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TranscriptomicsTranscription profiling of human primary effusion lymphoma cell lines reveals Kaposis sarcoma-associated herpesvirus encodes an ortholog of miR-155
MicroRNAs are small, non-coding RNAs that post-transcriptionally regulate gene expression by binding to 3’UTRs of target mRNAs. Kaposi’s sarcoma-associated herpesvirus (KSHV), a virus linked to malignancies including primary effusion lymphoma (PEL), encodes 12 miRNA genes, but only a few regulat...
ORGANISM(S): Homo sapiens 
2008-06-16 | E-GEOD-9264 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of Streptococcus agalactiae strain 2603 V/R and isogenic Delta_csrRS mutant grown in the presence or in the absence of glucose
Comparative global gene expression analysis of the 2603 V/R Streptococcus agalactiae (Group B streptococcus, GBS) strain grown in a medium devoid of sugars versus bacteria incubated for 30 min in 55 mM glucose medium. To investigate whether glucose-dependent regulation of gene expression was modulat...
ORGANISM(S): Streptococcus agalactiae 
2013-07-15 | E-MTAB-1100 | biostudies-arrayexpress
TranscriptomicsDetection and removal of barcode swapping in single-cell RNA-seq data
Barcode swapping results in the mislabeling of sequencing reads between multiplexed samples on the new patterned flow cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays, especially for single-cell studies where many samples are routinely multiplexed togeth...
ORGANISM(S): Mus musculus 
2018-06-25 | E-MTAB-6854 | biostudies-arrayexpress
TranscriptomicsPrediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells
Background: The ability to predict the spatial frequency of relapses in multiple sclerosis (MS) would enable treating physicians to decide when to intervene more aggressively and to plan clinical trials more accurately. Methods: In the current study our objective was to determine if subsets of gene...
ORGANISM(S): Homo sapiens 
2009-07-15 | E-GEOD-15245 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of Drosophila melanogaster transcription factors BCD, HB, KR, KNI, GT, CAD, HKB, TLL, D, FTZ, HRY, PRD, RUN, SLP1, DA, DL, MAD, MED, SHN, SNA, TWI, TFIIB and RNA polII
ChIP-chip was performed using chromatin isolated from formaldehyde crosslinked, staged embryos, and affinity purified antibodies against 21 transcription factors (including: BCD, HB, KR, KNI, GT, CAD, HKB, TLL, D, FTZ, HRY, PRD, RUN, SLP1, DA, DL, MAD, MED, SHN, SNA, TWI) that belong to 11 DNA bind...
ORGANISM(S): Drosophila melanogaster 
2009-07-27 | E-TABM-736 | biostudies-arrayexpress
TranscriptomicsHeLa cell response to overexpression of wild type and mutated forms of the P19 splice variant of c-H-ras
The c-H-ras proto-oncogene undergoes alternative splicing of the exon termed IDX giving rise to a novel protein of the Ras family, p19 (H-RasIDX). The experiment tests the effect on the transcriptome of overexpressing the wild type and W164A mutated forms of p19. Keywords: genetic modification Thre...
ORGANISM(S): Homo sapiens 
2009-12-29 | E-GEOD-12059 | biostudies-arrayexpress
TranscriptomicsMLL Fusion Proteins Preferentially Regulate a Small Set of Wild Type MLL Target Genes in the Leukemic Genome
MLL encodes a histone methyltransferase that is critical in maintaining gene expression during embryonic development and hematopoiesis. 11q23 translocations encode chimeric MLL fusions that act as potent drivers of acute leukemia. However, it remains unclear what portion of the leukemic genome is un...
ORGANISM(S): Mus musculus 
2011-04-28 | E-GEOD-24794 | biostudies-arrayexpress
TranscriptomicsCanonical and non-canonical EcfG sigma factors control the general stress response in Rhizobium etli
A core component of the M-NM-1-proteobacterial general stress response is the extracytoplasmic function (ECF) sigma factor EcfG, exclusively present in this taxonomic class. Half of the completed M-NM-1-proteobacterial genome sequences contain two or more copies of genes encoding M-OM-^CEcfG-like si...
ORGANISM(S): Rhizobium etli CFN 42 
2013-12-20 | E-GEOD-53517 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of human fetal hearts at 9, 12 and 16 weeks of gestation
RNA-Seq was used to study alterations in gene expression in the developing human heart across three gestational ages in the first and early second trimester. All tissue was acquired following elective termination of pregnancy and informed parental consent. Storage and use of tissue was in premises l...
ORGANISM(S): Homo sapiens 
2018-10-24 | E-MTAB-7031 | biostudies-arrayexpress
TranscriptomicsExpression data from WT (Columbia) and pifq (pif1pif3pif4pif5) mutant Arabidopsis seedlings
Plants respond to changes in the red:far red ratio (R:FR) of incident light. A reduction in this ratio (increase in FR) results in the Shade Avoidance Response (SAR) with associated changes in gene expression. The Phyotchrome-Interacting Factors (PIFs) are bHLH transcription factors known to be invo...
ORGANISM(S): Arabidopsis thaliana 
2012-08-01 | E-GEOD-28297 | biostudies-arrayexpress
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