|
| Status |
Public on May 23, 2024 |
| Title |
mdRCC2970, MeDIP, MeDIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Plasma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Plasma
histology: Epitehlioid
antibody: MeDIP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was fixed by 2mmol/L disuccinimidyl glutarate (DSG) for 10 minutes followed by 1% formaldehyde for 10 minutes, and quenched with glycine. Chromatin was sheared using the Covaris E220Ultrasonicator.
ChIP-seq libraries were generated from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit from TakaraBio. Libraries were sequenced using 150-base paired-end reads on an Illuminaplatform.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Data processing |
Paired-end sequencing reads were trimmed and aligned to the hg19 human reference genome using Burrows–Wheeler Aligner version 0.7.1740.
Non-uniquely mapping and duplicate reads were discarded. Peak calling was performed using MACS version 2.1.1.2014061641 with a q value (false discovery rate (FDR)) threshold of 0.01.
Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Fragment locations were inferred from mapped read pairs in BAM files and converted to BED format using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set.
bigWig files were generated using the genomicRanges R package.
circulating tumor DNA fraction in plasma samples was estimating using LP-WGS with ichorCNA.
Assembly: hg19
Supplementary files format and content: BigWig, narrowPeak (except for Input)
|
| |
|
| Submission date |
May 22, 2024 |
| Last update date |
May 23, 2024 |
| Contact name |
Karl Semaan |
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
Brookline Ave 450
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE268155 |
Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma |
|
| Relations |
| BioSample |
SAMN41495022 |
| SRA |
SRX24656384 |
