|
| Status |
Public on Feb 10, 2021 |
| Title |
P17103_1005 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6j
genotype: Sox10-Cre/RCE
antibody: Abcam Ab177178
tn5: In-house Tn5
|
| Growth protocol |
Cells were cultured in OPC proliferation medium (DMEM/Glutamax, 1xN2 supplement, 1x Penicilin-streptomycin, 1x NeuroBrew, 20ng/mL bFGF, 20ng/mL mPDGF-AA)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested using TrypLE and fixed with 1% formaldehyde prior to processing for HiChIP
Libraries were prepared as specified in Mumbach et.al. (2016) and with 0.75uL Tn5 enzyme.
Samples were sequenced on a single-lane of an SP flowcell on the NovaSeq6000 with the 2x50bp read setup
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
replicate 3
|
| Data processing |
Fastq files were aligned to the mm10 genome and filtered for duplcate reads using the HiC-Pro pipeline
allValidPairs files from the HiC-Pro pipeline for each replicate were merged together
hicpro2juicebox.sh from HiC-Pro was used on the merged allValidPairs file to generate the .hic file
Genome_build: mm10
Supplementary_files_format_and_content: Juicebox compatible .hic files, contains contact matrices at multiple resolutions
|
| |
|
| Submission date |
Sep 08, 2020 |
| Last update date |
Feb 10, 2021 |
| Contact name |
Marek Bartosovic |
| E-mail(s) |
bartosovic.marek@gmail.com
|
| Organization name |
Karolinska Institute
|
| Lab |
Goncalo Castelo-Branco
|
| Street address |
Solnavagen 9
|
| City |
Stockholm |
| ZIP/Postal code |
12432 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE157666 |
Single-cell profiling of histone modifications in the mouse brain |
| GSE163532 |
Single cell profiling of histone modifications and transcription factors in the mouse brain |
|
| Relations |
| BioSample |
SAMN16082474 |
| SRA |
SRX9093652 |
