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jurkat cells  (ATCC)
93
ATCC jurkat cells
(A) Schematic of MPRAs tiling through HIV genomes, saturation mutagenesis, and evaluation of different isolates. (B) Saturation mutagenesis MPRA experiments in unstimulated <t>Jurkat</t> <t>cells</t> for four tiles in the HIV-1 LTR from the clade B REJO strain that show transcriptional activity. Region coordinates are provided using standardized HXB2 genomic coordinates. TF motifs that contribute to activity are outlined. Inset shows MPRA activity tiling through the HIV-1 LTR. Blue indicates activity of tiles in the sense, and red in the antisense (opposite orientation) strand. (C) CASCADE-derived motifs for different cofactors at various regions of the HIV-1 LTR. (D) Regional distribution of HIV-1 isolates tested by MPRAs. (E) Violin plots showing the distribution of activity in unstimulated Jurkat cells across 5,569 isolates for different regions of the HIV-1 LTR across clades. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. The dots heatmaps below indicate the fold activation by stimulation of Jurkat cells with αCD3+PMA, TNFα, or IFNγ. The color indicates the median fold activation across isolates, whereas the size of the dots reflects the fold activity differences between the 5th and 95th percentiles. (F) Pearson correlation between the activity of different regions of the HIV-1 LTR across isolates. (G) Schematic of chimeric proviral constructs and reactivation experimental approach. (H-I) Fold change in GFP+ cells relative to DMSO control (H) or geometric mean fluorescence intensity of GFP+ cells (I) in Jurkat cells infected with chimeric proviruses carrying the U3 region of the indicated isolates from clades A, B, and C, and stimulated with TNFα for 2 days. (J) Comparison between fold activation of MPRA data from tile HXB2:250-431 in Jurkat cells activated with TNFα, and provirus reactivation by TNFα measured as fold change in GFP+ cells relative to DMSO control or geometric mean fluorescence intensity of GFP+ cells. Pearson correlation coefficients and one-tailed p-values are indicated for each comparison to MPRA data. (K) Dot heatmaps of recombinant HIV-1 viruses derived from clades B and C. Median baseline activity in tile HXB2:250-431 is shown in shades of green, whereas the median fold activation by αCD3+PMA, TNFα, or IFNγ is shown blue-white-red gradient. The size for the dots reflects the fold activity differences between the 5th and 95th percentiles.
Jurkat Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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jurkat cells - by Bioz Stars, 2026-06
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mpc 83 cells  (Dojindo Labs)
99
Dojindo Labs mpc 83 cells
(A) Schematic of MPRAs tiling through HIV genomes, saturation mutagenesis, and evaluation of different isolates. (B) Saturation mutagenesis MPRA experiments in unstimulated <t>Jurkat</t> <t>cells</t> for four tiles in the HIV-1 LTR from the clade B REJO strain that show transcriptional activity. Region coordinates are provided using standardized HXB2 genomic coordinates. TF motifs that contribute to activity are outlined. Inset shows MPRA activity tiling through the HIV-1 LTR. Blue indicates activity of tiles in the sense, and red in the antisense (opposite orientation) strand. (C) CASCADE-derived motifs for different cofactors at various regions of the HIV-1 LTR. (D) Regional distribution of HIV-1 isolates tested by MPRAs. (E) Violin plots showing the distribution of activity in unstimulated Jurkat cells across 5,569 isolates for different regions of the HIV-1 LTR across clades. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. The dots heatmaps below indicate the fold activation by stimulation of Jurkat cells with αCD3+PMA, TNFα, or IFNγ. The color indicates the median fold activation across isolates, whereas the size of the dots reflects the fold activity differences between the 5th and 95th percentiles. (F) Pearson correlation between the activity of different regions of the HIV-1 LTR across isolates. (G) Schematic of chimeric proviral constructs and reactivation experimental approach. (H-I) Fold change in GFP+ cells relative to DMSO control (H) or geometric mean fluorescence intensity of GFP+ cells (I) in Jurkat cells infected with chimeric proviruses carrying the U3 region of the indicated isolates from clades A, B, and C, and stimulated with TNFα for 2 days. (J) Comparison between fold activation of MPRA data from tile HXB2:250-431 in Jurkat cells activated with TNFα, and provirus reactivation by TNFα measured as fold change in GFP+ cells relative to DMSO control or geometric mean fluorescence intensity of GFP+ cells. Pearson correlation coefficients and one-tailed p-values are indicated for each comparison to MPRA data. (K) Dot heatmaps of recombinant HIV-1 viruses derived from clades B and C. Median baseline activity in tile HXB2:250-431 is shown in shades of green, whereas the median fold activation by αCD3+PMA, TNFα, or IFNγ is shown blue-white-red gradient. The size for the dots reflects the fold activity differences between the 5th and 95th percentiles.
