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| Status |
Public on Jun 05, 2021 |
| Title |
VH02001712_S1 |
| 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 |
SAMN19570138 |
| SRA |
SRX11067318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5357052_UMI_results_VH02001712.txt.gz |
4.9 Mb |
(ftp)(http) |
TXT |
| GSM5357052_flowcell_4000_UMI_decode_VH02001712.RData.gz |
10.2 Mb |
(ftp)(http) |
RDATA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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