Basic Information
| Dataset | E-MTAB-6204 |
|---|---|
| Status | 2018-05-01 |
| Species | Homo sapiens |
| Source | EBI ArrayExpress |
| Subcellular Localization | nuclear|cytoplasm |
| Title | Transcriptome profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination by siRNA |
| Experimental Design | We performed RNA-seq experiments on three biological replicates of HeLa cells depleted of MATR3, PTBP1/2, controls, or combined depletion of MATR3/PTBP1/2. Cells were fractionated into cytoplasmic and nuclear RNA. Library preparation was done with the TruSeq stranded RNAseq library kit (Illumina) according to manufacturer’s recommendations; RNA was depleted of rRNA using the RiboZero kit (Epicentre). All libraries were sequenced on Illumina HiSeq2 machines in a single-end manner with a read length of 100 nt. |
Sample Information
| BioProject | Sample Name | Localization | Genotype | Source | Label |
|---|---|---|---|---|---|
| PRJEB23439 | ERS2004161 | cytoplasmic RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD1 rep1 cytRNA |
| PRJEB23439 | ERS2004162 | nuclear RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD1 rep1 nucRNA |
| PRJEB23439 | ERS2004163 | cytoplasmic RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD1 rep2 cytRNA |
| PRJEB23439 | ERS2004164 | nuclear RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD1 rep2 nucRNA |
| PRJEB23439 | ERS2004165 | cytoplasmic RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD1 rep3 cytRNA |
| PRJEB23439 | ERS2004166 | nuclear RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD1 rep3 nucRNA |
| PRJEB23439 | ERS2004167 | cytoplasmic RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD2 rep1 cytRNA |
| PRJEB23439 | ERS2004168 | nuclear RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD2 rep1 nucRNA |
| PRJEB23439 | ERS2004169 | cytoplasmic RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD2 rep2 cytRNA |
| PRJEB23439 | ERS2004170 | nuclear RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD2 rep2 nucRNA |
| PRJEB23439 | ERS2004171 | cytoplasmic RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD2 rep3 cytRNA |
| PRJEB23439 | ERS2004172 | nuclear RNA | PTBP1/2 and MATR3 knock down by siRNA | HeLa cells | dKD2 rep3 nucRNA |
| PRJEB23439 | ERS2004173 | cytoplasmic RNA | scrambled siRNA | HeLa cells | siCtrl rep1 cytRNA |
| PRJEB23439 | ERS2004174 | cytoplasmic RNA | scrambled siRNA | HeLa cells | siCtrl rep2 cytRNA |
| PRJEB23439 | ERS2004175 | nuclear RNA | scrambled siRNA | HeLa cells | siCtrl rep2 nucRNA |
| PRJEB23439 | ERS2004176 | cytoplasmic RNA | scrambled siRNA | HeLa cells | siCtrl rep3 cytRNA |
| PRJEB23439 | ERS2004177 | nuclear RNA | scrambled siRNA | HeLa cells | siCtrl rep3 nucRNA |
| PRJEB23439 | ERS2004178 | nuclear RNA | scrambled siRNA | HeLa cells | siCtrl rep1 nucRNA |
| PRJEB23439 | ERS2004179 | cytoplasmic RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #1 rep1 cytRNA |
| PRJEB23439 | ERS2004180 | nuclear RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #1 rep1 nucRNA] |
| PRJEB23439 | ERS2004181 | cytoplasmic RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #1 rep2 cytRNA |
| PRJEB23439 | ERS2004182 | nuclear RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #1 rep2 nucRNA |
| PRJEB23439 | ERS2004183 | cytoplasmic RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #1 rep3 cytRNA |
| PRJEB23439 | ERS2004184 | nuclear RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #1 rep3 nucRNA |
| PRJEB23439 | ERS2004185 | cytoplasmic RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #2 rep1 cytRNA |
| PRJEB23439 | ERS2004186 | nuclear RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #2 rep1 nucRNA |
| PRJEB23439 | ERS2004187 | cytoplasmic RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #2 rep2 cytRNA |
| PRJEB23439 | ERS2004188 | nuclear RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #2 rep2 nucRNA |
| PRJEB23439 | ERS2004189 | cytoplasmic RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #2 rep3 cytRNA |
| PRJEB23439 | ERS2004190 | nuclear RNA | MATR3 knock down by siRNA | HeLa cells | siMATR3 #2 rep3 nucRNA |
| PRJEB23439 | ERS2004191 | cytoplasmic RNA | PTBP1/2 knock down by siRNA | HeLa cells | siPTBP1/2 rep1 cytRNA |
| PRJEB23439 | ERS2004192 | nuclear RNA | PTBP1/2 knock down by siRNA | HeLa cells | siPTBP1/2 rep1 nucRNA |
| PRJEB23439 | ERS2004193 | cytoplasmic RNA | PTBP1/2 knock down by siRNA | HeLa cells | siPTBP1/2 rep2 cytRNA |
| PRJEB23439 | ERS2004194 | nuclear RNA | PTBP1/2 knock down by siRNA | HeLa cells | siPTBP1/2 rep2 nucRNA |
| PRJEB23439 | ERS2004195 | cytoplasmic RNA | PTBP1/2 knock down by siRNA | HeLa cells | siPTBP1/2 rep3 cytRNA |
| PRJEB23439 | ERS2004196 | nuclear RNA | PTBP1/2 knock down by siRNA | HeLa cells | siPTBP1/2 rep3 nucRNA |
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