|
| Status |
Public on Nov 11, 2014 |
| Title |
TGIF1_4OHT_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
c-kit+ bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: MLL-AF9 transformed cells
feature: Transduced with pMIG-TGIF1-ER
treatment: 4-OHT
chip antibody: TGIF (H-172) (Santa Cruz Biotechnology, catalog# sc-9084, lot# K2608)
|
| Treatment protocol |
For induction of TGIF1-ER, the cells were treated with 4-OHT for 20 hrs
|
| Growth protocol |
c-kit+ bone marrow cells were transformed using the fusion oncogene MLL-AF9. The MLL-AF9 cells were further transduced with an inducible pMIG-TGIF1-ER construct.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lystaes were sonicated to an avarge fragment length of 300bp
Precipitated DNA was mixed with E. Coli DNA up to 2ng and libraries were prepared using the NEB Next ChIP-seq library prep master mix for Illumina according to manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3
|
| Data processing |
All data was mapped with bowtie v. 0.12.7, using standard parameters
All data was converted into BigWig format and vizualized in the UCSC genome browser
Peaks were called with MACS, v. 1.4 with an IgG mock sample as control and following settings: Band width = 300, model fold = 10,30 p-value cutoff < 10-9.
Genome_build: mm9
Supplementary_files_format_and_content: Raw data files in fastq and processed files as bigwig and txt
|
| |
|
| Submission date |
Feb 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Porse |
| E-mail(s) |
bo.porse@finsenlab.dk
|
| Organization name |
Rigshospitalet
|
| Department |
Finsen Centre
|
| Lab |
Finsen laboratory
|
| Street address |
Ole Maaloesvej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE55287 |
TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemias |
|
| Relations |
| BioSample |
SAMN02650343 |
| SRA |
SRX475270 |