Mpc 83 Cells, supplied by Dojindo Labs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mpc 83 cells - by Bioz Stars, 2026-06
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mpc 11 cell line  (ATCC)
96
ATCC mpc 11 cell line
(A) Schematic of MPRAs tiling through HIV genomes, saturation mutagenesis, and evaluation of different isolates. (B) Saturation mutagenesis MPRA experiments in unstimulated <t>Jurkat</t> <t>cells</t> for four tiles in the HIV-1 LTR from the clade B REJO strain that show transcriptional activity. Region coordinates are provided using standardized HXB2 genomic coordinates. TF motifs that contribute to activity are outlined. Inset shows MPRA activity tiling through the HIV-1 LTR. Blue indicates activity of tiles in the sense, and red in the antisense (opposite orientation) strand. (C) CASCADE-derived motifs for different cofactors at various regions of the HIV-1 LTR. (D) Regional distribution of HIV-1 isolates tested by MPRAs. (E) Violin plots showing the distribution of activity in unstimulated Jurkat cells across 5,569 isolates for different regions of the HIV-1 LTR across clades. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. The dots heatmaps below indicate the fold activation by stimulation of Jurkat cells with αCD3+PMA, TNFα, or IFNγ. The color indicates the median fold activation across isolates, whereas the size of the dots reflects the fold activity differences between the 5th and 95th percentiles. (F) Pearson correlation between the activity of different regions of the HIV-1 LTR across isolates. (G) Schematic of chimeric proviral constructs and reactivation experimental approach. (H-I) Fold change in GFP+ cells relative to DMSO control (H) or geometric mean fluorescence intensity of GFP+ cells (I) in Jurkat cells infected with chimeric proviruses carrying the U3 region of the indicated isolates from clades A, B, and C, and stimulated with TNFα for 2 days. (J) Comparison between fold activation of MPRA data from tile HXB2:250-431 in Jurkat cells activated with TNFα, and provirus reactivation by TNFα measured as fold change in GFP+ cells relative to DMSO control or geometric mean fluorescence intensity of GFP+ cells. Pearson correlation coefficients and one-tailed p-values are indicated for each comparison to MPRA data. (K) Dot heatmaps of recombinant HIV-1 viruses derived from clades B and C. Median baseline activity in tile HXB2:250-431 is shown in shades of green, whereas the median fold activation by αCD3+PMA, TNFα, or IFNγ is shown blue-white-red gradient. The size for the dots reflects the fold activity differences between the 5th and 95th percentiles.
Mpc 11 Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mpc 11 cell line - by Bioz Stars, 2026-06
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mpc11 murine mm cell line  (ATCC)
96
ATCC mpc11 murine mm cell line
The cell lines <t>MPC11,</t> L363 and KMS12-BM were seeded at 10,000 cells/well in a 96-well plate. The cells were stimulated with control medium or Met(-)- medium. For the positive control (death), the cells were stimulated with 1 µM staurosporine. After 24 h, 48 h and 72 h, measurements were performed with the EarlyTox Live/Dead Assay Kit (Molecular Devices). The staining solution (5 µg/mL Hoechst 33342 (Thermo Fisher, Darmstadt, Germany), 6 µM EthD-III, and 6 µM calcein AM (CAM) in DMEM (Gibco, Life Technologies; Darmstadt, Germany)) was added, and after 30 min of incubation, measurements were made with the ImageXpress Pico Automated Cell Imaging System. The number of cells was determined via Hoechst 33342. Living cells were stained with the nonfluorescent calcein AM, which permeates the intact cell membrane and is converted into calcein, the fluorescent form, by intracellular esterases (cells are shown in green). If compromised cell membrane integrity is associated with cell death, EthD-III enters cells and binds to nucleic acids (cells are shown in red). A representative area for cell viability is shown for each cell line. The cell numbers are not representative of every case. The white bar, representing 52.44 µm, is used for size classification.
Mpc11 Murine Mm Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mpc11 murine mm cell line - by Bioz Stars, 2026-06
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mouse mpc 11 myeloma plasmacytoma cell line  (ATCC)
96
