|
| Status |
Public on Mar 14, 2018 |
| Title |
21_wildtype_Input |
| Sample type |
SRA |
| |
|
| Source name |
wild type_Input
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
cell type: FACS sorted microglia
chip antibody: none (input DNA)
|
| 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 |
21_WT_Input
|
| 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 |
SAMN08105089 |
| SRA |
SRX3426478 |
