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| Status |
Public on Jan 29, 2018 |
| Title |
BE2C_ATAC |
| Sample type |
SRA |
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| Source name |
Neuroblastoma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: BE(2)-C
cell type: Neuroblastoma
growth condition: 10% FBS, DMEM
barcode: TCGCCTTA
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| Treatment protocol |
N/A
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| 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).
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATAC-seq of BE(2)-C
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| 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
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| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
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| Lab |
Bradner Lab
|
| Street address |
450 Brookline
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN04632521 |
| SRA |
SRX1690248 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2113544_BE2C_ATAC.wig.gz |
54.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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