ATCC mouse mpc 11 myeloma plasmacytoma cell line
The cell lines <t>MPC11,</t> L363 and KMS12-BM were seeded at 10,000 cells/well in a 96-well plate. The cells were stimulated with control medium or Met(-)- medium. For the positive control (death), the cells were stimulated with 1 µM staurosporine. After 24 h, 48 h and 72 h, measurements were performed with the EarlyTox Live/Dead Assay Kit (Molecular Devices). The staining solution (5 µg/mL Hoechst 33342 (Thermo Fisher, Darmstadt, Germany), 6 µM EthD-III, and 6 µM calcein AM (CAM) in DMEM (Gibco, Life Technologies; Darmstadt, Germany)) was added, and after 30 min of incubation, measurements were made with the ImageXpress Pico Automated Cell Imaging System. The number of cells was determined via Hoechst 33342. Living cells were stained with the nonfluorescent calcein AM, which permeates the intact cell membrane and is converted into calcein, the fluorescent form, by intracellular esterases (cells are shown in green). If compromised cell membrane integrity is associated with cell death, EthD-III enters cells and binds to nucleic acids (cells are shown in red). A representative area for cell viability is shown for each cell line. The cell numbers are not representative of every case. The white bar, representing 52.44 µm, is used for size classification.
Mouse Mpc 11 Myeloma Plasmacytoma Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mouse mpc 11 myeloma plasmacytoma cell line - by Bioz Stars, 2026-06
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balb c derived plasmacytoma cell line mpc 11  (ATCC)
96
ATCC balb c derived plasmacytoma cell line mpc 11
The cell lines <t>MPC11,</t> L363 and KMS12-BM were seeded at 10,000 cells/well in a 96-well plate. The cells were stimulated with control medium or Met(-)- medium. For the positive control (death), the cells were stimulated with 1 µM staurosporine. After 24 h, 48 h and 72 h, measurements were performed with the EarlyTox Live/Dead Assay Kit (Molecular Devices). The staining solution (5 µg/mL Hoechst 33342 (Thermo Fisher, Darmstadt, Germany), 6 µM EthD-III, and 6 µM calcein AM (CAM) in DMEM (Gibco, Life Technologies; Darmstadt, Germany)) was added, and after 30 min of incubation, measurements were made with the ImageXpress Pico Automated Cell Imaging System. The number of cells was determined via Hoechst 33342. Living cells were stained with the nonfluorescent calcein AM, which permeates the intact cell membrane and is converted into calcein, the fluorescent form, by intracellular esterases (cells are shown in green). If compromised cell membrane integrity is associated with cell death, EthD-III enters cells and binds to nucleic acids (cells are shown in red). A representative area for cell viability is shown for each cell line. The cell numbers are not representative of every case. The white bar, representing 52.44 µm, is used for size classification.
Balb C Derived Plasmacytoma Cell Line Mpc 11, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/balb c derived plasmacytoma cell line mpc 11/product/ATCC
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balb c derived plasmacytoma cell line mpc 11 - by Bioz Stars, 2026-06
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plasmacytoma cell line mpc 11  (ATCC)
96
ATCC plasmacytoma cell line mpc 11
The cell lines <t>MPC11,</t> L363 and KMS12-BM were seeded at 10,000 cells/well in a 96-well plate. The cells were stimulated with control medium or Met(-)- medium. For the positive control (death), the cells were stimulated with 1 µM staurosporine. After 24 h, 48 h and 72 h, measurements were performed with the EarlyTox Live/Dead Assay Kit (Molecular Devices). The staining solution (5 µg/mL Hoechst 33342 (Thermo Fisher, Darmstadt, Germany), 6 µM EthD-III, and 6 µM calcein AM (CAM) in DMEM (Gibco, Life Technologies; Darmstadt, Germany)) was added, and after 30 min of incubation, measurements were made with the ImageXpress Pico Automated Cell Imaging System. The number of cells was determined via Hoechst 33342. Living cells were stained with the nonfluorescent calcein AM, which permeates the intact cell membrane and is converted into calcein, the fluorescent form, by intracellular esterases (cells are shown in green). If compromised cell membrane integrity is associated with cell death, EthD-III enters cells and binds to nucleic acids (cells are shown in red). A representative area for cell viability is shown for each cell line. The cell numbers are not representative of every case. The white bar, representing 52.44 µm, is used for size classification.
Plasmacytoma Cell Line Mpc 11, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/plasmacytoma cell line mpc 11/product/ATCC
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Image Search Results


