|
| Status |
Public on Aug 08, 2017 |
| Title |
8h LPS DNase rep1 |
| Sample type |
SRA |
| |
|
| Source name |
8h LPS
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: Bone marrow derived macrophages
treatment: 8h LPS
|
| Treatment protocol |
Primary macrophages derived from bone marrow were stimulated with lipopolysaccharide and/or Dex for the indicated number of hours.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After treatment with Dex and/or LPS, nuclei of BMDMs were isolated, and chromatin were digested with 80 U/ml DNase I (Sigma) for 3 min at 37 ºC and incubated at 55 ºC overnight with 10 µg/ml of RNaseA (Invitrogen) and Proteinase K (Ambion). Digested DNA fragments were purified using phenol-chloroform and enriched by size selection over sucrose gradient. DNA fragments between 100 bp and 500 bp were precipitated and dissolved in nuclease free H2O.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GH1228
|
| Data processing |
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
DNase hypersensitive sites were identified as hotspots using DNase2Hotspots.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph, csv
|
| |
|
| Submission date |
Jan 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Songjoon Baek |
| Organization name |
NCI / NIH
|
| Department |
CCR
|
| Lab |
LRBGE
|
| Street address |
41 Library Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE93738 |
Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment [DNase-seq] |
| GSE93739 |
Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment |
|
| Relations |
| BioSample |
SAMN06236716 |
| SRA |
SRX2498815 |
