|
| Status |
Public on Oct 25, 2021 |
| Title |
BE2C_DMSO_IgG_MWZ8376 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: BE2C
chip antibody: IgG
antibody manu.: Proteintech
antibody catalog: 30000-0-AP
antibody lot: 22000001
agent: DMSO
|
| Growth protocol |
Cells were grown in T-75 flasks in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 12 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Purified DNA was prepared for sequencing using to the Swift 2S automated library preparation kit according to the manufacturers protocol.
Chromatin coupled primary antibodies in situ were retrieved with Cutana ProteinA/G-Mnase (Epicypher) according to the manufacturers protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: CUT&RUN-Seq
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: bigWig files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment.
|
| |
|
| Submission date |
Mar 25, 2021 |
| Last update date |
Oct 25, 2021 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE155002 |
Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN |
| GSE169616 |
Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN (CUT&RUN-Seq) |
|
| Relations |
| BioSample |
SAMN18490625 |
| SRA |
SRX10442782 |
