Project description:Characterization of three hepatocyte cell lines (2 parental and 1 clone), under two different media conditions. Parental cell lines HepG2 and HC-04, single cell cloned from HC-04 defined as HC-04.J7. The goal of the project initially was to investigate the invasion of hepatocytes by Plasmodium falciparum sporozoites, and once found that the HC-04 cell had a higher invasion than HepG2, single cell isolates were generated from HC-04 before being expanded. The resulting HC-04.J7 isolate further improved the invasion rate. Transcriptomic and proteomic data sets were generated from all cell lines in both media, than analyzed for potential receptors or biochemical pathways that play a role in the increased invasion of HC-04 and specifically, HC-04.J7.

2019-11-12 | PXD008613 | Pride

Candidatus Carsonella ruddii HC isolate Thao2000 strain:HC

Project description:Candidatus Carsonella ruddii HC Genome Sequencing

| PRJNA165187 | ENA

PfAP2-HC, an unusual, heterochromatin-associated ApiAP2 factor of Plasmodium falciparum

Project description:In this study we have investigated PfAP2-HC (PF3D7_1456000), a protein that was identified by co-immunoprecipitation with PfHP1 coupled with liquid chromatography-tandem mass spectrometry. PfAP2-HC belongs to the ApiAP2 family, the main transcription factor family in Apicomplexan parasites. We have confirmed that AP2-HC colocalises with HP1 with the use of immunofluorescence assays and chromatin immunoprecipitation-sequencing. We show that PfAP2-HC is not required for heterochromatin maintenance and inheritance with the use of PfAP2-HC Kock out and knockdown. We show with transcriptome-wide microarray time course analysis that PfAP2-HC does not act as a transcription factor in blood stage parasites. We demonstrate that the AP2 domain is dispensable for heterochromatin targeting by introducing a premature stop codon before the AP2 domain. We show that PfAP2-HC binding to heterochromatin dependents on PfHP1. and PfAP2-HC is likely not involved in de novo heterochromatin formation

2020-11-04 | GSE154840 | GEO

Oxalobacter formigenes strain:HC-1 | isolate:HC-1

Project description:Genome sequence of Oxalobacter formigenes Human Strain HC-1

| PRJNA353993 | ENA

Pectobacterium parmentieri strain:HC

Project description:Pectobacterium parmentieri strain:HC Genome sequencing

| PRJNA591387 | ENA

Control of agricultural traits by hc-siRNA associated MITEs in rice

Project description:Transposable elements (TEs) and repetitive sequences comprise over 40% of rice genome. Different TEs are tightly regulated by distinct epigenetic mechanisms. For example, the activities of LTR retrotransposon Tos17 and non-LTR retrotransposon LINE element Karma are uniquely regulated by histone H3K9 methylation and histone H3K4 demethylation, respectively. Miniature inverted repeat transposable elements (MITEs) are one of the most high-copy-number DNA transposons, which are interspersed around rice genome and might influence nearby gene expression. In plants, 24-nucleotide (24-nt) heterochromatic small interfering RNAs (hc-siRNAs) derived from repeats and TEs. To what extent hc-siRNA associated TEs affect gene expression and therefore contribute to agricultural traits in rice remains elusive. Here, we show that OsDCL3a, one of Dicer-Like 3 (DCL3) homolog, is primarily responsible for 24-nt hc-siRNA processing in rice. Impaired OsDCL3a displayed altered important agricultural traits in rice. We found that genome-wide (281,563) 24-nt hc-siRNA clusters were OsDCL3a-dependent, among which MITEs were significantly enriched. Impaired OsDCL3a caused significant overlapping between reduced hc-siRNAs from MITEs and elevated nearby gene expression. Intriguingly, genes involved in Gibberellin and Brassinosteroid homeostasis were identified as direct targets of OsDCL3a, which may attribute to dwarfism and enlarged flag leaf angle upon OsDCL3a deficiency. Our work uncovers OsDCL3a-dependent hc-siRNAs derived from MITEs as broad spectrum of regulators for fine-tuning gene expression, and this observation may reflect a conserved mechanism in other higher plants with dispersed repeat- or TE-rich genomes. Examination of OsDCL3a-dependent hc-siRNAs derived from MITEs.

2014-02-04 | E-GEOD-50778 | biostudies-arrayexpress

Vibrio cholerae HC-77A1

Project description:Vibrio cholerae HC-77A1 Genome sequencing project

| PRJNA63981 | ENA