|
| Status |
Public on Jun 20, 2024 |
| Title |
MeDIP-MGH1506-denovoSCLC |
| Sample type |
SRA |
| |
|
| Source name |
PDX
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PDX
sample id_(de-identified_id_for_the_originating_pdx): MGH1506
disease state: De novo SCLC
assay: MeDIP-seq
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp Circulating Nucleic Acid Kit (Qiagen)
KAPA HyperPrep Kit (KAPA Biosystems)
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA mem.
For peak calling MACS2 was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using MACS2 using the CHIPS pipeline
|
| |
|
| Submission date |
Jun 13, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Jacob Eli Berchuck |
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE269746 |
Detecting small cell transformation in patients with advanced EGFR mutant lung adenocarcinoma through epigenomic cfDNA profiling |
|
| Relations |
| BioSample |
SAMN41813826 |
| SRA |
SRX25166593 |
