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| Status |
Public on Nov 28, 2024 |
| Title |
BxPC3,plusIFNγ, Replicate9, ATAC-seq |
| Sample type |
SRA |
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| Source name |
BxPC-3
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| Organism |
Homo sapiens |
| Characteristics |
tissue: BxPC-3
cell line: PDAC
treatment: IFNgamma treatment
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| Treatment protocol |
For IFNγ-stimulated conditions, cells were cultured in medium supplemented with 100 IU/mL human IFNγ (BioLegend) for 48 hours.
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| Growth protocol |
BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed using homemade transposomes with minor modifications that are detailed below (Buenrostro et al.,2013; Picelli et al., 2014)). For each replicate, we trypsinized, washed, and resuspended 250,000 cells in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40, 0.1% tween-20, 0.01% digitonin) and lysed for 10 minutes on ice (Corces et al., 2017). After lysis, 50,000 cells were resuspended in transposase reaction mix (1ul Tn5 (0.5 µM), 4ul 5X TD-TAPS (50mM TAPS-NaOH, 25mM MgCl2, 50% DMF), 5ul dilution buffer (10mM Tris-HCl, pH 7.4, 100mM NaCl, 1mM DTT, 50% glycerol), 2ul 10% Tween, and 8ul PBS) and tagmentation was performed at 37°C for 30 minutes. Next, samples were purified using the Zymo Clean and Concentrate kit.
For the library preparation, DNA was amplified with NEBNext High-Fidelity 2× PCR Master Mix as previously described (Buenrostro et al.,2013). The PCR program was as followed: 72 °C for 5 minutes, 98 °C for 30 seconds, (98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 60 seconds) x 12 cycles. Samples were sequenced on both Illumina NextSeq 500 and Ultima Genomics platforms.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Ultima Genomics
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| Data processing |
For Illumina data, adaptors were trimmed with trimmomatic (version 0.39) with the options ILLUMINACLIP:Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:24 (Bolger, Lohse and Usadel, 2014). For Ultima data, cram files were converted to fastq using samtools (version 1.9), and trimmed using cutadapt (version 4.0) (Danecek et al., 2021; Martin, 2011).
Reads from both sequencing platforms were aligned to GRCh38 with bowtie2 (version 2.4.4) (Langmead and Salzberg, 2012), deduplicated with picard through gatk MarkDuplicates (version 4.2.5.0), and downsampled to the sample with the lowest reads using samtools, then peaks were called with MACS2 callpeak (version 2.2.7.1) with default parameters (Zhang.,2008).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
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| Submission date |
Feb 13, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Xinhe Xue |
| E-mail(s) |
[email protected]
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| Organization name |
New York Genome Center/New York University
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| Street address |
101 Avenue of the Americas
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| City |
NEW YORK |
| State/province |
New York |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE255698 |
Paired CRISPR screens to map gene regulation in cis and trans (ATAC-seq) |
| GSE255701 |
Paired CRISPR screens to map gene regulation in cis and trans |
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| Relations |
| BioSample |
SAMN39938756 |
| SRA |
SRX23617895 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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