 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 14, 2023 |
| Title |
MB099, G4, ATAC |
| Sample type |
SRA |
| |
|
| Source name |
medulloblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: medulloblastoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cryopreserved in DMSO. Nuclei were thawed, lysed, stained (Trypan Blue), counted (Countess, Invitrogen), and tagmented (1X Tagment DNA Buffer, Illumina). DNA was purified using DNeasy Blood & Tissue Kit (Qiagen), and quantified using NanoDrop 2000 (Thermo Scientific), and purified using the Nextera DNA Library Preparation Kit (Illumina).
Between 50,000 and 100,000 nuclei were used in library construction. DNA was amplified by PCR (8 cycles), size-selected for nucleosome-free fragments (175-250bp) by gel electrophoresis (2% agarose gel, Invitrogen), and purified using the QIAquick Gel Extraction Kit (Qiagen). A second PCR amplification (4 cycles) and purification (Agencourt AMPure XP beads, Beckman Coulter) was performed on the size-selected fragments. The final library was validated using a Fragment Analyzer™ instrument (Advanced Analytical) and the KAPA Library Quantification Kit for Illumina Sequencing Platforms.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ATAC-seq reads were trimmed on both ends using Trimmomatic v0.38, LEADING:15 TRAILING:15
ATAC-seq reads were aligned to the GRCh38 genome using bowtie v2.2.5 and deduplicated using Picard MarkDuplicates v2.18.27. Only primary alignments were retained.
Peaks were called using MACS2 v2.1.2 with significance cutoff q<0.05.
Coverage tracks were generated by extending reads to 200bp and shifting by 100bp, then converting to bigwig format using deeptools v3.5.1 bamCoverage.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak
|
| |
|
| Submission date |
Aug 14, 2023 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Lukas Chavez |
| E-mail(s) |
lchavez@sbpdiscovery.org
|
| Phone |
(858)952-3775
|
| Organization name |
Sanford Burnham Prebys Medical Discovery Institute
|
| Department |
Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center
|
| Street address |
10901 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE240830 |
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastomas [ATAC-seq] |
| GSE240985 |
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastomas |
|
| Relations |
| BioSample |
SAMN36985199 |
| SRA |
SRX21362311 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7710214_MB099_peaks.narrowPeak.gz |
241.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM7710214_MB099_treat_pileup.bw |
203.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
