|
| Status |
Public on Sep 15, 2022 |
| Title |
ATACseq_BT869_DMSO_48h |
| Sample type |
SRA |
| |
|
| Source name |
BT890
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT890
cell type: H3.3K27M-glioma
genotype: wildtype
treatment: DMSO
time: 48h
|
| Growth protocol |
BT869 cells were grown as neurospheres in tumor stem media base supplemented with B27 minus vitamin A (Thermo Fisher Scientific), human growth factors (EGF, FGF, PDGF-AA, PDGF-BB [Shenandoah Biotechnology]) and heparin (Stemcell Technologies) in ultra-low attachment flasks in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
40,000-50,000 live cells were sorted by FACS and lysed in 0.1% NP40 (Sigma/Roche 11332473001), 0.1% Tween-20 (Sigma/Roche 11332465001), and 0.01% digitonin (Promega, G9441), followed by tagmentation with 100 nM Tn5 transposase (Illumina, 15027865) for 30 min at 37 °C.
Tagmented DNA was purified using the MinElute PCR Cleanup kit (Qiagen) and PCR amplified using NEBNext-Fidelity 2X PCR Master Mix (NEB M0541S) and primers containing Illumina adapter sequences. Final library was purified by MinElute PCR Cleanup kit (Qiagen). Libraries were prepared and sequenced in two technical replicates on a Nextseq 500 sequencer (Illumina) using Nextseq High Output Cartridge kits by paired-end reads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw fastq reads were trimmed of adapters and aligned using Bowtie2 version 2.4.2. PCR duplicates were removed.
Chromatin accessibility peaks were called using MACS2 using custom parameters for ATAC-seq (–nomodel –nolambda –call-summits).
A signal track in .bdg form was emitted from the peak calling function that was subsequently converted into a .bigwig for visualization with the —SPMR flag.
To establish a uniform feature set, we used all 1 bp summits from the MACS2 peak calls per population and expanded these to uniform 500 bp.
Summits overlapping the same window were iteratively centered at the summit with the strongest signal (measured by -log10 FDR) until all summits were accounted. A peak x sample fragment counts matrix was completed using the getCounts function in chromVAR.
Assembly: hg19
Supplementary files format and content: bigwig in hg38
Supplementary files format and content: ATAC_500bp.counts.tsv - count matrix for all samples
|
| |
|
| Submission date |
Sep 04, 2022 |
| Last update date |
Sep 15, 2022 |
| Contact name |
Joana Graca Marques |
| E-mail(s) |
joanagracamarques@gmail.com
|
| Phone |
8572506823
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
360 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE212679 |
BAF complex maintains glioma stem cells in pediatric H3K27M-glioma [ATAC-seq] |
| GSE212786 |
BAF complex maintains glioma stem cells in pediatric H3K27M-glioma |
|
| Relations |
| BioSample |
SAMN30671057 |
| SRA |
SRX17423037 |
