 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 01, 2024 |
| Title |
U2,Mus musculus,Liver,293,57 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
vector treatment: 293
timepoint _(weeks): 57
genotype: C57BL/6J
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Flash-Frozen mouse liver tissue was manually disassociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017) using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PE42 protocol
|
| Data processing |
BWA-mem
MACS2
Assembly: GRCm38.p6
Supplementary files format and content: bam- aligned reads
Supplementary files format and content: narrowPeak- MACS2 output from bam files
|
| |
|
| Submission date |
Jan 29, 2024 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Evan Witt |
| E-mail(s) |
evan.witt@bmrn.com
|
| Organization name |
Biomarin Pharmaceutical
|
| Street address |
791 Lindaro Street
|
| City |
San Rafael |
| State/province |
California |
| ZIP/Postal code |
94901 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE254503 |
The longitudinal kinetics of AAV5 vector integration profiles and evaluation of clonal expansion in mice |
|
| Relations |
| BioSample |
SAMN39659188 |
| SRA |
SRX23431135 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8043553_18_0DAS_01XGBiomarin_S18-U2_ATAC_mm10_i213_peaks.narrowPeak.gz |
2.8 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
