|
| Status |
Public on Jan 28, 2022 |
| Title |
DIPG4_DOX input |
| Sample type |
SRA |
| |
|
| Source name |
DIPG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SU-DIPG-IV
antibody: none
treatment: DOX
|
| Treatment protocol |
Cells were treated with doxycycline to induce shRNA expression
|
| Growth protocol |
Diffuse intrinsic pontine glioma cells (SU-DIPG-IV) were lenti-virally infected with doxycyline inducible shRNA constructs targeting MAT2A followed by antibiotic selection
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitations (ChIP), using H3K36me3 antibodies, were carried out using the Diagenode SX-8G IP-Star Compact (Diagenode automated Ideal ChIP-seq Kit).
KAPA Hyper prep kit (Cat# KK8504, KAPA Biosystems) and KAPA Dual-indexed adapter kit (Cat# KK8722 KAPA Biosystems) were used to construct the ChIP-RX DNA library for sequencing on an Illumina platform following the manufacturer’s instructions. A
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed using trimGalore and quality was assessed using FastQC
The resulting reads were aligned to hg19 using Bowtie2 (v2.3.5.1)
Spike-in normalization was performed by aligning the reads to the dm6 genome.
Epic2 was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bigwig files
|
| |
|
| Submission date |
Aug 05, 2021 |
| Last update date |
Jan 28, 2022 |
| Contact name |
Stephen C Mack |
| E-mail(s) |
stephen.mack@stjude.org
|
| Organization name |
St. Jude Children’s Research Hospital
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE160006 |
MAT2A and methionine dependency are indispensible for H3K27M mutant gliomas. |
|
| Relations |
| BioSample |
SAMN20593746 |
| SRA |
SRX11657260 |
