|
| Status |
Public on Jun 12, 2018 |
| Title |
Tamoxifen.3nM.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Ishikawa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Ishikawa
treatment: Tamoxifen
dosage: 3nM
|
| Treatment protocol |
Cells were treated with indicated compounds at 3nM and 30nM for 24 hours before collection.
|
| Growth protocol |
Ishikawa cell were cultured in DMEM supplemented with 5% CSS, trypsinized, washed with basal media (DMEM/F12 + 15 mM HEPES) 3 times for 5 minutes each. Cells were then seeded at 800,000 cells/well in basal medium in a 6-well plate. Compounds were added seven hours post plating.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected using Trizol extraction
Non-stranded polyA mRNA library constructed at BGI
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FASTQ file sequenced by Illumina HiSeqTM4000
After sequencing ,the raw reads were filtered.Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads
Transcript per million (TPM) were calculated using kallisto with default settings
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files generated by Kallisto with fields: gene_name: name of gene; length: length of the gene; eff_length: effective length of the gene; est_counts: estimated read count; tpm: transcript per million
|
| |
|
| Submission date |
Jun 11, 2018 |
| Last update date |
Jun 12, 2018 |
| Contact name |
Zhenhua Wu |
| E-mail(s) |
zhenhuawu75@gmail.com
|
| Phone |
6179592279
|
| Organization name |
H3 Biomedicine
|
| Street address |
300 Technology Square floor 5
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE115608 |
Transcriptional profiling of Ishikawa cells treated with H3B-5942, E2, or standard of care compounds |
| GSE115611 |
Discovery of Selective Estrogen Receptor Covalent Antagonists (SERCAs) for the treatment of ERa(WT) and ERa(MUT) breast cancer. |
|
| Relations |
| BioSample |
SAMN09394327 |
| SRA |
SRX4193308 |
