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TranscriptomicsMetaphase-Chromosome-Organization
Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two alternative three-dimensional folding state...
ORGANISM(S): Homo sapiens 
2013-11-05 | E-MTAB-1948 | biostudies-arrayexpress
TranscriptomicsChromatin accessibility by ATAC-seq in WT and HIRA KO HeLa cells
We profiled accessibility by ATAC-seq of G1/S-synchronised 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-14415 | biostudies-arrayexpress
TranscriptomicsTotal RNA-seq in WT and HIRA KO HeLa cells
We performed total RNA-seq of G1/S-synchronised 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-14417 | 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
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
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
UnknownA pathway for mitotic chromosome formation.
Not available
S-EPMC5924687 | biostudies-literature
UnknownSpatial organization of transcribed eukaryotic genes.
Not available
S-EPMC9380065 | biostudies-literature
TranscriptomicsTranscription profiling of embryonic and hematopoietic stem cells lacking the transcription factor Zfx to provide insight into the role of Zfx in embryonic and adult stem cell self-renewal
Stem cells (SC) exhibit a unique capacity for self-renewal in an undifferentiated state. It is unclear whether the self-renewal of pluripotent embryonic SC (ESC) and of tissue-specific adult SC such as hematopoietic SC (HSC) is controlled by common mechanisms. The deletion of transcription factor Zf...
ORGANISM(S): Mus musculus 
2007-11-07 | E-GEOD-7069 | biostudies-arrayexpress
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