|
| Status |
Public on Jun 23, 2015 |
| Title |
ChIP RUNX1 |
| Sample type |
SRA |
| |
|
| Source name |
TSU-1621-MT_ChIP RUNX1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TSU-1621-MT
antibody target: RUNX1
chip antibody vendor: Abcam
chip antibody cat. #: ab23980
|
| Treatment protocol |
ChIP-seq: ChIP seq experiments of ATRA treated cells were performed in TSU-1621-MT cells treated with 1 uM ATRA for 24 hours.
For shRNA from RNA-seq experiments: TSU-1621-MT FUS-ERG cells were grown in the absence of tetracycline for induction of shRNA targeting FUS-ERG. shRNA expression was induced in TSU-1621-MT using dox.
|
| Growth protocol |
TSU-1621-MT cells were cultured in RPMI 1640 supplemented with 10% FCS, 10 ng/ml of G-CSF and incubated at 37 °C and 5% CO2 (Shikami et al., 1999).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sonicated and used for ChIP seq using specific antibodies.
RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.
ChIP seq and RNA-seq libraries were prepared according to Illumina's standard protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
C35TNACXX_6_4983
|
| Data processing |
Basecalls performed using CASAVA
Reads were aligned to the hg18 genome assembly BWA/ELAND
Peaks were called using MACS2 on settings: p value = 10-6
Genome_build: All ChIP-seq tracks were mapped to genome build HG18
Supplementary_files_format_and_content: wig files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps
|
| |
|
| Submission date |
Aug 18, 2014 |
| Last update date |
Nov 11, 2021 |
| Contact name |
Joost Martens |
| E-mail(s) |
j.martens@science.ru.nl
|
| Phone |
0243780645
|
| Organization name |
Radboud University
|
| Department |
RIMLS
|
| Lab |
Molecular Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| State/province |
Nederland |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE60477 |
The oncofusion protein FUS-ERG targets key hematopoietic regulators and modulates the all-trans retinoic acid signaling pathway in t(16;21) acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN02996885 |
| SRA |
SRX682384 |
