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Sample GSM1954318 Query DataSets for GSM1954318
Status Public on Feb 28, 2017
Title STATegra Ikaros cells 0h Batch12
Sample type SRA
 
Source name pre-B lymphocyte
Organism Mus musculus
Characteristics transfection: inducible Ikaros
time: 0h
#replicate: 5
#batch: 12
treatment: 4-OHT
dose: 0.5 uM
cell line: B3
cell type: pre-B lymphocyte
Treatment protocol Cells containing inducible Ikaros were generated by transducing mouse pre-B cell line B3 with mouse stem cell virus (MSCV) retroviral vectors encoding a fusion protein of haemagglutinin-tagged wild type Ikaros (HA-Ikaros) and the estrogen receptor hormone-binding domain (ERt2), followed by an internal ribosomal entry site (IRES) and GFP. B3 cells containing inducible Ikaros (HA-Ikaros-ERt2-IRES-GFP) were plated at a density of 0.5 million cells/ml in IMDM medium containing 10% FCS and 1% penicillin-streptomycin. 0.5uM 4 hydroxy-tamoxifen was added to the cells 2h before collection.
Extracted molecule genomic DNA
Extraction protocol B3 cells containing inducible Ikaros were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Time point samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80. Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80.
DNase-seq libraries were generatedas previously described (Myers protocol: http://myers.hudsonalpha.org/documents/Myers%20Lab%20Sequencing%20Library%20Protocol%20061508.pdf). Libraries were sequenced as 43bp paired-end on the NextSeq 500 Illumina platform. DNase-seq libraries were sequenced to a minimum depth of ~20 million reads per each biological replicate.
 
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina NextSeq 500
 
Description corresponding processed data file header: Ik0h_rep5
0h after Taxomifen induction in Ikaros/ERt2 cells
R5
Data processing Data were aligned to the mm10 reference using Bowtie
Capture narrow and broad chromatin elements using HOMER
Sort and merge with Bedtools software
Quantitate read counts over regions using coverageBed options (Bedtools)
Region counts were normalized with both RPKM and TMM methods
Unknown sources of variation were removed by using ARSyN method (Batch correction)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing DHS regions for each Sample (matrix) formatted as chr_start_end (i.e. Chromosome number, Start position and End position).
 
Submission date Nov 25, 2015
Last update date May 15, 2019
Contact name Ana Conesa
E-mail(s) info@stategra.eu
Organization name Centro de Investigaciones Príncipe Felipe (CIPF)
Department Computational Genomics Program
Lab Genomics and Gene Expression Lab
Street address C/ Eduardo Primo Yúfera 3
City Valencia
State/province Valencia
ZIP/Postal code 46012
Country Spain
 
Platform ID GPL19057
Series (2)
GSE75390 DNase-seq analysis of B3 pre-B cell line from STATegra Project
GSE75395 Omics analyses of B3 pre-B cell line from STATegra Project
Relations
BioSample SAMN04295059
SRA SRX1452093

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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