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| Status |
Public on Feb 13, 2023 |
| Title |
SN4741_ATACseq_39_rep4 |
| Sample type |
SRA |
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| Source name |
SN4741
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| Organism |
Mus musculus |
| Characteristics |
cell line: SN4741
cell type: Neural precursor cells
genotype: WT
treatment: 39°C Incubation
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| Treatment protocol |
To induce differentiation, 24 hours after the cells were passaged, media was replaced by DMEM supplemented with 1% penicillin–streptomycin and 0.5% FBS at 39°C. Cells were allowed to grow and differentiate in these conditions for 48 hours before harvesting for experimentation.
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| Growth protocol |
SN4741 cells were maintained in high glucose Dulbecco's Modified Eagle Medium, supplemented with 1% penicillin–streptomycin and 10% fetal bovine serum in a humidified 5% CO2 incubator at 37°C. Cells at 80% confluence were passaged by trypsinization approximately every 2-3 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following the Omni-ATAC protocol, aliquots of 50,000 cells were centrifuged at 2000 x g for 20 mins at 4°C, and the resulting pellets were resuspended in 50μL of resuspension buffer. Cells were left to lyse for 3 minutes on ice before being centrifuged again at 2000 x g for 20 minutes at 4°C. The resulting nuclei pellets were then tagmented, as written, using 50μL of transposition mixture and then incubated at 37°C for 30 mins in a 1000 RPM thermomixer. After transposition, DNA was purified with the Zymo DNA Clean and Concentrator -5 Kit and eluted in 21μL of elution buffer.
Pre-amplification of transposed fragments was performed according to the conditions outlined in the Omni-ATAC protocol. 12 pre-amplification cycles were run in lieu of qPCR amplification to determine additional cycles. The amplified libraries were prepared according to the Nextera DNA Library Prep Protocol Guide, except that libraries were purified with 40.5μL AMPure XP beads, and 27.5μL of resuspension buffer was added to each sample. All libraries were quantified with the Qubit dsDNA High Sensitivity Assay (Invitrogen) in combination with the High Sensitivity DNA Assay (Agilent) on the Agilent 2100 Bioanalyzer.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads were aligned to the mouse reference genome (mm10) in local mode with Bowtie2 (v2.4.1), using –X 1000 to specify an increased pair distance to 1000bp.
Samtools (v1.15.1) and Picard (v2.26.11; http://broadinstitute.github.io/picard/) were used to sort, deduplicate and index reads.
Peaks were called with MACS3 (v3.0.0a7; https://github.com/macs3-project/MACS) and specifying --nomodel and --nolambda for the `callpeaks()` command.
Peaks overlapping mm10 blacklisted/block listed regions called by ENCODE and in the original ATAC-seq paper were also removed with BEDTools (v2.30.0).
Assembly: mm10
Supplementary files format and content: xls peak files
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| Submission date |
Feb 10, 2023 |
| Last update date |
Feb 14, 2023 |
| Contact name |
Andrew S. McCallion |
| E-mail(s) |
andy@jhmi.edu
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| Organization name |
Johns Hopkins University School of Medicine
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| Department |
Genetic Medicine
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| Lab |
McCallion
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| Street address |
733 North Broadway
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE225069 |
Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons [ATAC-seq] |
| GSE225084 |
Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons |
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| Relations |
| BioSample |
SAMN33244596 |
| SRA |
SRX19333616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7038917_39-4_SN4741_S6_peaks.xls.gz |
1.3 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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