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933 results for “shRNA”
Synthetic datasets reflecting the shRNA-seq knockdown ENCODE data for HepG2 and K562 with coresponding GRN
<p>Synthetic data correspond to the ENCODE data for cell lines HepG2 (https://www.encodeproject.org/biosamples/ENCBS282XVK/) and K562 (https://www.encodeproject.org/biosamples/ENCBS023XVB/). The data and networks were generated using GeneSPIDER (publicly available at https://bitbucket.org/sonnhammergrni/genespider/).</p> <p> </p> <p><strong>Table.1 </strong>Description of the files</p> <table> <tbody> <tr> <td>data_HepG2like_SNR_L=0.0054699_diff=1.6188e-05.txt</td> <td>Synthetic gene expression knockdown (shRNA-seq) data immitating the ENCODE data for HepG2 cell line. Data size: 232 RBPs vs 464 experiments (2 replicates). SNR_L is the value of signal to noise ratio. Difference (diff) value tells the difference between replicate correlation coefficients of real and synthetic ENCODE data. Columns represent experiments, rows represent genes.</td> </tr> <tr> <td>data_K562like_SNR_L=0.0028692_diff=0.00017339.txt</td> <td>Synthetic gene expression knockdown (shRNA-seq) data immitating the ENCODE data for K562 cell line. Data size: 232 RBPs vs 464 experiments (2 replicates). SNR_L is the value of signal to noise ratio. Difference (diff) value tells the difference between replicate correlation coefficients of real and synthetic ENCODE data. Columns represent experiments, rows represent genes.</td> </tr> <tr> <td>network_HEPG2like_sparsity4.txt</td> <td>Synthetic scale-free gene regulatory network compatibile with data_HepG2like_SNR_L=0.0054699_diff=1.6188e-05.txt. Sparsity (average node degree) is 4 including selfloops. Direction should be read from columns to rows.</td> </tr> <tr> <td>network_K562like_sparsity4.txt</td> <td>Synthetic scale-free gene regulatory network compatibile with data_K562like_SNR_L=0.0028692_diff=0.00017339.txt. Sparsity (average node degree) is 4 including selfloops. Direction should be read from columns to rows.</td> </tr> <tr> <td>perturbations_HepG2&K562_2replicates.txt</td> <td>Perturbation matrix including information about knockeddown RBPs. Data size: 232 RBPs vs 464 experiments (2 replicates).</td> </tr> </tbody> </table> <p> </p> <p>Created by Garbulowski et al. (2024) as a part of the work entitled "Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer"</p>
BRG1 shRNA knockdown in ALCL cell lines
<p>To determine the consequences of Brg1 expression in ALCL, cells were transfected with shRNA to Brg1 leading to a decrease in Brg1 transcript and protein levels. RNA was isolated 72 hours later from the shRNA5 (TRCN0000015551) expressing cells and sequencing conducted to examine changes to the transcriptome mediated by Brg1. Following differential gene expression analysis of the scrambled shRNA versus shRNA5, the transcriptome was identified as being dramatically altered showing both downregulation (2,527 mRNA transcripts: of a cumulative 26,833 genes, adj. <em>p</em> ≤ 0.05) and upregulation (2,900 mRNA transcripts, of a cumulative 26,833 genes, adj. <em>p</em> ≤ 0.05) of genes. When analysing the the 15,285 protein-coding genes alone, 1,934 (13%) were downregulated while 2,797 (18%) were upregulated (adj. <em>p</em> ≤ 0.05). To establish which physiological processes are most affected by the activity of BRG1, pathway enrichment analyses were undertaken. The input comprised of the significant (adj. <em>p</em> ≤ 0.05) protein-coding targets, where the absolute log2 fold change of expression was ± 1.5. Transcripts whose expression was either induced (n=33) or repressed (n=243) by BRG1 were investigated. Reactome analysis suggests that BRG1 plays roles in upregulating genes associated with the cell cycle, while suppressing genes associated with epigenetic regulation. </p>
Pbi-shRNA™ EWS/FLI1 Type 1 LPX in Subjects With Advanced Ewing's Sarcoma
ClinicalTrials.gov study NCT02736565. IPD Sharing: NO. Countries: 1. Publications: 4.
Trial of Bi-shRNA-furin and GMCSF Augmented Autologous Tumor Cell Vaccine for Advanced Cancer
ClinicalTrials.gov study NCT01061840. IPD Sharing: NO. Countries: 1. Publications: 6.
Phase I Intratumoral Pbi-shRNA STMN1 LP in Advanced and/or Metastatic Cancer
ClinicalTrials.gov study NCT01505153. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Esterase- responsive SLC7A11 shRNA Delivery System Induced Ferroptosis and Suppressed Hepatocellular Carcinoma Progression
Open the record for dataset details and reuse information.
shRNA RNA-seq from K562 (ENCSR481YXD)
GEO Series GSE88302. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from HepG2 (ENCSR741YCA)
GEO Series GSE88502. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Illumina bead array -/+ UV ASCC3 long isoform shRNA knockdown cells
GEO Series GSE92327. Homo sapiens. 12 samples. Type: Expression profiling by array.
shRNA RNA-seq from HepG2 (ENCSR471GIS)
GEO Series GSE88292. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from K562 (ENCSR555LCE)
GEO Series GSE177341. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from HepG2 (ENCSR457WBK)
GEO Series GSE88285. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from HepG2 (ENCSR674KDQ)
GEO Series GSE88452. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from K562 (ENCSR958NDU)
GEO Series GSE88671. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from K562 (ENCSR815CVQ)
GEO Series GSE88563. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from K562 (ENCSR792XFP)
GEO Series GSE80927. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from HepG2 (ENCSR116YMU)
GEO Series GSE88045. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from HepG2 (ENCSR104ABF)
GEO Series GSE88031. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from K562 (ENCSR949RMX)
GEO Series GSE177924. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
shRNA RNA-seq from K562 (ENCSR379VXW)
GEO Series GSE88233. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.