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Sample GSM4605987 Query DataSets for GSM4605987
Status Public on Dec 17, 2020
Title 3_DLD1_siVPS37A#1
Sample type SRA
 
Source name DLD1_siVPS37A#1
Organism Homo sapiens
Characteristics cell line: DLD1
sirna: siVPS37A#1
batch: 3
Treatment protocol Cells were plated in 12-well plate format at the density 60,000 cells/ml in 1 and 2 ml of medium, respectively. After 16-24 h cells were left non-transfected or differentially transfected according to the forward transfection protocol with combinations of siRNA molecules specified in Table S4. The following PreDesigned or Validated Ambion Silencer Select siRNAs (Thermo Fisher Scientific) were used: Negative Control No. 1 (siNC#1, 4390843), on-target siVPS37A#1 (s44037), siVPS37B#1 (s36177), and siVPS37C#1 (s30059). Additionally, two custom-ordered Silencer Select duplexes were used: Negative Control No. 3 (NC3, sense strand 5’->3’ UACGACCGGUCUAUCGUAGtt, antisense strand 5’->3’ CUACGAUAGACCGGUCGUAtt) and Negative Control No. 4 (NC4, sense strand 5’->3’ UUCUCCGAACGUGUCACGUtt, antisense strand 5’->3’ ACGUGACACGUUCGGAGAAtt). 72h later, cells were washed with PBS and cell pellet was collected.
Growth protocol Human colorectal carcinoma cell line DLD1 was obtained fom American Type Culture Collection (ATCC). DLD1 were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich, M2279) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma-Aldrich, F7524) and 2 mM L-Glutamine (Sigma-Aldrich, G7513). Cells were cultured in an incubator at 37°C in a humidified atmosphere containing 5% CO2. During the study, cells were regularly tested for mycoplasma and the identities of DLD1 and RKO were confirmed by short tandem repeat (STR) profiling performed by the ATCC Cell Authentication Service.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with RNeasy Mini Kit (Qiagen, 74104) followed by on-column DNase digestion according to manufacturer’s protocol.
Library was prepared with the Ion AmpliSeq Transcriptome Human Gene Expression Panel (Thermo Fisher, USA)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description IonXpress_052_rawlib.89
Data processing torrent mapper, version 5.0.4
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
removal of features with less then 100 counts based on the sum of normalized counts across all samples, removal of non-protein coding features
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix
 
Submission date Jun 10, 2020
Last update date Dec 17, 2020
Contact name Krzysztof Goryca
Organization name Uniwersytet Warszawski
Department CeNT
Street address Banacha 2c
City Warszawa
ZIP/Postal code 02-097
Country Poland
 
Platform ID GPL17303
Series (1)
GSE152195 Concurrent depletion of Vps37 proteins evokes inflammatory response and cell growth inhibition via ESCRT-I destabilization.
Relations
BioSample SAMN15198387
SRA SRX8518626

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

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