|
| Status |
Public on Jan 29, 2018 |
| Title |
SHEP21_24HR_INPUT_NOSPIKE_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SHEP-21N_Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SHEP-21N
cell type: neuroblastoma cell line
growth condition: 10% Tet-Free FBS, RPMI
treated with: 0.2 ug/mL DOX for 24HR
chip antibody: NA
chip antibody vendor: NA
chip antibody cat. #: NA
input: NA
barcode: CGATGTTT
|
| Treatment protocol |
Tet-Off MYCN shutdown was performed by addition of doxycycline (0.2μg/mL) to growth media
|
| Growth protocol |
SK-N-AS, SH-SY5Y, NGP, BE(2)-C, and KELLY cells were kindly provided by Dr. Kimberly Stegmaier (Dana Farber Cancer Institute) and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS. SHEP-21N cells were kindly provided by Dr. William Weiss (University of California, San Francisco) and cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech). Tet-Off MYCN shutdown was performed by addition of doxycycline (0.2μg/mL) to growth media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Input for SHEP21-N, 24hr (replicate 2)
|
| Data processing |
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format
|
| |
|
| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE80151 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [ChIP-seq] |
| GSE80154 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma |
|
| Relations |
| BioSample |
SAMN04632512 |
| SRA |
SRX1690221 |
