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Sample GSM5983271 Query DataSets for GSM5983271
Status Public on Mar 30, 2022
Title LN7-1112AR ATAC
Sample type SRA
 
Source name melanoma cell line
Organism Mus musculus
Characteristics strain: C57BL/6
Growth protocol All cell lines are grown in DMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin
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
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
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.
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
 
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
Organization name Stanford University
Department Pathology
Lab Engleman Lab
Street address 3373 Hillview Ave
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platform ID GPL24247
Series (1)
GSE117529 RNA/WES/ATAC/scRNA sequencing of murine melanoma primary and LN metastases
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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