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| Status |
Public on Feb 08, 2015 |
| Title |
input_1 for BCL6 and E2A |
| Sample type |
SRA |
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| Source name |
ICN12 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: primary pre-B acute lymphomablastic leukemia
chip antibody: NA
chip antibody host, amount, catelog number and provider: Rabbit, 2ug, 2729, Cell Signaling
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| Treatment protocol |
ICN12 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.
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| Growth protocol |
Leukemia cells from bone marrow biopsy of patients with pre-B ALL (ICN12) were xenografted into sublethally irradiated NOD/SCID mice via tail vein injection. After passaging, leukemia cells were harvested and cultured on OP9 stroma cells in Alpha Minimum Essential medium (Alpha-MEM, Invitrogen, Carlsbad, CA) without ribonucleotides and deoxyribonucleotides, supplemented with 20% fetal bovine serum, 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
ICN12_input.bigWIG: hg18
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| Submission date |
Jul 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Huimin Geng |
| E-mail(s) |
huimin.geng@ucsf.edu
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| Organization name |
UCSF
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| Department |
Department of Laboratory Medicine
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| Street address |
513 Parnassus Ave., MSB S-1480
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE59538 |
Self-enforcing Feedback Activation between BCL6 and Pre-B Cell Receptor Signaling Defines a Distinct Subtype of Acute Lymphoblastic Leukemia |
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| Relations |
| BioSample |
SAMN02924334 |
| SRA |
SRX656348 |
| Named Annotation |
GSM1438988_ICN12_input.bigWIG |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1438988_ICN12_input.bigWIG |
263.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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