|
| Status |
Public on Aug 29, 2012 |
| Title |
H4K20me3_untreated_NB4_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
NB4 cells (leukemic), untreated, H4K20me3 ChIP-Seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NB4
cell type: leukemic cells
treatment: none
chip antibody: anti-H4K20me3
antibody vendor: Upstate
antibody catalog #: 07-463
antibody lot: 24475
|
| Treatment protocol |
Leukemic cells (NB4) were treated with ATRA for 48 hours.
|
| Growth protocol |
Leukemic cells NB4 and SKNO-1 were cultured in normal cell culture containing 10% serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For NA-seq, isolated nuclei from different AML leukemic cells were treated for a very short time with Nlalll or Hpall restriction enzymes. Purified DNA was further shortened using Sau3A1 enzyme (Gargiulo et al. 2009 (PMID 19289091)). Size-selected library was sequenced from the respective restriction enzyme side. ChIP-seq was performed as before (Martens et al. 2010 (PMID 20159609)).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
SS14
Chromatin IP against H4K20me3 (Upstate).
|
| Data processing |
Reads (32 bp) were aligned to the human (Homo sapiens) reference genome (hg18, NCBI Build 36) using the GERALD (Eland) application from the Casava 1.7 tool provided by Illumina. Sequenced tags were extended back to reconstitute the restriction enzyme sites. Those reads not starting with the respective enzyme site were filtered out. The Fisher test was applied to call accessible regions. All of the bed files contain hg18 chromosomal coordinates of the tags (first three columns are chromosome, start, end). For NA-seq, wiggle files were generated using Fseq (Boyle et al. 2008). Wiggle files for ChIP-seq data were produced as before (Martens et al. 2010).
|
| |
|
| Submission date |
Jun 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
|
| Phone |
+31-24-3610520
|
| Organization name |
Radboud University
|
| Department |
Department of Molecular Biology (274)
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE30254 |
Chromatin accessibility, p300 and histone acetylation define PML-RARalpha- and AML1-ETO-binding sites |
|
| Relations |
| SRA |
SRX080050 |
| BioSample |
SAMN00631099 |
