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TranscriptomicsThe polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq
We have examined the nuclear (nuc) and cytoplasmic (cyt) polyA+ transcriptomes of undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5) using strand-specific RNA-Seq. The 46C mouse embryonic stem cell line was used for this study. Two cell types were exa...
ORGANISM(S): Mus musculus 
2012-08-01 | E-GEOD-38990 | biostudies-arrayexpress
TranscriptomicsFragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
To accelerate previous RNA structure probing approaches, which focus on analyzing one RNA sequence at a time, we have developed FragSeq, a high-throughput RNA structure probing method that uses high-throughput RNA sequencing to identify single-stranded RNA (ssRNA) regions from fragments generated by...
ORGANISM(S): Mus musculus 
2010-11-07 | E-GEOD-24622 | biostudies-arrayexpress
TranscriptomicsA Central Role for RAF-MEK-ERK Signaling in the Genesis and Maintenance of Pancreatic Ductal Adenocarcinoma.
Although KRAS mutation is a hallmark of pancreatic ductal adenocarcinoma (PDA), mutated KRAS remains an intractable pharmacological target. Consequently, an understanding of the RAS effector pathway(s) required for PDA maintenance is critical for improved strategies to treat this disease. Here we ...
ORGANISM(S): Mus musculus 
2012-07-09 | E-GEOD-30562 | biostudies-arrayexpress
TranscriptomicsMutation independent activation of the Notch pathway is associated with Lapatinib resistance in Her2+ breast cancer cell lines
We compared untreated HCC1419 cells with Lapatinib resistant HCC1419 cells that were either treated with Lapatinib for only 9 days before harvesting (drug tolerant persisters, DTPs) or were growing in the presence of Lapatinib (>70 days) (drug tolerant expanded persisters, DTEPs). We show that the N...
ORGANISM(S): Homo sapiens 
2015-01-15 | E-GEOD-62074 | biostudies-arrayexpress
TranscriptomicsHuman embryonic stem cell, rhesus embryonic stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) RNA-seq
We compared the expression in embryonic stem cells of KRAB ZNF proteins and retrotransposon elements in the human genome under several conditions. Native human stem cells. Mouse stem cells containing a transchromosomic copy of human chromosome 11, with and without the introduction of plasmids contai...
ORGANISM(S): Macaca mulatta 
2014-09-29 | E-GEOD-60178 | biostudies-arrayexpress
GenomicsHuman stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) ChIP-seq
We compared the binding patterns in embryonic stem cells of KAP1 and KRAB Zinc Finger (KZNF) proteins as well as H3K4me3 DNA under several conditions. Native human stem cells. Mouse stem cells containing a transchromosomic copy of human chromosome 11, with and without the introduction of plasmids co...
ORGANISM(S): Mus musculus 
2014-09-29 | E-GEOD-60210 | biostudies-arrayexpress
GenomicsEGAD00000000119
Genotypes from cell lines derived from breast carcinoma tissue
EGAD00000000119 | EGA
GenomicsAssessment of genomic copy number alterations in breast cancer
The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.
EGAS00000000059 | EGA
GenomicsBreast Cancer Cell Line Data Access Committee
Access to data is available by emailing application to the data access committee and will be granted to qualified investigators for appropriate use.
EGAC00000000015 | EGA
UnknownKey Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
Not available
S-EPMC7652061 | biostudies-literature
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