer cells was performed using TRIzol™ Reagent (Invitrogen) and Rneasy kit (Qiagen) according to manufacturer’s protocol.
Libraries were generated using Truseq RNA stranded polyA (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
n/a
|
| Data processing |
RNA-seq
Reads were alighed to human genome assembly hg19 and processed using Bowtie2 and Tophat2.
Counts were generated using Cufflinks.
Assembly: GRCh37 (hg19)
Supplementary files format and content: counts.txt
ChIP-Seq reads were aligned to human genome assembly hg19 using bowtie 2.1.0 with default parameters.
Peaks were called by using HOMER v4.2 with "-style histone" to its input and default parameters.
Assembly: GRCh37 (hg19)
Supplementary files format and content: bedgraph
|
| |
|
| Submission date |
Oct 13, 2022 |
| Last update date |
Apr 06, 2023 |
| Contact name |
Zhaoyu Li |
| E-mail(s) |
zhaoyu.li@uwa.edu.au
|
| Organization name |
University of Western Australia
|
| Department |
School of Biomedical Sciences
|
| Street address |
QE II, M block, 225C
|
| City |
Perth |
| State/province |
Western Australia |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE215384 |
Estrogen receptor alpha targeting in liver cancer and breast cancer |
|
| Relations |
| BioSample |
SAMN31269247 |
| SRA |
SRX17877463 |
