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| Status |
Public on Nov 18, 2020 |
| Title |
ATACseq of MA1L_vector, 10_IFNG replicate 2 |
| Sample type |
SRA |
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| Source name |
MA1L liver cancer cells
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| Organism |
Mus musculus |
| Characteristics |
transduction: Vector
treatment: 10 ng/ml IFNG
genetic background: p53-/-, Myc overexpression; C57BL/6J
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
200,000 of vector or sgKmt2d transduced primary liver tumor cells (MA1L) were seeded into 12-well plate, and 0, or 10 ng/ml IFN-γ were added to treated them for 24 h. After treatment, the cell nuclei were collected for ATAC-seq using a protocol as previously described. Briefly, cells from different treatment group were counted and 50,000 cells were collected by centrifuge at 500g for 5 min. After washing once with 50 μl of cold 1× PBS, the cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630).
Immediately after lysis, nuclei were spun at 500 g for 10 min using a refrigerated centrifuge, and the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37°C. After transposition reaction, the sample was purified using a Qiagen MinElute kit, and using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. To assure the PCR cycles, the full libraries were amplified for five cycles, and then 5 μl was used for Sybr Green qPCR. After determing the cycle number, the remaining 45 μl were amplified. The libraries were purified using AMPure XP beads.
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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 mm10 genome with Bowtie v2.2.9
ATAC-seq accessible regions were called with MACS2.
Reads spanning ATAC-seq regions were quantified and tabulated across all samples using DiffBind.
Differential accessibility was determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: peak calls for each sample
Supplementary_files_format_and_content: Read counts for all ATAC-seq regions across all samples
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| Submission date |
May 26, 2020 |
| Last update date |
Nov 18, 2020 |
| Contact name |
Ryan D Chow |
| E-mail(s) |
ryan.chow@yale.edu
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| Organization name |
Yale University
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| Street address |
850 West Campus Drive
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| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE151226 |
CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade (ATAC-Seq) |
| GSE151227 |
CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade |
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| Relations |
| BioSample |
SAMN15027675 |
| SRA |
SRX8401766 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4568833_Gwatac_5_peaks.narrowPeak.gz |
1.6 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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