|
| Status |
Public on Jul 05, 2019 |
| Title |
A2-CTRL-K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
CTRL-K4me3
|
| Organism |
Bos taurus |
| Characteristics |
animal id: Animal 2
condition: Control
cell type: Bovine alveolar macrophages
chip antibody: H3K4me3
chip antibody vendor: Millipore
chip antibody cat. #: 05-745R
|
| Treatment protocol |
2 x 10^6 macrophages were seeded in 60 mm tissue culture plates and challenged with M. bovis at an MOI of 10:1 (2 X 107 bacteria per plate) for 24 hours, parallel non-infected controls were prepared simultaneously.
|
| Growth protocol |
Centrifuged cell pellet was resuspended in 15 ml of R10+ media and placed in a 75 cm [2] vented culture flask (CELLSTAR®, Greiner Bio-One Ltd., Stonehouse, UK) and incubated for 24 h at 37 °C, 5% CO2. After incubation, media was removed together with non-adherent cells and adherent cells were washed with 15 ml HBSS pre-warmed to 37 °C (Note: all pre-warmed media and solutions were heated to 37 °C prior to use). Adherent cells were dissociated by adding 10 ml pre-warmed 1× non-enzymatic cell dissociation solution (Sigma–Aldrich Ltd.) to each culture flask and incubating at room temperature for 10 min. Cells were then pelleted (200× g for 5 min at room temperature), resuspended in 10 ml pre-warmed R10+ media and the number of viable cells was counted using a Beckman Coulter® Vi-CELL™ XR Cell Viability Analyzer and reagent kit (Beckman Coulter Inc., High Wycombe, UK).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEB Next Ultra ChIPseq Library Prep (New England Biolabs) for ChIP-seq library preparations.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
batch number: 0212_BHJ77HBBXX
|
| Data processing |
At each step of data processing, read quality was assessed via fastqc version 0.11.5
ChIP-seq reads aligned to bovine reference genome via Bowtie2 version 2.3.0
All resulting SAM files converted into sorted BAM files via Samtools (version 1.3.1)
The peak calling was carried out via macs (version 2.1.1.20160309), normalised by input samples. Broadpeak or narrowpeak calls based on mark. Peaks filtered based on pvalue < 0.05 and fold enrichment > 2.5
BEDgraph files generated via MACS2 and compared via MACS2 bdgcmp
Genome_build: UMD 3.1
Supplementary_files_format_and_content: BEDgraph converted to bigwig via bedtools
|
| |
|
| Submission date |
Jul 06, 2018 |
| Last update date |
Jul 05, 2019 |
| Contact name |
Thomas Hall |
| E-mail(s) |
tjhall1688@gmail.com
|
| Phone |
857168930
|
| Organization name |
UCD
|
| Department |
Vet sciences
|
| Street address |
2, Taney Grove
|
| City |
Dublin |
| State/province |
Select One |
| ZIP/Postal code |
D14 KW14 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL23295 |
| Series (2) |
| GSE116731 |
Initial host response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes [ChIP-seq] |
| GSE116734 |
Initial host response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes. |
|
| Relations |
| BioSample |
SAMN09623390 |
| SRA |
SRX4348286 |
