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| Status |
Public on Mar 30, 2022 |
| Title |
B16-F0 #4 ATAC |
| Sample type |
SRA |
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| Source name |
melanoma cell line
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
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| Growth protocol |
All cell lines are grown in DMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lines were trypsinized, washed with complete serum, centrifuged, and washed with PBS. Following washing cell pellets were frozen at -80C. After thawing, cells were resuspended in buffer RLT and lysed using QiaShredders. Extraction was performed using the Qiagen RNEasy Plus mini kit according to the manufacturer's protocol.
Library construction (RNA-seq) was performed by MedGenome using the Illumina TruSeq stranded mRNA kit
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Samples were prepared for ATAC-seq following the Omni-ATAC protocol (Corces et al., 2017). Briefly, cells detached with Accutase, washed in PBS, and resuspended in 50μL of ATAC-Resuspension Buffer (RSB, water with 10mM Tris-HCL, 10mM NaCl, and 3mM MhCl2) supplemented with 0.1% NP40 (Sigma), 0.1% Tween-20 (Sigma), and 0.01% Digitonin (Promega). Cells were incubated on ice for 3 minutes prior to adding 1mL RSB + 0.1% Tween-20. Samples were centrifuged and resuspended in 50μL of transposition mixture (2X TDE buffer + 2.5μL Tn5 Transposase (Illumina Tagment DNA Enzyme) + PBS + Digitonin + Tween-20 + water) incubated for 30min at 37°C on an orbital shaker. Samples were cleaned with the Zymo DNA Clean and Concentrator-5 Kit. Samples were amplified for 5 cycles using the NEBNext 2X Master Mix, after which 5μL of the reaction was subjected to qRT-PCR amplification to determine the optimum number of additional cycles for each sample. The remainder of the initial reactions were then amplified these additional number of cycles (ranging from 5 to 7). Library cleanup was performed using the Zymo DNA Clean and Concentrator-5 Kit, samples were eluted in water, and library quantification was performed using the KAPA Library Quantification Kit according to the manufacturer’s protocol.
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| Data processing |
Raw sequencing reads were filtered and adapters trimmed using Trimmomatic v0.36. Quality was assessed using FastQC v0.11.3.
Transcript abundance was quantified using Salmon v0.7.2 in quasi-mapping mode and using the sequence, GC, and position bias correction parameters.
Differential expression analysis was performed using DESeq2.
Assembly: GRCm38 GENCODE release M11
Supplementary files format and content: tab-delimeted files contain TPM values for each sample generated by Salmon
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| Submission date |
Mar 29, 2022 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Nathan Edward Reticker-Flynn |
| E-mail(s) |
naterf@stanford.edu, retickerflynn@stanford.edu
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| Organization name |
Stanford University
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| Department |
Pathology
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| Lab |
Engleman Lab
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| Street address |
3373 Hillview Ave
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE117529 |
RNA/WES/ATAC/scRNA sequencing of murine melanoma primary and LN metastases |
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| Relations |
| BioSample |
SAMN27064464 |
| SRA |
SRX14660733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5983266_B16_F0_Luc_4-coverage-tss-norm.bw |
404.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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