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| Status |
Public on Sep 11, 2023 |
| Title |
maxillary process, e13.5, input |
| Sample type |
SRA |
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| Source name |
maxillary process
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| Organism |
Mus musculus |
| Characteristics |
tissue: maxillary process
antibody: none
cell type: mixed
genotype: WT
developmental stage: e13.5
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly dissected mouse embryonic face tissue.
Tissue was dissociated and crosslinked, cells lyzed and chromatin was sonicated to obtain DNA fragments ranging between 100-600bp. Chromatin was immunoprecipitated with an anti-H3K27ac antibody (Active Motif, Cat#39133), reverse crosslinked and the samples were assessed for DNA concentration and fragment size distribution. Sequencing libraries were prepared with Illumina TruSeq kit.
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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 |
ChIP-seq data was analyzed using the ENCODE histone ChIP-seq Unary Control Unreplicated pipeline (https://www.encodeproject.org/pipelines/ENCPL841HGV/) implemented at DNAnexus (https://www.dnanexus.com).
Reads were mapped to the mouse reference genome version mm10 using BWA (v0.7.7) and sorted bam file generated using samtools (v0.1.19). Peak calling was performed using MACS2 (v2.2.4; --broad flag, q-value < 0.05), and overlapping peaks identified using overlap_peaks.py.
Assembly: mm10
Supplementary files format and content: broadPeak, bigWig
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| Submission date |
Jun 26, 2023 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Laura E Cook |
| E-mail(s) |
lecook@lbl.gov
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| Organization name |
Lawrence Berkeley National Laboratory
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| Department |
Biosciences
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| Lab |
MFGL
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| Street address |
1 Cyclotron Road
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| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE235748 |
Dynamic enhancer landscapes in human craniofacial development [mouse ChIP] |
| GSE235858 |
Dynamic enhancer landscapes in human craniofacial development |
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| Relations |
| BioSample |
SAMN35990872 |
| SRA |
SRX20784858 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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