|
| Status |
Public on Jun 12, 2017 |
| Title |
600cells_AD_mic_12 |
| Sample type |
SRA |
| |
|
| Source name |
Whole brain
|
| Organism |
Mus musculus |
| Characteristics |
enrichment: CD45-intCD11bintGr1-
tissue: Brain
strain: 5XFAD
chip antibody: H3K4me2
|
| Growth protocol |
Either whole brains, spinal cords, or specific parts of the brain (cortex or cerebellum), not excluding meninges and choroid plexus, were collected from mice following perfusion.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Reverse crosslinking and purify ChIPed DNA with AMPure beads
High troughput reChIP, developed from the iChIP protocol (Lara-Astiaso, Weiner et al. Science 2014
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sorted cells enriched for from brain of AD mouse
|
| Data processing |
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108). In case of paired end samples if single end protocol was used a short read in R2 was used as a UMI
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
May 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE98970 |
Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [ChIP] |
| GSE98971 |
Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease |
|
| Relations |
| BioSample |
SAMN07134156 |
| SRA |
SRX2830118 |