(A) Schematic of MPRAs tiling through HIV genomes, saturation mutagenesis, and evaluation of different isolates. (B) Saturation mutagenesis MPRA experiments in unstimulated Jurkat cells for four tiles in the HIV-1 LTR from the clade B REJO strain that show transcriptional activity. Region coordinates are provided using standardized HXB2 genomic coordinates. TF motifs that contribute to activity are outlined. Inset shows MPRA activity tiling through the HIV-1 LTR. Blue indicates activity of tiles in the sense, and red in the antisense (opposite orientation) strand. (C) CASCADE-derived motifs for different cofactors at various regions of the HIV-1 LTR. (D) Regional distribution of HIV-1 isolates tested by MPRAs. (E) Violin plots showing the distribution of activity in unstimulated Jurkat cells across 5,569 isolates for different regions of the HIV-1 LTR across clades. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. The dots heatmaps below indicate the fold activation by stimulation of Jurkat cells with αCD3+PMA, TNFα, or IFNγ. The color indicates the median fold activation across isolates, whereas the size of the dots reflects the fold activity differences between the 5th and 95th percentiles. (F) Pearson correlation between the activity of different regions of the HIV-1 LTR across isolates. (G) Schematic of chimeric proviral constructs and reactivation experimental approach. (H-I) Fold change in GFP+ cells relative to DMSO control (H) or geometric mean fluorescence intensity of GFP+ cells (I) in Jurkat cells infected with chimeric proviruses carrying the U3 region of the indicated isolates from clades A, B, and C, and stimulated with TNFα for 2 days. (J) Comparison between fold activation of MPRA data from tile HXB2:250-431 in Jurkat cells activated with TNFα, and provirus reactivation by TNFα measured as fold change in GFP+ cells relative to DMSO control or geometric mean fluorescence intensity of GFP+ cells. Pearson correlation coefficients and one-tailed p-values are indicated for each comparison to MPRA data. (K) Dot heatmaps of recombinant HIV-1 viruses derived from clades B and C. Median baseline activity in tile HXB2:250-431 is shown in shades of green, whereas the median fold activation by αCD3+PMA, TNFα, or IFNγ is shown blue-white-red gradient. The size for the dots reflects the fold activity differences between the 5th and 95th percentiles.

