GEO series

miRNA34 expression in SW480 cells

GSE7678 Homo sapiens (human) Expression microarray 8 samples Submitted 2007/08/20 Platform GPL570

At a glance

Expression microarray · human · 8 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 8 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

SW480 were stably transfected with an episomal plasmid expressing GFP and miRNA34 from a bidirectional doxycyclin regulatable promoter (Bornkamm et al Nucleic Acids Res. 2005 Sep 7;33(16)). Polyclonal cell lines were obtained by selection with Hygromycin at 350ug/ml for 10 days. The cell llnes identified as GFP only express GFP, whereas the cell lines identified as miRNA34a express both GFP and miRNA34 under doxycyclin control.

Read the full summary ↓

For the present experiment, cells were treated with 1ug/ml Docycyclin for 72h. Cells were harvested and total RNA was isolated using Trizol (Invitrogen). After RNA cleanup (RNeasy, Qiagen) Affymetrix 133 Plus 2.0 micorarrays were hybridized using standard techniques. Keywords: Cell line transfection

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE7678_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA99475. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 17656095) ↗

Samples in this study

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+ 8 more — browse all 8 samples with per-sample file links →

Datasets on a similar topic

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GSE253110 The SW480 cell line as a model of resident and migrating colon cancer stem cells 8 samples shares sw480
GSE266220 RNA sequencing analysis of SW480 cells treated with Amuc_0904 6 samples shares sw480
GSE312195 MEK inhibition induces AXIN1 loss in colorectal cancer by mTOR associated suppression of protein synthesis [RNASeq_SW480] 27 samples shares sw480
GSE299428 RNA-seq of oxaliplatin resistant HCT116 and SW480 24 samples shares sw480
GSE254891 Deep transcriptional profiling of the two cancer stem cell populations present in the SW480 cell line as presented in "Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments" [bulk RNA-seq] 10 samples shares sw480
GSE314387 Recurrent ZC3H18 mutations stabilize oncogenic endogenous retroviral RNA [SW480_pA] 6 samples shares sw480

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