|
| Status |
Public on Jan 29, 2018 |
| Title |
SHEP21_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SHEP-21N
cell type: Neuroblastoma
growth condition: 10% Tet-Free FBS, RPMI
barcode: CCTCTCTG
|
| Treatment protocol |
N/A
|
| 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).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A total of 50,000 cells were lysed, subject to transposition reaction using transposase enzyme (Illumina Nextera DNA preparation kit, cat#: FC-121-1030), and purified using Qiagen MinElute PCR purification kit.
Library amplification was performed using custom Nextera primers and the number of total cycles determined by running a SYBR-dye based qPCR reaction and calucalting the cycle number that corresponds to ¼ the maximum. Amplified libraries were purified using a Qiagen PCR purification kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC-seq of SHEP-21N, 0hr
|
| Data processing |
library strategy: ATAC-seq
Paired end reads were aligned to HG19 referenece genome using bowtie2 with the following parameters: --end-to-end --sensitive --no-unal --no-discordant --mm
Aligned bams were filtered and sorted using samtools by removing chrM, filtering against the ENCODE blacklist, and removing discordant reads.
Peaks were called using MACS1.4 with p-val =1e-9
Genome_build: hg19
Supplementary_files_format_and_content: Processed ATAC 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) |
| GSE80152 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [ATAC-seq] |
| GSE80154 |
Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma |
|
| Relations |
| BioSample |
SAMN04632519 |
| SRA |
SRX1690251 |
