|
Status |
Public on Jun 12, 2018 |
Title |
H3B5942.3nM.rep1 |
Sample type |
SRA |
|
|
Source name |
Ishikawa
|
Organism |
Homo sapiens |
Characteristics |
cell line: Ishikawa treatment: H3B5942 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 |
SAMN09394324 |
SRA |
SRX4193311 |