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| Status |
Public on Jun 17, 2024 |
| Title |
Ptf1aERT;K*, 10 weeks, replicate 1 |
| Sample type |
SRA |
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| Source name |
Pancreas
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| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
time: 10 weeks after Tamoxifen
gender: Female
genotype: Ptf1aERT;K*
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| Treatment protocol |
To induce Ptf1aCreERT-dependent recombination, animals were treated with Tamoxifen (T5648, Sigma). Tamoxifen was dissolved in corn oil and administered by oral gavage, 5mg daily for a total of five days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen tissue was pulverized by using the CP02 pulverizer (Covaris). Pulver was washed with PBS containing 0.04% BSA and 1X protease inhibitor and centrifuged (5 min, 500 g, 4 °C). Supernatant was discarded, pellet was resuspended in 0.1 U/μl DNase solution (EN0521, Thermo Fisher Scientific) and incubated on ice for 5 minutes. Tissue was washed twice with PBS containing 0.04% BSA and 1X protease inhibitor. After the last centrifugation step (5 min, 500 g, 4 °C), supernatant was discarded, pellet was resuspended in freshly prepared lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonident P40, 0.01% Digitonin (BN2006, Thermo Fisher Scientific), 1% BSA and 1X protease inhibitor) and incubated on ice for 10 minutes. Nuclei were isolated by using a 2 ml Dounce homogenizer. Sample was filtrated through a 70 μm cell strainer, followed by centrifugation (1 min, 100 g, 4 °C). Supernatant was transferred to a new tube and washed with wash buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA and 1X protease inhibitor) followed by centrifugation (5 min, 500 g, 4°C) for three times. Before the final washing step, suspension was filtered through a 40 μm Flowmi cell strainer. Nuclei were resuspended in Nuclei Buffer (10X Genomics).
Library preparation and sequencing was performed at the Advanced Genomics Core of the University of Michigan. Single nucleus suspensions were counted on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and snATAC libraries were generated using the 10x Genomics Chromium instrument following the manufacturer’s protocol. Final library quality was assessed using the LabChip GX (PerkinElmer).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics, Sequencing Batch 2
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| Data processing |
Bcl2fastq2 Conversion Software (Illumina) was used to generate demultiplexed fastq files.
Raw sequencing data was processed using cellranger-atac-2.0.0 (10X Genomics).
Assembly: mm10
Supplementary files format and content: Fragment files, peak data in bed format and barcode information (singlecell.csv)
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| Submission date |
Jan 18, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Simone Benitz |
| Organization name |
Henry Ford Health System
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| Street address |
2799 W Grand Blvd
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| City |
Detroit |
| ZIP/Postal code |
48202 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE253597 |
ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma (snATAC-Seq) |
| GSE253600 |
ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma |
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| Relations |
| BioSample |
SAMN39486470 |
| SRA |
SRX23277841 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8023965_Sample9_5581-FB-1_fragments.tsv.gz |
1.5 Gb |
(ftp)(http) |
TSV |
| GSM8023965_Sample9_5581-FB-1_fragments.tsv.gz.tbi.gz |
847.3 Kb |
(ftp)(http) |
TBI |
| GSM8023965_Sample9_5581-FB-1_peaks.bed.gz |
950.8 Kb |
(ftp)(http) |
BED |
| GSM8023965_Sample9_5581-FB-1_singlecell.csv.gz |
5.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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