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| Status |
Public on Jun 14, 2024 |
| Title |
AP2-Regenerated, replicate 1, scATAC |
| Sample type |
SRA |
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| Source name |
Prostate
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| Organism |
Mus musculus |
| Characteristics |
tissue: Prostate
cell type: all prostatic cells
genotype: C57BL/6J
treatment: 96 hours of testosterone induced regeneration
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cell tissue dissociations were performed as previously described (Lukacs et al., 2010). Briefly, in dissecting medium (DMEM (#10-027-CV, Corning) with 10% (vol/vol) FBS (#10437028, ThermoFisher), 1X glutaMAX (#35050061, ThermoFisher), and 1X penicillin-streptomycin (#15070063, ThermoFisher)) prostates were dissected away from the GU tract into individual lobes from 4-6 independent mice (N=4-6). Dorsal, lateral, and ventral prostatic lobes were pooled together, and anterior lobes were processed separately. Pooled prostatic tissue was minced and transferred to digestion solution containing 1mg/ml collagenase (#17100017, ThermoFisher Scientific). Tissue was digested at 37 °C for 2 hours with constant inversion. After digestion, tissue was spun down, resuspended in Trypsin-EDTA (#25300120, ThermoFisher), and digested for an additional 5 minutes at 37 °C. Trypsin digestions was inhibited by addition of dissecting medium supplemented with 500 U DNase I (#10104159001, Millipore-Sigma). Digested tissue was next passed through 18-G and then 20-G syringes to facilitate dissociation. Dissociated tissue was finally passed through a mesh filter with a 40 mm pore size to isolate single cells. All solutions used for tissue digestion/dissociation contained 10 mM Y-27632 dihydrochloride (#1254, Tocris) to prevent anoikis. Cell viability was greater than 80% for all downstream assays.
Single cell ATAC-Seq libraries are generated using the 10X Genomics platform. Isolated nuclei suspensions are treated with Transposase to preferentially fragment open DNA and add partial adapter sequences to the ends of the DNA fragments. Nuclei are loaded into the Chromium Controller (10X Genomics) where they are partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell. Libraries are completed by PCR amplification incorporate remaining Illumina adapter sequences and unique sample indexes. The resulting libraries are evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies), and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina. They are then pooled, denatured, and diluted to 300pM with 1% PhiX control library added. The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).
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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
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| Data processing |
The demultiplex, reads alignment and aggregation were made using the Cell Ranger cellranger-arc software v1.2.0
Note: each sample has two lanes of sequenced data which were pooled/aggregated.
Assembly: mm10
Supplementary files format and content: fragments.tsv.gz files are gzipped files containing the tab-seperated values of chromosome, start, end locations of the sequenced reads after alignment associated with each cell barcode
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| Submission date |
Mar 10, 2023 |
| Last update date |
Jun 14, 2024 |
| Contact name |
Tao Liu |
| E-mail(s) |
[email protected]
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| Phone |
7168451300
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| Organization name |
Roswell Park Comprehensive Cancer Institute
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| Department |
Biostatistics and Bioinformatics
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| Street address |
Elm and Carlton St
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE227107 |
Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells (scATAC-seq) |
| GSE227109 |
Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells. |
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| Relations |
| BioSample |
SAMN33714937 |
| SRA |
SRX19634977 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7091753_mAP2-scATAC-Regenerated-1-fragments.tsv.gz |
1.7 Gb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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