|
| Status |
Public on Oct 03, 2019 |
| Title |
dipg38.3-h3.3: SU-DIPG38 patient-derived DIPG culture |
| Sample type |
SRA |
| |
|
| Source name |
SU-DIPG38 patient-derived DIPG culture
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Diffuse intrinsic pontine glioma (DIPG)
antibody: H3.3 (Millipore #09-838)
|
| Growth protocol |
TSM base + EGF/FGF/PDGF-AA/PDGF-BB, see Grasso 2015
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are fixed with 1% FA. Following ChIP and washes, DNA is purified using PCI purification
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
cell culture ChIP-seq
SU-DIPG38 patient-derived DIPG culture
dipg38.3,dipg38.4
|
| Data processing |
ChIP-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Peaks were called using macs2 version 2.1.1.20160309 callpeak on full depth bam files over input controls. Broad peak calling was used for H3K27me3 and EED
genome build: hg19
processed data files format and content: RPM bigwig
|
| |
|
| Submission date |
Jun 16, 2019 |
| Last update date |
Oct 05, 2019 |
| Contact name |
Michelle Monje |
| E-mail(s) |
mmonje@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
265 Campus Drive, SIM1 G3035
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE126319 |
Variant and cell-context specific H3K27M reprogramming results in distinct enhancer architecture and oncogenic states |
|
| Relations |
| BioSample |
SAMN12070297 |
| SRA |
SRX6075156 |
