|
| Status |
Public on Feb 16, 2021 |
| Title |
6658_0.01ng of synthetic DNA in 10ng of AML sample: Patient 5 |
| Sample type |
SRA |
| |
|
| Source name |
AML plasma + synthetic spike-in DNA
|
| Organism |
Homo sapiens |
| Characteristics |
experiment: Assessing batch effects
tissue: AML - plasma
treatment: output
molecule subtype: cfDNA
|
| Growth protocol |
HCT116 cells were grown with McCoy Media supplemented with 10% FBS and 1% Penicillin/Streptomycin in 75cm2 flasks at 37˚C and 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA of the collected cells were extracted using Thermofisher PureLink® Genomic DNA Kit and eluted in EB buffer, prior to being sheared using a Covaris M220 shearing instrument to a target size of 150 bp.The sheared product was size selected via AMPure XP to an average size of ~180bp. Synthetic spike-in control DNA waws obtained through commercial means (IDT)
The libraries were prepared using the Kapa Hyper Prep Kit using IDT xGen Stubby adapters.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AML plasma + synthetic spike-in DNA
Multiple identifiers for this sample are: 6658, A64, A64_DT, Sample 1, Princess Margaret Cancer Biobank ID 150197
|
| Data processing |
Library strategy: cfMeDIP-seq
Adapters were trimmed using fastp v. 0.11.5
Alignment to our synthetic fragments and subsequently to hg38 was performed using BowTie2 v. 2.4.5.
Genome_build: hg38 pr alignment to synthetic fragment sequence
Supplementary_files_format_and_content: bed
The column headers for the bed files are:
1. read 1 chromosome or scaffold
2. read 1 start position
3. read 1 end position
4. read 2 chromosome or scaffold
5. read 2 start position
6. read 2 end position
7. strand
8. strand
9. read count
|
| |
|
| Submission date |
Feb 05, 2021 |
| Last update date |
Jul 29, 2022 |
| Contact name |
Michael Hoffman |
| E-mail(s) |
[email protected]
|
| Organization name |
Princess Margaret Cancer Centre
|
| Department |
Research
|
| Lab |
Hoffman lab
|
| Street address |
101 College St.
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE166259 |
Synthetic spike-in controls enable sensitive and reproducible cell-free methylome interrogation |
|
| Relations |
| BioSample |
SAMN17813896 |
