|
| Status |
Public on Jul 02, 2021 |
| Title |
MDA_INPUT_rep1 [m6A-seq] |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: None
cell culture: DMEM + 10% FBS
|
| Growth protocol |
Standard
|
| Extracted molecule |
total RNA |
| Extraction protocol |
250 ug RNA was phenol-chloroform extracted, rRNA depleted, and fragmented to ~100 nt. 1 ug fragmented RNA was saved as input and the rest was immunoprecipitated. RNA was precipitated and libraries were prepared with TruSeq Stranded Total RNA Preparation Kit according to manufacturer’s instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
macs2_mda_filtered.bed
|
| Data processing |
Library strategy: m6A-seq
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. Read densities were calculated to identify m6A peaks using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs).
|
| |
|
| Submission date |
Sep 11, 2019 |
| Last update date |
Jul 03, 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 |
SAMN12727121 |
| SRA |
SRX6830228 |
