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Questions tagged [cell-line]

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6
votes
2answers
169 views

How can the cell line contribution be estimated from RNASeq data?

Using a laser-capture microdissection of cells a group of cells stained with the marker of interest was sequenced. In another cohort of patients (this is all human liver tissue) the whole tissue was ...
6
votes
2answers
321 views

Searching for gene expression data by cell line

I have two cancer cell lines (OCI-Ly18 & riva) that I want to find gene expression data for, but I'm not aware of many gene expression databases that allow searching by cell-line without searching ...
5
votes
1answer
61 views

Should the cell sorting marker genes be excluded during clustering?

We sort different populations of blood cells using a number of fluorescent flow cytometry markers and then sequence RNA. We want to see what the transcriptome tells us about the similarity and ...
3
votes
2answers
47 views

Where can I find gene expression data on one of the cell lines in NCI-60?

I'm trying to retrieve the most expressed genes from a cell line from the NCI-60, lets say cell line NCI-H23, but I'm not sure where to find the gene expression data. My main goal is to create a ...
3
votes
2answers
97 views

How to link GDC ids to CCLE cell line names?

Hello bioinformaticians, I've recently downloaded few RNAseq data files from Genomic Data Commons Data (GDC) portal. These files belong to Broad institutes CCLE project. Now the problem is that GDC ...
2
votes
0answers
29 views

Working with the additional cell lines in NCI-60

NCI-60 has additional cell lines, but when I get results from CellMiner they are not included in there. Namely, the genes such as: DLD-1(Colon), ...
1
vote
1answer
46 views

How to access the patient-derived xenografts (PDXs) repository?

I saw this nature news item, it sounds that Cellminer is obsolete, is it right? What are the new tools to analyze the "new cell lines"? Where's the PDX repository? What about the European initiative ...
1
vote
1answer
28 views

semantic similarity measurement for cell line ontologies

I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies. The problem I have is that I have found a Python library called Fastsemsim, but it ...
1
vote
0answers
74 views

Help with generating network from gene expression data

I'm struggling to figure out how to go from gene expression data to be able to create a network out of the most expressed genes in a cell line. Ok, I have developed an application for Cytoscape where ...