|
| Status |
Public on Jul 24, 2019 |
| Title |
H3K4m3_CO |
| Sample type |
SRA |
| |
|
| Source name |
09_Rumen-primC_H3K4me3_bosTau8
|
| Organism |
Bos taurus |
| Characteristics |
breed: Hostein
treatmnet: Control
cell type: Rumen Epithelial Primary Cells (REPC)
chip antibody: H3K4m3
chip antibody vendor: Active Motif
chip antibody cat. #: 39159
chip antibody lot/batch #: 25817005
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
CTCF-seq and ChIP-Seq of H3K27ac, H3K27m3, H3K4m1, H3K4m3, of rumen primary epithelial cells (RPEC) were performed at Active Motif according to proprietary methods. For ChIP-seq, CTCF-seq, the 75-nt sequence reads
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
09_03P3_00GMUSDA_Rumen-primC_H3K4me3_Btau_i78
|
| Data processing |
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trim_Galore (version 0.4.1)
We then mapped clean reads to the cattle reference genome (UMD3.1.1) using BWA algorithm with default settings. We only kept reads uniquely aligned with less than two mismatches for the subsequent analysis. We employed MACS2.1.1 for peak-calling with default parameter settings by looking for significant enrichment in the studied samples when compared to the input data file (i.e., random background)
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: xlsx
|
| |
|
| Submission date |
Apr 05, 2019 |
| Last update date |
Jul 24, 2019 |
| Contact name |
George E. Liu |
| E-mail(s) |
george.liu@usda.gov
|
| Phone |
301-504-9843
|
| Organization name |
USDA-ARS
|
| Lab |
Animal Genomics and improvement Lab.
|
| Street address |
10300 Baltimore Ave Bldg 306
|
| City |
Beltsville |
| State/province |
Maryland (MD) |
| ZIP/Postal code |
20705 |
| Country |
USA |
| |
|
| Platform ID |
GPL23055 |
| Series (2) |
| GSE129419 |
Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 4] |
| GSE129423 |
Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation |
|
| Relations |
| BioSample |
SAMN11352776 |
| SRA |
SRX5649084 |
