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Sample GSM1333565 Query DataSets for GSM1333565
Status Public on Nov 11, 2014
Title IgG
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: none
chip antibody: IgG (Sigma, catalog# I8140, lot# 115k7551)
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 Genome Analyzer IIx
 
Description Sample 9
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 GPL11002
Series (1)
GSE55287 TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemias
Relations
BioSample SAMN02650340
SRA SRX475276

Supplementary file Size Download File type/resource
GSM1333565_IgG.bw 247.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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