|
| Status |
Public on Sep 08, 2016 |
| Title |
SH-SY5Y-MYCN-OFF H3K4me3_ChIP_seq |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y-MYCN-OFF
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neuroblastoma cell line with stable tet-inducible MYCN, minus tet
chip antibody: H3K4me3
chip antibody catalog/vender: ab8580 (Abcam, Cambridge, UK)
|
| Treatment protocol |
For modulation of MYCN levels, stable neuroblastoma cell models were used where MYCN can be either up- or downregulated upon addition of 1µg/ml tetracycline (SH-SY5Y-MYCN and IMR5-75-shMYCN, respectively)
|
| Growth protocol |
Cells were grown in RPMI medium (10%FCS) under standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies. Antibodies against H3K4me1 (ab8895, Abcam, Cambridge, UK), H3K27ac (ab4729), H3K4me3 (ab8580, Abcam) and H3K27me3 (ab6002, Abcam) were used for precipitation.
Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, US) according to the manufacturer’s protocol. Libraries were sequenced (50 bases single-end) on the Illumina sequencing platform (German Cancer Research Center Core facility).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq single-end reads were aligned to the hg19 genome using Bowtie and only uniquely aligned reads were kept.
The HOMER tool suite (version 4.6) was used for H3K27me3 bedgraph file generation.
H3K4me1, H3K27ac and H3K4me3 peaks were called using the MACS 1.4 tool using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files are generated by HOMER.
|
| |
|
| Submission date |
Apr 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunxuan Shao |
| E-mail(s) |
c.shao@Dkfz-Heidelberg.de
|
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE80197 |
ChIP-seq-based analysis of i) K27me3 promoter coverage and ii) enhancer elements in neuroblastoma cell lines |
|
| Relations |
| BioSample |
SAMN04692567 |
| SRA |
SRX1694149 |
