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Status |
Public on Jun 05, 2021 |
Title |
VH02001704_S4 |
Sample type |
SRA |
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Source name |
U2OS
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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
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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
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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
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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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
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Submission date |
Jun 04, 2021 |
Last update date |
Jun 06, 2021 |
Contact name |
Daniel Ho |
E-mail(s) |
daniel.ho@novartis.com
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Organization name |
Novartis Institutes for Biomedical Research
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Street address |
250 Massachusetts Avenue
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City |
Cambridge |
ZIP/Postal code |
02139 |
Country |
USA |
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Platform ID |
GPL20301 |
Series (1) |
GSE176150 |
DRUGseq U2OS cells treated with small molecules |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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