|
| Status |
Public on Jul 02, 2021 |
| Title |
MYC_HMEC_SHY2_rep1 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
MYC-ER HMEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MYC-ER HMEC
cell culture: Medium 171/ MEGS supplement
|
| Treatment protocol |
4-Hydroxytamoxifen at 15nM for 48 hours
|
| Growth protocol |
Standard.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using Trizol and Zymo's Directzol RNA extraction kit.
1ug total RNA was rRNA depleted and processed using the TruSeq Stranded Total RNA Preparation Kit by Illumina according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file: featurecounts.txt
MYC_HMEC_R1_SHY-2_1_S5_L007
|
| Data processing |
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner.
Genome_build: hg19
Supplementary_files_format_and_content: Featurecounts
|
| |
|
| Submission date |
Sep 18, 2020 |
| Last update date |
Jul 02, 2021 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE137258 |
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer |
|
| Relations |
| BioSample |
SAMN16207176 |
| SRA |
SRX9149655 |
