Journal: PLoS ONE

Article Title: Biologically Active Polymers from Spontaneous Carotenoid Oxidation: A New Frontier in Carotenoid Activity

doi: 10.1371/journal.pone.0111346

Figure Lengend Snippet: Human THP-1 monocytes (A), fibroblasts (B), and endothelial cells (C), were treated with the indicated concentrations of OxC-beta or vehicle control (DMSO) for 24 hours. Immune receptor content was measured 24 hours post-treatment by FACS analysis. OxC-beta-induced increase in receptor level was assessed relative to untreated control cells using a one-way analysis of variance with Tukey’s post test for multiple comparisons. DMSO had no effect on receptor level (result not shown). Phorbol myristate acetate (PMA) was used as a positive control in experiments with THP-1 cells (hatched bars).

Article Snippet: Fibroblasts (ATCC CRL-2097) were cultured in Eagle’s Minimum Essential Media (EMEM) supplemented with 0.1 mM non-essential amino acids, 0.1 mM sodium pyruvate, 10% FBS and antibiotics.

Techniques: Control, Positive Control

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: Ribosome biogenesis (GO#, 0042254) was more robust in human embryonic stem cells (ESCs) than in the reprogramming starting cells, fibroblasts. ( A ) Box plots showing that the full set of ribosome biogenesis (RB) genes was expressed at higher levels in human ESCs than in fibroblasts. ( B ) Pie charts showing the expression categories of the RB gene set in human ESCs (hESCs) and fibroblasts. The grey sector in the left pie chart indicates that 11 genes were enriched at least twofold in fibroblasts in comparison with human ESCs (q < 0.01). The right pie chart is a further classification of the uncertain sector in the left pie using less stringent criteria (>1.5×, q < 0.05). ( C ) A heat map showing that 170 out of 291 RB genes were enriched in human ESCs by at least 1.5-fold (q < 0.05). ( D ) Quantification of expression differences for the RB gene set between hESCs and fibroblasts. H1 and H9, human embryonic stem cell (hESC) lines H1 and H9, respectively; hESC is a subline of H1. The first number after the fibroblast designation is the time of RNA harvesting after seeding of cells, and the second number is the lane number of RNA-seq flow cells. The boxes and labels of hESCs are highlighted in green. hESC = 3; fibroblasts = 4. See also .

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques: Expressing, Comparison, RNA Sequencing

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: Proper reprogramming of ribosome biogenesis at the early stage of Yamanaka reprogramming. ( A ) A heat map showing that the 170 hPSC-enriched (>1.5×, q < 0.05) RB genes were upreprogrammed to the pluripotent state within 48 h. ( B ) A heat map showing that the 11 fibroblast-enriched RB genes were not downreprogrammed to the pluripotent state up to 72 h of OSKM induction and remained clustered with fibroblasts. ( C ) A heat map showing that the entire set of 298 RB genes became clustered with the hPSCs upon OSKM reprogramming. H1 and H9, human embryonic stem cell lines H1 and H9, respectively. The first number after the fibroblast or treatment designations is the time of RNA harvesting after seeding of cells or treatment time by OSKM or GFP, and the second number is the lane number of RNA-seq flow cells. hESCs are highlighted in green while OSKM samples are in red. hESC = 3; fibroblasts = 4; OSKM = 2. See also .

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques: RNA Sequencing

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: The key mesenchymal transcriptional factors (TFs) maintained high levels of expressions and the epithelial marker CDH1 remained silenced at the time of proper RB reprogramming. ( A ) Box plots for individual genes showing little reprogramming of mesenchymal TFs, and of the epithelial marker gene CDH1 at the early time of OSKM reprogramming (log2-transformed averaged read counts for time points of 48 and 72 h). ( B ) Clustering and the associated heat map showing lack of substantial downreprogramming of the five mesenchymal TFs. ( C ) Violin plots of each sample for the six mesenchymal TFs showing little reprogramming as a group upon OSKM induction. ( D ) Log2 (fold differences) relative to ESCs (blue and orange bars) or to the threshold level read counts (50) for the expressed genes (grey bars). F in ( A ) and ( D ) stands for fibroblasts. Dashed red lines in ( A ) and ( C ) mark the threshold level of the expressed genes. Sample labels are the same as in . See also .

