|
| Status |
Public on Sep 26, 2022 |
| Title |
βRicKO+Ad-GFP-2(KO2) |
| Sample type |
SRA |
| |
|
| Source name |
islet
|
| Organism |
Mus musculus |
| Characteristics |
age: 16-week-old
tissue: islet
genotype: BetaRicKO
|
| Treatment protocol |
Adenovirus packaged with Acsl4 or control was transfected with 48h ex vivo
|
| Growth protocol |
Individual islets were hand-picked and cultured in RPMI 1640, isolated islets were digested by 0.25% trypsin with EDTA .
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Selected 50 average size islets were lysed in lysis buffer.Nuclei were then incubated with the Tn5 transposome and tagmentation.
Libaray was prepared according to protocols of TruePrep DNA Library Prep Kit V2 for illumina(Vazyme Biotech, Nanjing, China) .PCR was performed to amplify the library for 12 cycles.The libraries were sequenced on HiSeq (X Ten) platform and using PE50 sequencing strategy
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using Trimmomatic.
Quality filtered reads were then mapped to hg38/GRCh38 reference genome using BWA(0.7.10), and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools and used for peak calling. MACS2(2.1.1)was used to call peaks and an initial threshold q-value of 0.05 as cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Genome_build: hg38
|
| |
|
| Submission date |
Sep 25, 2019 |
| Last update date |
Sep 26, 2022 |
| Contact name |
canqi cui |
| E-mail(s) |
guyanyun@hotmail.com
|
| Organization name |
shanghai national reaearch center for endocrine and metabolic diseases
|
| Street address |
197 Ruijin 2nd Road
|
| City |
Shanghai |
| ZIP/Postal code |
20025 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE138014 |
Enhancing Acsl4 in absence of mTORC2/Rictor drove β-cell dedifferentiation via inhibiting FoxO1 and promoting ROS production |
|
| Relations |
| BioSample |
SAMN12842486 |
| SRA |
SRX6902405 |
