NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2866991 Query DataSets for GSM2866991
Status Public on Mar 14, 2018
Title 12_HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_H3K9ac
Sample type SRA
 
Source name HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre_H3K9ac
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: HDAC1-2lox-HDAC2-2lox-Cx3cr1-Cre
cell type: FACS sorted microglia
chip antibody: H3K9ac
chip antibody vendor: abcam
chip antibody cat. #: ab10812
chip antibody lot #: GR287797-2
Treatment protocol no treatment prior to FACS sorting
Growth protocol A myleoid lineage specific constitutive knockout mouse line was generated by crossing Hdac1-2lox, Hdac2-2lox and Cx3cr1-Cre mice.
Extracted molecule genomic DNA
Extraction protocol Mice were sacrificed at an age of 6 weeks and microglia were isolated by FACS sorting of brain homogenate for CD11bhi CD45lo cells.
Sequencing library preparation was performed using the KAPA Library Preparation Kit with Real-time PCR Library Amplification for Illumina Platforms Kit (Kapa Biosystems) as per the manufacturer’s protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description 12_HDACDKO_H3K9ac
Data processing bcl2fastq version: 2.17.1.14 was used to convert RTA files generated from a Hiseq2000 run to Fastq files.
STAR 2.5.2b was used to align sequences to the mouse genome with parameters --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignIntronMax 1 --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10
Picard Tools 2.7.1 markDuplicates was performed with standard settings to remove duplicate reads
Deeptools 2.4.0 bamCoverage was used to generate bigWig files with parameters --normalizeTo1x (mm10 genome size) --normalizeUsingRPKM -e -bs 10 --smoothLength 50
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig files containing coverage information for ChIP and input DNA samples respectively.
 
Submission date Nov 28, 2017
Last update date May 15, 2019
Contact name Ori Staszewski
E-mail(s) ori.staszewski@uniklinik-freiburg.de
Organization name University Medical Center Freiburg
Department Institute of Neuropathology
Street address Breisacher Str. 64
City Freiburg
ZIP/Postal code D-79106
Country Germany
 
Platform ID GPL13112
Series (2)
GSE98823 Knockout of HDAC1 and HDAC2 in Microglia
GSE107436 HDAC1/2 are required for microglia identity during development, homeostasis and neurodegeneration in a context-dependent manner [ChIP-seq constitutive knockout]
Relations
BioSample SAMN08105079
SRA SRX3426468

Supplementary file Size Download File type/resource
GSM2866991_12_HDACDKO_H3K9ac.20170314.bw 205.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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