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Sample GSM5357049 Query DataSets for GSM5357049
Status Public on Jun 05, 2021
Title VH02001704_S4
Sample type SRA
 
Source name U2OS
Organism Homo sapiens
Characteristics cell line: U2OS
cell type: osteosarcoma cell line
treatment: DMSO, ND-09-QY33, CA-90-VK59, JC-68-AL90, MB-03-IE36, JC-43-ZO95, PA-33-CK45, KA-73-NB69, QC-05-UB63, SE-15-AV21, NV-67-DX31, DB-85-YA47, NA-37-JQ34, VA-76-OV33, & LD-22-SA99 for 24 hrs
Treatment protocol U2OS cells were treated with 3.18nM, 10.04nM, 31.74nM, 100.29nM, 316.91nM, 1001.44nM, 3164.56nM, and 10000nM of DMSO, ND-09-QY33, CA-90-VK59, JC-68-AL90, MB-03-IE36, JC-43-ZO95, PA-33-CK45, KA-73-NB69, QC-05-UB63, SE-15-AV21, NV-67-DX31, DB-85-YA47, NA-37-JQ34, VA-76-OV33, & LD-22-SA99 for 24 hrs
Growth protocol Cells were plated down at 5000 cells per well in 384-well plates in DMEM + 10% FBS + 1% penicillin/streptomycin the day prior to compound treatment
Extracted molecule total RNA
Extraction protocol direct cell lysis was performed using custom-made 1x DRUGseq lysis buffer (containing 1M Tris-HCl, 2M KCl, 20% of 20% Ficoll PM-400, Triton-100, RNase Inhibitor)
DRUGseq library construction protocol using reagents from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit and Illumina Nextera XT DNA Library Preparation Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Aligned raw data using Star with reference genome GRCh38
Custom scripts to perform UMI counting and filtering out UMI duplicates
Performed differential expression using limma trend
Genome_build: ensembl human GRch38
Supplementary_files_format_and_content: Rdata object containing UMI counts data; Tab-delimited UMI counts data
 
Submission date Jun 04, 2021
Last update date Jun 06, 2021
Contact name Daniel Ho
E-mail(s) daniel.ho@novartis.com
Organization name Novartis Institutes for Biomedical Research
Street address 250 Massachusetts Avenue
City Cambridge
ZIP/Postal code 02139
Country USA
 
Platform ID GPL20301
Series (1)
GSE176150 DRUGseq U2OS cells treated with small molecules
Relations
BioSample SAMN19570141
SRA SRX11067315

Supplementary file Size Download File type/resource
GSM5357049_UMI_results_VH02001704.txt.gz 4.7 Mb (ftp)(http) TXT
GSM5357049_flowcell_4000_UMI_decode_VH02001704.RData.gz 9.6 Mb (ftp)(http) RDATA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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