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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 17, 2020 |
| Title |
2_DLD1_siVPS37ABC#1 |
| Sample type |
SRA |
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| Source name |
DLD1_siVPS37ABC#1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1
sirna: siVPS37ABC#1
batch: 2
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| 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.
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| 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.
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
IonXpress_013_rawlib.84
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| 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
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| Submission date |
Jun 10, 2020 |
| Last update date |
Dec 17, 2020 |
| Contact name |
Krzysztof Goryca |
| Organization name |
Uniwersytet Warszawski
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| Department |
CeNT
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| Street address |
Banacha 2c
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| City |
Warszawa |
| ZIP/Postal code |
02-097 |
| Country |
Poland |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE152195 |
Concurrent depletion of Vps37 proteins evokes inflammatory response and cell growth inhibition via ESCRT-I destabilization. |
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| Relations |
| BioSample |
SAMN15198392 |
| SRA |
SRX8518619 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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