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TranscriptomicsChromatin position effects assayed by thousands of reporters integrated in parallel (cell lines with mPGK IRs)
Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcripti...
ORGANISM(S): Mus musculus 
2013-08-16 | E-GEOD-49807 | biostudies-arrayexpress
TranscriptomicsChromatin position effects assayed by thousands of reporters integrated in parallel (mPGK TRIP pools)
Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcripti...
ORGANISM(S): Mus musculus 
2013-08-16 | E-GEOD-48608 | biostudies-arrayexpress
TranscriptomicsChromatin position effects assayed by thousands of reporters integrated in parallel (tet-Off TRIP pools)
Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcripti...
ORGANISM(S): Mus musculus 
2013-08-16 | E-GEOD-49806 | biostudies-arrayexpress
TranscriptomicsReorganization of nuclear lamina – genome interactions upon differentiation of embryonic stem cells.
The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. We present a genome-wide analysis of the interactions between chromatin and the nuclear lamina during differentiation of mouse embryonic stem cells (ESCs) into lineage-co...
ORGANISM(S): Mus musculus 
2010-05-27 | E-GEOD-17051 | biostudies-arrayexpress
GenomicsHigh-throughput semi-quantitative analysis of insertional mutations in heterogeneous tumors
Exploiting the full potential of insertional mutagenesis screens with retroviruses and transposons requires methods for distinguishing clonal from subclonal insertion events within heterogeneous tumor cell populations. Current protocols, based on ligation mediated PCR, depend on endonuclease based f...
ORGANISM(S): Mus musculus 
2011-08-11 | E-GEOD-22657 | biostudies-arrayexpress
TranscriptomicsChromatin position effects assayed by thousands of reporters integrated in parallel (RNA-Seq)
Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcripti...
ORGANISM(S): Mus musculus 
2013-08-16 | E-GEOD-48607 | biostudies-arrayexpress
TranscriptomicsSERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B are markers of resistance to neoadjuvant chemotherapy in HER2-negative breast cancer
Abstract Introduction Response rates to chemotherapy remain highly variable in breast cancer patients. We set out to identify genes associated with chemotherapy resistance. We analyzed what is currently the largest single-institute set of gene expression profiles derived from breast cancers prior t...
ORGANISM(S): Homo sapiens 
2012-12-01 | E-GEOD-34138 | biostudies-arrayexpress
TranscriptomicsVariation in RNA expression in a panel of 30 breast cancer cell lines
RNA expression was measured using RNA sequencing in 30 different breast cancer cell lines, under untreated, exponentially growing conditions.
ORGANISM(S): Homo sapiens 
2019-01-09 | E-MTAB-4801 | biostudies-arrayexpress
TranscriptomicsComparison of lymph node negative (N0) and lymph node metastasis (N+) head and neck squamous-cell carcinomas (HNSCC)
A classifier was build on 82 training samples to differentiate between lymph node negative (N0) and lymph node metastasis (N+) head and neck squamous-cell carcinomas (HNSCC). The 102 predictor genes that resulted from this classifier where then validated against a independent validation set.
ORGANISM(S): Homo sapiens 
2005-01-09 | E-UMCU-11 | biostudies-arrayexpress
TranscriptomicsFra1 silencing in MDA-MB-231 cells
Fra1 silencing in MDA-MB-231 cells
ORGANISM(S): Homo sapiens 
2013-07-24 | E-MTAB-1230 | biostudies-arrayexpress
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