Journal: bioRxiv

Article Title: Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

doi: 10.64898/2026.04.03.716403

Figure Lengend Snippet: (A) Schematic of MPRAs tiling through HIV genomes, saturation mutagenesis, and evaluation of different isolates. (B) Saturation mutagenesis MPRA experiments in unstimulated Jurkat cells for four tiles in the HIV-1 LTR from the clade B REJO strain that show transcriptional activity. Region coordinates are provided using standardized HXB2 genomic coordinates. TF motifs that contribute to activity are outlined. Inset shows MPRA activity tiling through the HIV-1 LTR. Blue indicates activity of tiles in the sense, and red in the antisense (opposite orientation) strand. (C) CASCADE-derived motifs for different cofactors at various regions of the HIV-1 LTR. (D) Regional distribution of HIV-1 isolates tested by MPRAs. (E) Violin plots showing the distribution of activity in unstimulated Jurkat cells across 5,569 isolates for different regions of the HIV-1 LTR across clades. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. The dots heatmaps below indicate the fold activation by stimulation of Jurkat cells with αCD3+PMA, TNFα, or IFNγ. The color indicates the median fold activation across isolates, whereas the size of the dots reflects the fold activity differences between the 5th and 95th percentiles. (F) Pearson correlation between the activity of different regions of the HIV-1 LTR across isolates. (G) Schematic of chimeric proviral constructs and reactivation experimental approach. (H-I) Fold change in GFP+ cells relative to DMSO control (H) or geometric mean fluorescence intensity of GFP+ cells (I) in Jurkat cells infected with chimeric proviruses carrying the U3 region of the indicated isolates from clades A, B, and C, and stimulated with TNFα for 2 days. (J) Comparison between fold activation of MPRA data from tile HXB2:250-431 in Jurkat cells activated with TNFα, and provirus reactivation by TNFα measured as fold change in GFP+ cells relative to DMSO control or geometric mean fluorescence intensity of GFP+ cells. Pearson correlation coefficients and one-tailed p-values are indicated for each comparison to MPRA data. (K) Dot heatmaps of recombinant HIV-1 viruses derived from clades B and C. Median baseline activity in tile HXB2:250-431 is shown in shades of green, whereas the median fold activation by αCD3+PMA, TNFα, or IFNγ is shown blue-white-red gradient. The size for the dots reflects the fold activity differences between the 5th and 95th percentiles.

Article Snippet: Jurkat cells (ATCC-TIB-15) were cultured in RPMI media (Fisher Scientific, Catalogue # A1049101) with 10% Fetal Bovine Serum (R&D Systems, Catalog # S12450H) and 1% Antibiotic-antimicotic (Thermofisher Scientific, Catalogue #15240062) up to a density of 1 million cells per mL prior to transfection.

Techniques: Mutagenesis, Activity Assay, Derivative Assay, Activation Assay, Construct, Control, Fluorescence, Infection, Comparison, One-tailed Test, Recombinant

(A) Distribution of the number of TF binding sites across HIV-1 isolates in tiles HXB2:250-431 and HXB2:581-780. Each pie chart shows the proportion of isolates with different number of binding sites for the indicated TFs. (B-C) Violin plots of baseline activity or fold activation by αCD3+PMA or TNFα for tile HXB2:250-431 across HIV-1 isolates based on the number of NF-κB (B) or SP/KLF sites (C). The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (D, H) Activity distribution in Jurkat cells across HIV-1 isolates with different TF configurations in tiles HXB2:250-431 (D) and HXB2:581-780 (H). The left boxes represent the TF configurations based on aligned TF positions. The distribution of isolates from different clades across TF configurations is shown as pie chats. Violin plots indicate the distributions of activity in unstimulated Jurkat cells (baseline), and cells stimulated with αCD3+PMA, TNFα, or IFNγ. In the case tile HXB2:250-431 only configurations with at least 10 isolates are shown. (E) Alphafold3 model of the HIV-1 REJO LTR including three SP1 and two sets of NF-κB (p65 and p50) proteins. (F-G) Violin plots of baseline activity or fold activation by IFNγ for tile HXB2:581-780 across HIV-1 isolates based on the number of IRF (F) or SP/KLF sites (G). The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (I) Violin plots of F-statistic showing the variability in activity for each isolate for tile HXB2:581-780 across four donors in CD4+ T cells. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (J) Activity distribution and donor variability (F-statistic) in CD4+ T cells in Jurkat cells across HIV-1 isolates with different TF configurations in tile HXB2:581-780. The left boxes represent the TF configurations based on aligned TF positions. The distribution of isolates from different clades across TF configurations is shown as pie charts. (K) Distribution of donor variability (F-statistic) in tile HXB2:581-780 for isolates that contain or lack an SP/KLF site across four CD4+T cell donors or five replicates of Jurkat cells. Statistical significance determined by two-tailed Brunner-Munzel test.

