|
| Status |
Public on Feb 04, 2020 |
| Title |
Nx 3 H3K4me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
N9 microglia
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Normoxia
passages: 3-9
antibody: Abcam ab8580
|
| Treatment protocol |
Cells were treated for 16 hours with either 1% O2 or 21% O2, in an incubator maintained at 5% CO2 and 37 °C.
|
| Growth protocol |
N9 microglia cultured in DMEM and supplemented with 10% fetal bovine serum and 1% penicillin streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, lysates were sonicated manually and cleared prior to antibody incubation.For RNA seq, cells were lysed in Trizol.
ChIP-seq libraries prepared according to Illumina's instructions; RNA stranded libraries prepared according to Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq: Base calls were made using Illumina 1.9 software
ChIP-seq: Alignment was performed by ProteinCT using bowtie2
ChIP-seq: Homer v4.8 was used to create normalized genome coverage files with duplicate removal
ChIP-seq: Homer v4.8 vwas used to generate tag directories and perform peak calling
ChiP-seq: Homer v4.8 was used to perform differential peak analysis between Nx and Hx samples
RNAseq: Base calls made using Illumina 1.9 software
RNAseq: Alignment made using Tophat v2.1
RNAseq: Differential expression analyses performed using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: ChIP bedGraph files for each individual sample and consensus files for all samples in treatment;
|
| |
|
| Submission date |
Jan 04, 2018 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Jyoti Watters |
| E-mail(s) |
jjwatters@wisc.edu
|
| Phone |
6082656092
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
CBS
|
| Lab |
Jyoti Watters
|
| Street address |
2015 Linden Drive
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE108770 |
Hypoxia-induced priming of microglial inflammatory gene expression is associated with TLR4 signaling H3K4me3 enrichment |
|
| Relations |
| BioSample |
SAMN08321114 |
| SRA |
SRX3583281 |
