NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5507880 Query DataSets for GSM5507880
Status Public on Aug 08, 2021
Title DM2_2541
Sample type SRA
 
Source name MP41
Organism Homo sapiens
Characteristics cell type: Uveal melanoma cells
cell line: MP41
treatment: DMSO
Treatment protocol Cells were grown under regular conditions until they reached approximately 80% confluence. Culture media (RPMI) containing the following compounds dissolved in DMSO (Fisher BioReagents), or an equal volume of DMSO, were added to the cells; 50 μM PRT (PRT4165, Sigma-Aldrich), 1 μM UMK57 (Aobious) and 0.5 μM reversine (Cayman Chemical). For experiments with treatment extending beyond 2 hours, culture media were supplemented with 10% FBS and replenished after the first 24 hours, with the applicable compound.
Growth protocol Melanoma cells were grown in RPMI-1640 media (Gibco) supplemented with 10% fetal bovine serum (FBS, Sigma). Cell culture media were supplemented with 1% penicillin/streptomycin and cells were maintained at 37 °C and 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was the extracted using the QIAShredder and the RNeasy extraction kit (Qiagen) and sequenced on NovaSeq (Illumina) to generate 150 bp pair-end reads. CUT&RUN were prepared using the CUTANA kit (EpiCypher, 14-1048)
RNA libraries were prepared for sequencing using standard Illumina protocols, CUT&RUN Library preparation was performed using the NEBNext Ultra II Library Prep Kit for Illumina (New England BioLabs, E7103S)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Exp1_Gene_normalized_counts.txt
Data processing Raw reads (FASTQ) were aligned to the human reference genome (Ch38) using STAR on Partek Flow software, version 8.0. Aligned reads were mapped to transcripts (Ensembl Transcripts release 102) using Partek’s modified expectation-maximization (EM) algorithm for transcript quantification, with strict paired-end compatibility. Gene counts were normalized per sample to generate fragments Per Kilobase of transcript per Million mapped reads (FPKM) values.
Raw reads (FASTQ) were aligned to the human reference genome (Ch38), using STAR on Partek Flow software, version 10.0 (Partek). Genomic peaks were called using MACS2 with the following parameters (BAM, cutoff q-value 0.05, no down-sampling).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample
 
Submission date Aug 06, 2021
Last update date Aug 08, 2021
Contact name Mathieu F Bakhoum
Organization name Yale University
Department Ophthalmology
Lab Bakhoum Laboratory
Street address 300 George St.
City New Haven
State/province CT
ZIP/Postal code 06510
Country USA
 
Platform ID GPL24676
Series (1)
GSE181600 Loss of PRC1 in Uveal melanoma
Relations
BioSample SAMN20603340
SRA SRX11664661

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap