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Sample GSM2026219 Query DataSets for GSM2026219
Status Public on Jan 03, 2017
Title KLF-4 ChIP-Seq
Sample type SRA
 
Source name Bone Marrow
Organism Mus musculus
Characteristics tissue: Bone Marrow
genotype/variation: KLF-4 KO
strain: Klf4flox/flox vav-Cre in C57BL/6 background.
chip antibody: KLF4
Treatment protocol na
Growth protocol na
Extracted molecule genomic DNA
Extraction protocol Sorted cells were fixed and then genomic DNA was extracted and sheared. DNA was reverse crosslinked after KLF4 antibody pulldown and was subjected to seuqencing.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description Klf4flox/flox vav-Cre in C57BL/6 background.
Data processing Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (v0.6.1, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7. --- or e.g.: Peak calling was done with the SICER script (SICER v1.1; FDR 1E-10, gap=600).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: wig
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks
 
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Toni-Ann Mistretta
E-mail(s) toniannm@bcm.edu
Organization name Baylor College of Medicine
Department Pathology
Lab TCH Pathology\TCMC
Street address 1 Baylor Plaza, BCM 315
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL17021
Series (2)
GSE76473 Inactivation of KLF4 in T cell acute lymphoblastic leukemia promotes the expansion of leukemia cells by activating the Map2k7/Jnk pathway. [ChIP-Seq]
GSE76474 nactivation of KLF4 in T cell acute lymphoblastic leukemia promotes the expansion of leukemia cells by activating the Map2k7/Jnk pathway.
Relations
BioSample SAMN04382566
SRA SRX1513505

Supplementary file Size Download File type/resource
GSM2026219_1_TALL-BM_prep3_KLF4_i4_uniqnorm_signal.wig.gz 122.1 Mb (ftp)(http) WIG
GSM2026219_2079BCM_KLF4_ucsctracks.bed.gz 154.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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