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Status |
Public on Jan 03, 2017 |
Title |
KLF-4 ChIP-Seq |
Sample type |
SRA |
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Source name |
Bone Marrow
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Organism |
Mus musculus |
Characteristics |
tissue: Bone Marrow genotype/variation: KLF-4 KO strain: Klf4flox/flox vav-Cre in C57BL/6 background. chip antibody: KLF4
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Treatment protocol |
na
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Growth protocol |
na
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Description |
Klf4flox/flox vav-Cre in C57BL/6 background.
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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
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Submission date |
Jan 04, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Toni-Ann Mistretta |
E-mail(s) |
toniannm@bcm.edu
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Organization name |
Baylor College of Medicine
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Department |
Pathology
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Lab |
TCH Pathology\TCMC
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Street address |
1 Baylor Plaza, BCM 315
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City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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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. |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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