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| Status |
Public on Apr 03, 2023 |
| Title |
siCon-input |
| Sample type |
SRA |
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| Source name |
Beta-TC6
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| Organism |
Mus musculus |
| Characteristics |
cell line: Beta-TC6
cell type: beta cell
genotype: WT
treatment: control siRNA
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| Treatment protocol |
Cells synchronized using 1 hour 10 micromolar forskolin pulse
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| Growth protocol |
DMEM + 15% FBS (cells), RPMI + 10% FBS or human AB serum (islets)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Omni-ATAC protocol for bulk ATAC-seq, 10X Protocol for snATAC-seq, DirectZol MicroPrep (Zymo) for RNA, AQuA HiChIP for HiChIP
10X Protocol for snATAC-seq. NEBNext Ultra II for RNA, ChIP, and HiChIP-seq. Nextera (Tn5) for ATAC-Seq
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10
Supplementary files format and content: bigWig files (*.bw.gz)
Supplementary files format and content: HiCPro validPair files (*.validPairs)
Supplementary files format and content: Homer peak files (*peaks.txt)
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| Submission date |
Oct 03, 2022 |
| Last update date |
Apr 03, 2023 |
| Contact name |
Benjamin J Weidemann |
| E-mail(s) |
benjamin.weidemann@northwestern.edu
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| Phone |
3127920532
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| Organization name |
NORTHWESTERN UNIVERSITY
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| Department |
Medicine
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| Lab |
Joseph Bass
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| Street address |
303 E. Superior St.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60613 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE214674 |
NF-kB and Circadian Enhancers Link β-cell Function with Anti-IL1B Therapy [ChIP/HiChIP-seq] |
| GSE214678 |
NF-kB and Circadian Enhancers Link β-cell Function with Anti-IL1B Therapy. |
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| Relations |
| BioSample |
SAMN31137591 |
| SRA |
SRX17781282 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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