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques: Marker, Transformation Assay

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: Defining the subreprogramomes for the mesenchymal-to-epithelial (MET) transition during the iPSC reprogramming process from human fibroblasts. ( A ) A pie chart for classification of the MET/EMT genes in the context of human fibroblast-to-iPSC reprogramming. ( B ) sub-classification for the sector of “at similar levels” in ( A ). ( C ) Sub-classification for the sector of fibroblast-enriched genes in pie chart ( A ). ( D ) Sub-classification for the sector of hPSC-enriched genes in pie chart ( A ). ( E ) Quantification of reprogrammikng for the MET subreprogramomes. LFC, log2 (fold changes); U, uncertain genes based on the sorting criteria. See also .

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques:

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: MET reprogramome and its subreprogramomes were not reprogrammed at the time of proper RB reprogramming. Clustering analyses and associated heat maps showing similarity of the reprogramming cells to the starting fibroblasts and GFP-transduced fibroblast controls and dissimilarity to hESCs for the entire MET reprogramome ( A ), upreprogramome ( B ), downreprogramome ( C ), activatome ( D ), and erasome ( E ). G1 to G4: GFP-5, GFP72-8a, GFP48-5, and GFP72-8; F1 to F4: BJ48-4, BJ72-7, BJ48-1, and BJ72-4; E1 to E3: human embryonic stem cell H1, H9, and hESC; 48 and 72: RNA harvested from human fibroblasts 48 and 72 h post transduction with lentiviral reprogramming factors OSKM.

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques: Transduction

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: A Proper, Insufficient, Aberrant, and NO reprogramming (PIANO) response of the annotated MET genes to OSKM reprogramming at the time of proper RB reprogramming. ( A ) insufficient downreprogramming (56 genes); ( B ) insufficient upreprogramming (11 genes); ( C ) 104 fibroblast-enriched genes were irresponsive to OSKM reprogramming; ( D ) 99 hPSC-enriched genes were irresponsive to OSKM reprogramming; ( E ) 5 common MET genes were downregulated when they should have not been; ( F ) 11 common MET genes were upregulated when they should have not been; ( G ) 2 MET genes were wrongly downregulated when they should have been upreprogrammed; ( H ) 5 MET genes were wrongly upregulated when they should have been downreprogrammed; ( I ) 22 fibroblast-enriched genes were properly downreprogrammed; ( J ) 17 hPSC-enriched genes were properly upreprogrammed. Color scales of read counts are the same as shown by heat map ( A ), except for ( B ), ( G ), and ( H ) that share the second color scales as shown by ( H ). See also .

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques:

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: Ribosome biogenesis was more robust in human iPSCs than in fibroblasts. ( A ) Out of 298 RB genes, 176 were significantly enriched in human iPSCs compared to fibroblasts (>1.3×, q < 0.05). ( B ) Out of 298 RB genes, only 10 were enriched in human fibroblasts compared to iPSCs (>2×, q < 0.01). ( C ) Quantification of expression enrichment of the RB genes in iPSCs relative to fibroblasts. LFC, log2 fold changes.

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques: Expressing

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: Ribosome biogenesis remained more robust in human ESCs compared with an independent fibroblast line. ( A ) Out of 298 RB genes, 156 were expressed significantly higher in ESCs (>1.3×, q < 0.05). ( B ) Out of 298 RB genes, only 11 RB genes were expressed significantly higher in fibroblasts than in ESCs (>2×, q < 0.01). ( C ) Quantification of expression enrichment of RB genes in ESCs relative to fibroblasts. H1P43 and hESH1 are human ESC line H1 at different passage numbers; H9P69 and hESH9 are human ESC line H9 at different passage numbers.

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques: Expressing

Journal: Cells

Article Title: Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming

doi: 10.3390/cells9112484

Figure Lengend Snippet: OSKM quickly reprogrammed RB to the pluripotent state in an independent fibroblast line. ( A ) Pie diagram showing predominant upregulation of RB genes during early iPSC reprogramming of the CCD fibroblasts. ( B ) Out of the 200 OSKM-upregulated genes, 123 were ESC-enriched (q < 0.05. >1.3×). Note the clustering of RB genes with ESCs and away from fibroblasts. ( C ) The fibroblast-enriched RB genes predominantly underwent legitimate downreprogramming, although insufficiently. Human ESC samples are indicated by green text; CCD fibroblasts underwent OSKM-mediated reprogramming are indicated by red color.

Article Snippet: Human primary fibroblasts (BJ, ATCC, Cat#, CRL-2522; CCD-1079Sk, ATCC, Cat#, CRL-2097) were culture in the fibroblast medium, Dulbecco’s modified Eagle’s medium, with high glucose, supplemented with 10% heat-inactivated fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1× penicillin–streptomycin, 0.1 mM minimum essential medium non-essential amino acids, and 4 ng/mL human fibroblast growth factor 2 (FGF2).

Techniques: