|
| Status |
Public on Jul 02, 2021 |
| Title |
MYC_HMEC_TAM_SMINPUT_rep1 [eCLIP-seq] |
| Sample type |
SRA |
| |
|
| Source name |
MYC-ER HMEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MYC-ER HMEC
treatment: 4-Hydroxytamoxifen
cell culture: Medium 171/ MEGS supplement
|
| Treatment protocol |
4-Hydroxytamoxifen at 15nM for 48 hours
|
| Growth protocol |
Standard
|
| Extracted molecule |
total RNA |
| Extraction protocol |
20M cells were UV-crosslinked, lysed and sonicated. RNA was fragmented and protein-RNA complexes were immunoprecipitated with a YTHDF2 antibody. Inputs (2% of lysate) were saved and run alongside IP samples. IP samples were stringently washed, and for all samples the RNA was dephosphorylated, followed by on-bead ligation of barcoded RNA adapters to the 3’ end. RNA-protein complexes were run on standard protein gels and transferred to nitrocellulose membranes where the RNA in the region 65 kDa – 140kDa was excised off the membrane and proteinase K treated. RNA was then reverse transcribed followed by treatment with ExoSAP-IT to remove excess oligonucleotides. Samples were cleaned up with Dynabeads MyOne Silane and subject to qPCR to determine the appropriate number of PCR cycles.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
MYC_HMEC_TAM_1-MYC_HMEC_TAM_2.idr.final.bed
|
| Data processing |
Library strategy: eCLIP-seq
Raw sequencing reads were trimmed for adapter sequences and barcode 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 eCLIP peaks.
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 |
SAMN12727092 |
| SRA |
SRX6830196 |
