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| Status |
Public on Aug 31, 2020 |
| Title |
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) assess genome-wide chromatin accessibility of Runx2fl/fl Mouse Molar Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: To study the function of Runx2 on mouse tooth root development. The goals of this study are to assess genome-wide chromatin accessibility of Runx2fl/fl Mouse Molar Transcriptomes to identify the potential downstream target of Runx2. Methods: the apical halves of lower 1st molars of PN7.5 control mice were lysed to get a single cell suspension. 50000 cells 50,000 cells were lysed, and followed by transposition reaction and purification, and PCR amplification. The library construction and sequencing were performed by NextSeq 500 platform.
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| Overall design |
Briefly, the apical halves of 8 mandibular first molars of PN7.5 Runx2fl/fl control mice were collected in PBS on ice. Then the tissues were treated to obtain a single-cell suspension. 50,000 cells were lysed, and followed by transposition reaction and purification, and PCR amplification. The library construction and sequencing were performed by NextSeq 500 platform. The raw data was analyzed using Partek® Flow® software. Briefly, raw reads were aligned using Bowtie2 with the mm10 genome; MACS2 was used for detecting genomic enrichment regions; Runx2 binding motifs were analyzed using HOMER
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| Contributor(s) |
Wen Q, Chai Y |
| Citation missing |
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| Submission date |
Jun 01, 2020 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Quan Wen |
| E-mail(s) |
qw_354@usc.edu
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| Organization name |
University of Southern California
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| Street address |
2250 Alcazar St. CSA 123
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| City |
Los Angeles |
| State/province |
Ca |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA636372 |
| SRA |
SRP265494 |
