|
| Status |
Public on Jan 16, 2024 |
| Title |
34_LXR-aKO_LPS_3h_(p65)_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell type: bone marrow-derived macrophage
chip antibody: NF-κB p65 (Cell Signaling, #6956 & #8242)
genotype: LXR-aKO
treatment: Lipopolysaccharide 100 nM 3 hours
|
| Growth protocol |
For bone marrow-derived macrophage (BMDM) cell differentiation, bone marrow from femurs and tibias of 8-10 week-old WT or LXRβ-/- mice were isolated and cultured for 7 days in RPMI supplemented with 10% conditioned media from L-929 cells expressing M-CSF and 1% antibiotics (penicillin and streptomycin). To analyze LXRα-dependent response, cells were cultured in RPMI supplemented with 10% FBS, 1% antibiotics (penicillin and streptomycin) and 100 nM of Lipopolysachaaride (LPS) during 3 or 24 hours. Genome-wide locations of LXRα, p65 (NF-κB) and H3K27ac acetylation mark were analized in response to treatment with LPS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with DSG (2 mM) for 30 minutes and 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorruptor plus (Diagenode) and LXR-DNA, p65-DNA or H3K27ac-DNA complexes were isolated with indicated antibodies.
to create the sequencing library, DNA was end-repaired and ligated to stem-loop adaptors (DNA Library Prep kit for Illumina (Ref.:#7370) following the manufacture instructions). Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using Casava version 1.8.4
For ChIP-Seq, reads were aligned to the mm10 genome using default parameter for bowtie2 (v2.2.9).
Aligned read files were analyzed with HOMER software (v4.9) to find peaks, perform sequence motif finding and other analyses in the study.
Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
annotation was performed with HOMER software v4.9 annotatePeaks.pl using default parameters
Assembly: mm10
Supplementary files format and content: Processed files include bed files
|
| |
|
| Submission date |
Jan 15, 2024 |
| Last update date |
Jan 16, 2024 |
| Contact name |
ANTONIO CASTRILLO |
| Organization name |
Instituto Investigaciones Biomedicas Alberto Sols CSIC
|
| Department |
metabolism and cellular signaling
|
| Lab |
Lab B11
|
| Street address |
Arturo Duperier 4
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE200922 |
TLR-dependent transcriptional reprogramming of LXRα cistrome in bone marrow-derived macrophages |
|
| Relations |
| BioSample |
SAMN39446954 |
| SRA |
SRX23223136 |
