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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 01, 2018 |
| Title |
HL1_input_gDNA |
| Sample type |
SRA |
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| Source name |
input DNA
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell line: HL-1 cells
cell type: cardiac muscle cell line
chip antibody: none
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| Growth protocol |
Cells were grown in Claycomb Medium (Sigma) supplemented with 10% Fetal bovine serum (Sigma, Lot #116K8400), 2 mM L-Glutamine, 0.1 mM Norepinephrine and antibiotics in gelatin/fibronectin coated flasks upto 95% confluency.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101). After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~320 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
input DNA
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| Data processing |
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
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| Submission date |
Apr 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Elizaveta V Benevolenskaya |
| E-mail(s) |
evb@uic.edu
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| Phone |
312-413-8947
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| Organization name |
University of Illinois at Chicago
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| Department |
Biochemistry and Molecular Genetics
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| Street address |
900 S. Ashland Ave.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE28341 |
Genome-wide maps of KDM5A/JARID1A/RBP2 and JARID2/JMJ in HL-1 cardiomyocytes. |
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| Relations |
| SRA |
SRX055316 |
| BioSample |
SAMN00255009 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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