Journal: bioRxiv

Article Title: Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

doi: 10.64898/2026.04.03.716403

Figure Lengend Snippet: (A) Distribution of the number of TF binding sites across HIV-1 isolates in tiles HXB2:250-431 and HXB2:581-780. Each pie chart shows the proportion of isolates with different number of binding sites for the indicated TFs. (B-C) Violin plots of baseline activity or fold activation by αCD3+PMA or TNFα for tile HXB2:250-431 across HIV-1 isolates based on the number of NF-κB (B) or SP/KLF sites (C). The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (D, H) Activity distribution in Jurkat cells across HIV-1 isolates with different TF configurations in tiles HXB2:250-431 (D) and HXB2:581-780 (H). The left boxes represent the TF configurations based on aligned TF positions. The distribution of isolates from different clades across TF configurations is shown as pie chats. Violin plots indicate the distributions of activity in unstimulated Jurkat cells (baseline), and cells stimulated with αCD3+PMA, TNFα, or IFNγ. In the case tile HXB2:250-431 only configurations with at least 10 isolates are shown. (E) Alphafold3 model of the HIV-1 REJO LTR including three SP1 and two sets of NF-κB (p65 and p50) proteins. (F-G) Violin plots of baseline activity or fold activation by IFNγ for tile HXB2:581-780 across HIV-1 isolates based on the number of IRF (F) or SP/KLF sites (G). The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (I) Violin plots of F-statistic showing the variability in activity for each isolate for tile HXB2:581-780 across four donors in CD4+ T cells. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (J) Activity distribution and donor variability (F-statistic) in CD4+ T cells in Jurkat cells across HIV-1 isolates with different TF configurations in tile HXB2:581-780. The left boxes represent the TF configurations based on aligned TF positions. The distribution of isolates from different clades across TF configurations is shown as pie charts. (K) Distribution of donor variability (F-statistic) in tile HXB2:581-780 for isolates that contain or lack an SP/KLF site across four CD4+T cell donors or five replicates of Jurkat cells. Statistical significance determined by two-tailed Brunner-Munzel test.

Article Snippet: Jurkat cells (ATCC-TIB-15) were cultured in RPMI media (Fisher Scientific, Catalogue # A1049101) with 10% Fetal Bovine Serum (R&D Systems, Catalog # S12450H) and 1% Antibiotic-antimicotic (Thermofisher Scientific, Catalogue #15240062) up to a density of 1 million cells per mL prior to transfection.

