|
| Status |
Public on Mar 14, 2018 |
| Title |
61_5xFAD_HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2_H3K9ac |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted microglia
|
| Organism |
Mus musculus |
| Characteristics |
genotype: 5xFAD-HDAC1-2lox-HDAC2-2lox-Cx3cr1-CreERT2
chromatin_mark: H3K9ac
|
| Treatment protocol |
HDAC1 and HDAC2 knockout was induced at an age of 6 weeks and animals tehreafter aged to 12 months prioor to FACS sorting of microglia.
|
| Growth protocol |
A microglia specific inducible knockout mouse line was generated by crossing Hdac1-2lox, Hdac2-2lox and Cx3cr1-CreERT2 mice. Mice were then crossed to the 5xFAD mouse line.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mice were sacrificed at an age of 12 months 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 3000 |
| |
|
| Data processing |
bcl2fastq version: 2.17.1.14 was used to convert RTA files generated from a Hiseq3000 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 |
Feb 05, 2018 |
| Last update date |
Mar 14, 2018 |
| 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 |
GPL21493 |
| Series (2) |
| GSE98823 |
Knockout of HDAC1 and HDAC2 in Microglia |
| GSE110166 |
HDAC1/2 are required for microglia identity during development, homeostasis and neurodegeneration in a context-dependent manner [ChIP inducible knockout on FAD background] |
|
| Relations |
| BioSample |
SAMN08469379 |
| SRA |
SRX3651357 |
