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Status |
Public on Mar 30, 2022 |
Title |
LN7-1112AR 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 |
SAMN27064469 |
SRA |
SRX14660738 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5983271_LN7_1112AR-coverage-tss-norm.bw |
575.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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