|
| Status |
Public on Oct 01, 2022 |
| Title |
T47D 4uM MI503 24h H3K4me3 C&R BioRep 2 |
| Sample type |
SRA |
| |
|
| Source name |
not applicable
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: not applicable
cell line: T47D
cell type: Hormone receptor + breast cancer
genotype: WT
treatment: 4uM MI503 24h
|
| Treatment protocol |
T47D were treated with 4uM MI503 or DMSO for 24h
|
| Growth protocol |
T47D were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were detatched using accutase
Libraries were constructed following the manufacturer's protocol (Epicypher). 5ng of DNA was used as starting material for library preparation. Following the Epicypher protocol, libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were confirmed to be 200-500bp in length via bioanalyzer.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed from 3' end until the PHRED quality score was >33 using Trim Galore version 0.6.7. All read with PHRED quality score <20 were discarded.
Reads were aligned to the GRCh38.p14 genome using Bowtie2 version 2.2.5. All reads that did not have concordant alignment overlap between both paired end sequences were removed
Aligned sequences were sorted using samtools version 1.6 and duplicate reads were removed using the Picard Tools version 2.27.4.
To generate coverage plots, deeptools was used to normalize the bam files using the e. coli abundance which produced bigwig and bedGraph files.
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Sep 28, 2022 |
| Last update date |
Oct 02, 2022 |
| Contact name |
Jennifer Marie Spangle |
| E-mail(s) |
jennifer.spangle@emory.edu
|
| Organization name |
Emory University
|
| Street address |
1365C Clifton Rd NE
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30311 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE214329 |
Targeting MLL methyltransferases enhance the anti-tumor effects of PI3K inhibition in hormone receptor-positive breast cancer [Cut & Run] |
| GSE214333 |
Targeting MLL methyltransferases enhance the anti-tumor effects of PI3K inhibition in hormone receptor-positive breast cancer |
|
| Relations |
| BioSample |
SAMN31062417 |
| SRA |
SRX17732089 |
