|
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.
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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|
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.
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|
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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 |