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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 28, 2017 |
| Title |
Input (Lhx6) |
| Sample type |
SRA |
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| Source name |
E11.5 Maxillary Arch
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| Organism |
Mus musculus |
| Characteristics |
genotype: Wild-type (CD1)
chip antibody: None
tissue: E11.5 Maxillary Arch
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| Treatment protocol |
Not applicable.
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| Growth protocol |
Not applicable.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The maxillary arches were dissected from 47 of E11.5 CD-1 wild-type embryos in phosphate-buffered saline and snap-frozen on dry ice. The tissue was then sent to Active Motif, Inc. (Carlsbad, CA) for FactorPath™ service, which included chromatin preparation, ChIP-seq for LHX6, and bioinformatics analysis of the sequencing result to identify LHX6-enriched genomic regions (peaks). Twenty micrograms of the maxillary arch chromatin was used for ChIP with a rabbit polyclonal anti-LHX6 antibody The tissue was then sent to Active Motif, Inc. (Carlsbad, CA) for HistonePathTM service, which included chromatin preparation, ChIP-seq for H3K27ac, and bioinformatics analysis of the sequencing result to identify H3K27ac-enriched genomic regions (peaks). 20 μg of the maxillary arch chromatin was used for ChIP with a rabbit polyclonal anti-H3K27Ac antibody (Active Motif, cat# AM 39133). Libraries for Illumina sequencing (Hi-Seq) were prepared from ChIP DNA and input chromatin as described (Labhart et al., 2005)
Libraries for Illumina sequencing (Hi-Seq) were prepared from ChIP DNA and input chromatin, and the sequence reads from each sample were aligned to the mouse genome (NCBI Build 37, mm 9) using BWA algorithm (73). The aligned sequence tags were extended in silico at the 3′-ends into 150-bp fragments, and the histograms of the fragment density along the genome were stored in BAR (Binary Analysis Results) files and visualized using Integrated Genome Browser (IGB).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
The sequence reads from each sample were aligned to the mouse genome (NCBI Build 37, mm9) using BWA algorithm (Li and Durbin, 2009) The aligned sequence tags were extended in silico at the 3′-ends into 150-bp fragments, and the histograms of the fragment density along the genome were stored in BAR (Binary Analysis Results) files and visualized using Integrated Genome Browser (IGB) (Nicol et al., 2009)
LHX6 peaks were identified using MACS peak-finding algorithm (39) with the following parameters: band width = 150, model fold = 8,24, P-value cutoff = 1E-7.
Genome_build: mm9
Supplementary_files_format_and_content: peak
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| Submission date |
Jul 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Juhee Jeong |
| Organization name |
New York University College of Dentistry
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| Department |
Basic sciences and Craniofacial development
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| Lab |
902D (Jeong Lab)
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| Street address |
345 E 24th St
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10010 |
| Country |
USA |
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| Platform ID |
GPL15103 |
| Series (1) |
| GSE71497 |
Identification of an LHX target cis-regulatory element through LHX6 ChIP-seq. |
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| Relations |
| BioSample |
SAMN03943711 |
| SRA |
SRX1123622 |
| 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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