NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3716998 Query DataSets for GSM3716998
Status Public on Feb 12, 2020
Title Naive_MAFG_IP_Replicate3
Sample type SRA
 
Source name Naive_IP_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: MAFG antibody (Genetex, GTX114541)
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 SAMN11391743
SRA SRX5664990

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap