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TranscriptomicsSelect microRNAs are essential for early development in the sea urchin.
microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many developmental events. The transcriptional network during early embryogenesis of the purple sea urchin, Strongylocentrotus purpuratus, is well described and w...
ORGANISM(S): Strongylocentrotus purpuratus 
2012-02-17 | E-GEOD-35876 | biostudies-arrayexpress
TranscriptomicsRNA-seq of Mycobacterium tuberculosis H37Rv treated with alpibectir or a combination of alpibectir and ethionamide against untreated controls
Alpibectir potentiates the activity of ethionamide and prothionamide, which are second-line antibiotics used for tuberculosis treatment. Both are prodrugs whose antibacterial activity depends on bioactivation by oxidases, including the Baeyer-Villiger monooxygenase MymA. Alpibectir binds the transcr...
ORGANISM(S): Mycobacterium tuberculosis 
2025-12-10 | E-MTAB-16253 | biostudies-arrayexpress
TranscriptomicsHi-C to compare 3D genome organisation in WT to HIRA KO HeLa cells
We performed Hi-C in asynchronous HeLa cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene.
ORGANISM(S): Homo sapiens 
2025-08-07 | E-MTAB-14433 | biostudies-arrayexpress
TranscriptomicsHi-C to compare 3D genome organisation in HIRA KO HeLa cells rescued with HIRA
We performed Hi-C in asynchronous HeLa cells that knock-out (KO) for the H3.3-specific chaperone HIRA and bear an exogenous H3.1-SNAP and H3.3-SNAP gene transfected with HIRA-YFP (HIRA) or YFP only (control) plasmid.
ORGANISM(S): Homo sapiens 
2025-08-07 | E-MTAB-14431 | biostudies-arrayexpress
GenomicsEdU-seq and H3 variant SNAP capture-seq in HIRA KO HeLa cells rescued with HIRA
Our previous work on the histone H3.3 chaperone HIRA revealed its importance for maintaining the targeting of H3.3 to its pre-existing sites. In concert with replication fork-coupled deposition of the replicative H3.1 variant, this establishes boundaries of H3.3/H3.1, which define early replication ...
ORGANISM(S): Homo sapiens 
2025-08-07 | E-MTAB-14419 | biostudies-arrayexpress
TranscriptomicsIllumina sequencing of small RNAs from C. elegans embryos
Caenorhabditis elegans is one of the most prominent model systems to study embryogenesis. However, it has been impractical to collect large amounts of precisely staged embryos. Thus, early C. elegans embryogenesis has not been amenable to most modern high-throughput genomics or biochemistry assays. ...
ORGANISM(S): Caenorhabditis elegans 
2009-09-06 | E-GEOD-17153 | biostudies-arrayexpress
GenomicsDistribution of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in WT and HIRA KO HeLa cells
We profiled the enrichment of active (H3K4me1, H3K4me3, H3K27ac) and inactive (H3K9me3, H3K27me3) histone PTMs in cells that are wild-type (WT) or knock-out (KO) for the H3.3-specific chaperone HIRA. We performed native ChIP-seq following MNase digestion to isolate nucleosomes in H3.1-SNAP and H3.3-...
ORGANISM(S): Homo sapiens 
2025-08-07 | E-MTAB-14416 | biostudies-arrayexpress
Transcriptomics454 Life Sciences/Roche and Illumina sequencing of small RNAs from planarian samples
Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule required for piRNA expression in planarians....
ORGANISM(S): Schmidtea mediterranea 
2009-06-30 | E-GEOD-16159 | biostudies-arrayexpress
TranscriptomicsmiRNA expression profile in breast cancer cells
We performed microRNA sequencing (miRNA-seq) according to Illumina sequencing protocols. Total RNA extracted from MCF-7 cells expressing human ER-beta in absence of estrogen stimuli was subjected to size selection labrary preparation ond retrotranscribed. Obtained DNA was sequenced with the Illumina...
ORGANISM(S): Homo sapiens 
2014-11-13 | E-MTAB-2085 | biostudies-arrayexpress
TranscriptomicsmiRNA expression profile in breast cancer cells
We performed microRNA sequencing (miRNA-seq) according to Illumina sequencing protocols. Total RNA extracted from MCF-7 cells expressing or not human Erbeta in absence of estrogen stimuli was subjected to size selection labrary preparation ond retrotranscribed. Obtained DNA was sequenced with the Il...
ORGANISM(S): Homo sapiens 
2014-04-09 | E-MTAB-1495 | biostudies-arrayexpress
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