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TranscriptomicsTranscription profiling of Bordetella pertussis from mid-log phase cultures diluted to two concentrations and grown beyond the log to stationary phase transition to determine growth phase-associated patterns of transcript abundance
B. pertussis mid-log phase cultures were diluted in modified Stainer-Scholte medium to a starting optical density at 600 nm of 0.03 to 0.05, then grown at 37 C with shaking until three hours beyond the log to stationary phase transition.
ORGANISM(S): Bordetella parapertussis 
2006-12-31 | E-TABM-100 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Bordetella pertussis from mid-log phase cultures diluted to two concentrations and sampled at multiple points along the growth curve to determine growth phase-associated patterns of transcript abundance
B. pertussis mid-log phase cultures were diluted in modified Stainer-Scholte medium to a starting optical density at 600 nm of 0.03 to 0.05, then grown at 37 C with shaking until stationary phase. Samples were taken at multiple points along the growth curve.
ORGANISM(S): Bordetella pertussis 
2006-12-31 | E-TABM-101 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Bordetella pertussis strains in response to glutamate availablility
B. pertussis mid-log phase cultures were washed twice and resuspended at a starting OD at 600 nm of 0.05 in media containing various concentrations of glutamate.
ORGANISM(S): Bordetella parapertussis 
2006-12-04 | E-TABM-99 | biostudies-arrayexpress
TranscriptomicsSpt6 Levels are Modulated by PAAF1 and 26S Proteasome to Regulate the HIV-1 LTR and a Subset of Cellular Genes involved in Cancer.
Effect of PAAF1 and Spt6 knock-down on gene expression. Total RNAs were extracted from HeLa-LTR-Luc cells in which PAAF1 or Spt6 had been knock down by a specific siRNA or HeLa-LTR-Luc cells that had been transfected with a control siRNA (“si Neg”). Differentially expressed genes in PAAF1 knock-down...
ORGANISM(S): Homo sapiens 
2012-05-28 | E-GEOD-32033 | biostudies-arrayexpress
GenomicsCritical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency (Chip-Seq)
We recently showed that some human induced pluripotent stem cell (iPSC) clones were defective in neural differentiation and were marked with the activation of long term repeats (LTRs) of human endogenous retroviruses (HERVs). We herein demonstrated that these LTRs were transiently overexpressed duri...
ORGANISM(S): Homo sapiens 
2014-08-04 | E-GEOD-56567 | biostudies-arrayexpress
TranscriptomicsCritical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency (RNA-Seq)
We recently showed that some human induced pluripotent stem cell (iPSC) clones were defective in neural differentiation and were marked with the activation of long term repeats (LTRs) of human endogenous retroviruses (HERVs). We herein demonstrated that these LTRs were transiently overexpressed duri...
ORGANISM(S): Homo sapiens 
2014-08-04 | E-GEOD-56568 | biostudies-arrayexpress
UnknownSpt6 levels are modulated by PAAF1 and proteasome to regulate the HIV-1 LTR.
Not available
S-EPMC3305501 | biostudies-literature
MetabolomicsGNPS - Targeting FSP1 triggers ferroptosis in lung cancer
Raw mass spectrometry data were acquired via LC-MS to quantify oxidized lipids and Coenzyme Q9 (CoQ9) in mouse lung tumor and cell line samples. A Parallel Reaction Monitoring (PRM) strategy was employed for oxidized lipids, while a Data-Dependent Acquisition (DDA) method was used for CoQ9.
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2025-08-19 | MSV000098883 | GNPS
ProteomicsUltra-fast proteome analysis of HEK293T cells using Q-Orbitrap MS
We established an ultrafast proteomic method based on a 5-min gradient LC and quadrupole-Orbitrap mass spectrometer.
ORGANISM(S): Homo Sapiens (human) 
2022-07-28 | PXD034227 | JPOST Repository
ProteomicsBioID-based mass spectrometry data
BioID-based mass spectrometry data on stress granules
ORGANISM(S): Homo Sapiens (human) 
2023-04-20 | PXD030039 | JPOST Repository
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