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| Status |
Public on Mar 24, 2017 |
| Title |
MO1043_ICN1_HA_H3K27Ac_b |
| Sample type |
SRA |
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| Source name |
CLL cell line MO1043
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| Organism |
Homo sapiens |
| Characteristics |
antibody: Histone H3K27ac antibody Active Motif, cat#39133
tissue: Chronic Lymphocytic Leukemia (CLL) cell line
cell line: MO1043
conditions: MO1043 CLL cells induced to express ICN1-HA
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| Treatment protocol |
CLL cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature and quenched by the addition of glycine to a final concentration of 0.125M.
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| Growth protocol |
MO1043-ICN1-HA cells were induced to express ICN1-HA with 1 ug/ml of Doxycycline for 36 hours; primary CLL cells were thawed in Iscove's Modified Dulbecco's Medium (Life Technologies) supplemented with 20% fetal bovine serum (FBS) (Sigma-Aldrich), penicillin (100 U/ml) and streptomycin (100 μg/ml) and immediately crosslinked.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked chromatin was fragmented by sonication with the Bioruptor sonicator (Diagenode) to achieve fragment sizes of ~200–500 base pairs using the following sonication buffer: 10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine.
ChIP-seq libraries were constructed starting from 4ng of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 101 bp reads.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10-5 for NOTCH1, and 10-15 for H3K4me1, H3K4me3 and H3K27Ac.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively. The fourth column is the maximum peak height normalized per million mapped reads in each library.
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| Submission date |
Dec 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Riccardo Dalla-Favera |
| E-mail(s) |
rd10@cumc.columbia.edu
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| Organization name |
Columbia University
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| Street address |
1130 St Nicholas Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE92701 |
Identification of NOTCH1 bound genes in chronic lymphocytic leukaemia (CLL) cells |
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| Relations |
| BioSample |
SAMN06172565 |
| SRA |
SRX2438587 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2435531_MO1043_ICN1_HA_H3K27Ac_b_RG019_peaks.bed.gz |
446.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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