|
| Status |
Public on Feb 12, 2020 |
| Title |
Naive_MAFG_Input_Replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
Naive_Input_astrocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype/variation: wild type
Sex: female
sample group: naïve
cell type: Flow cytometry sorted astrocytes
chip antibody: none (input)
|
| Treatment protocol |
Induction of EAE or Naïve. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Each CNS was isolated per mouse. A cell suspension was generated by trypsinization, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, chromatin was isolated using the Active Motif ChIP-IT Express Enzymatic shearing kit. Chromatin complexes were IPed with MAFG antibody (Genetex, GTX114541), cross-links were reversed, and DNA was cleaned up for library prep using QIAquick PCR purification kit.
NEBNext Ultra II DNA Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file:
Naive_merged_p0.01_peaks.narrowPeak
|
| Data processing |
ChIP-seq Reads were aligned using BWA mem (v0.7.8) against the GRCm38 genome with default settings.
Duplicated reads were removed using Picard (v2.5.0).
Alignments were filtered with SAMtools (v1.3) to exclude reads with mapping quality <30, not properly aligned, and aligned to the mitochondrial genome.
For peak calling, MACS2 callpeaks (V2.1.1) were called using IP as treatment and Input as control sample, with pval 0.01 as threshold.
Fold enrichment tracks were generated in MACS using bdgcmp to compare treatment against control and were visualized using IGV (v 2.3.59).
Genome_build: GRCm38
Supplementary_files_format_and_content: narrowPeaks output from MACS2
|
| |
|
| Submission date |
Apr 10, 2019 |
| Last update date |
Feb 12, 2020 |
| Contact name |
Michael Wheeler |
| E-mail(s) |
mwheeler0@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Neurology
|
| Street address |
60 Fenwood Rd.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE129607 |
Genome-wide analysis of MAFG binding in astrocytes during EAE [ChIP-seq] |
| GSE130119 |
MAFG-driven astrocytes promote CNS inflammation |
|
| Relations |
| BioSample |
SAMN11391738 |
| SRA |
SRX5664996 |
