|
| Status |
Public on May 03, 2024 |
| Title |
20211116C-msTumor-NFIB_S8_R1.fastq.gz |
| Sample type |
SRA |
| |
|
| Source name |
primary
|
| Organism |
Mus musculus |
| Characteristics |
tissue: primary
cell type: medulloblastoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GNPs, PNCs and tumor cells were isolated from P7, P28 and adult cerebellum by percoll gradient centrifugation, respectively. These isolated 1 x 105 cells were directly subjected to CUT & Tag library preparation.
CUT & Tag was performed according to the online protocol from EpiCypher
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to mm10 genome by bowtie2
Peak call was performed by MACS2
Assembly: mm10
Supplementary files format and content: peak summit data
Library strategy: Cut&Tag
|
| |
|
| Submission date |
Aug 08, 2023 |
| Last update date |
May 03, 2024 |
| Contact name |
Kohei Kumegawa |
| E-mail(s) |
kohei.kumegawa@gmail.com
|
| Organization name |
Japanese Foundation for Cancer Research
|
| Street address |
3-8-31 Ariake, Koto-ku
|
| City |
Tokyo |
| ZIP/Postal code |
135-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE240359 |
Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Essential Transcriptional Factors during Medulloblastoma Tumorigenesis [CUT&Tag] |
| GSE240362 |
Cancer-Specific Epigenome Identifies Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression |
|
| Relations |
| BioSample |
SAMN36890714 |
| SRA |
SRX21298896 |