Techniques: Binding Assay, Activity Assay, Activation Assay, Two Tailed Test

(A) Schematic of CREST and LARM models. CREST predicts baseline activity in Jurkat cells from DNA sequence. LARM predicts fold-activation by αCD3+PMA or TNFα for sequences corresponding to tile HXB2:250-431. (B) Pearson correlation between baseline activity in Jurkat cells measured by MPRAs and predicted using CREST for the validation and test sets. (C) Pearson correlation between TNFα-induced fold activation of tile HXB2:250-431 isolates in Jurkat cells measured by MPRAs and the corresponding values predicted by LARM for the validation and test sets. (D-E) Baseline activity predicted by CREST in tile HXB2:250-431 for isolates heterosexual (D) or mother-to-infant (E) transmission pairs. , The activity of the predicted founder sequence is indicated for infants. (F) Baseline activity predicted by CREST in tile HXB2:250-431 for isolates from 7 PWH from samples obtained at different days post infection. Error bars indicate the standard deviation, dots indicate the average value. (G) Baseline activity predicted by CREST for tile HXB2:250-431 of two PWH. Isolates are shown within their respective evolutionary trees. Node color represents the activity and node size indicates the average day post infection for the corresponding haplotype. Square nodes correspond to predicted ancestral sequences. (H) Baseline activity predicted by CREST for tile HXB2:250-431 for samples from Los Alamos database plotted versus the date of sample collection. Isolates are colored by clade. (I) Fold activation in Jurkat cells stimulated with TNFα predicted by LARM in tile HXB2:250-431 for isolates from 7 PWH from samples obtained at different days post infection. Error bars indicate the standard deviation, dots indicate the average value.

Journal: bioRxiv

Article Title: Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

doi: 10.64898/2026.04.03.716403

Figure Lengend Snippet: (A) Schematic of CREST and LARM models. CREST predicts baseline activity in Jurkat cells from DNA sequence. LARM predicts fold-activation by αCD3+PMA or TNFα for sequences corresponding to tile HXB2:250-431. (B) Pearson correlation between baseline activity in Jurkat cells measured by MPRAs and predicted using CREST for the validation and test sets. (C) Pearson correlation between TNFα-induced fold activation of tile HXB2:250-431 isolates in Jurkat cells measured by MPRAs and the corresponding values predicted by LARM for the validation and test sets. (D-E) Baseline activity predicted by CREST in tile HXB2:250-431 for isolates heterosexual (D) or mother-to-infant (E) transmission pairs. , The activity of the predicted founder sequence is indicated for infants. (F) Baseline activity predicted by CREST in tile HXB2:250-431 for isolates from 7 PWH from samples obtained at different days post infection. Error bars indicate the standard deviation, dots indicate the average value. (G) Baseline activity predicted by CREST for tile HXB2:250-431 of two PWH. Isolates are shown within their respective evolutionary trees. Node color represents the activity and node size indicates the average day post infection for the corresponding haplotype. Square nodes correspond to predicted ancestral sequences. (H) Baseline activity predicted by CREST for tile HXB2:250-431 for samples from Los Alamos database plotted versus the date of sample collection. Isolates are colored by clade. (I) Fold activation in Jurkat cells stimulated with TNFα predicted by LARM in tile HXB2:250-431 for isolates from 7 PWH from samples obtained at different days post infection. Error bars indicate the standard deviation, dots indicate the average value.

Article Snippet: Jurkat cells (ATCC-TIB-15) were cultured in RPMI media (Fisher Scientific, Catalogue # A1049101) with 10% Fetal Bovine Serum (R&D Systems, Catalog # S12450H) and 1% Antibiotic-antimicotic (Thermofisher Scientific, Catalogue #15240062) up to a density of 1 million cells per mL prior to transfection.

Techniques: Activity Assay, Sequencing, Activation Assay, Biomarker Discovery, Transmission Assay, Infection, Standard Deviation

(A) MPRA activity map across the genome of HIV-1 clade B REJO strain in unstimulated Jurkat cells. The genome organization is shown below. (B) Saturation mutagenesis MPRA experiments in unstimulated Jurkat cells for HIV-1 intragenic CREs at HXB2:1330-1530 and HXB2:7784-7984. TF motifs that contribute to activity are outlined. (C-D) Violin plots showing the distribution of activity across isolates for intragenic CREs from HIV-1 across clades: HXB2:1330-1530 (C) and HXB2:7784-7984 (D). The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (E) Entropy decomposition across the ETS–bZIP region in HIV-1 Gag aligned to HXB2 coordinates (codon start positions). Codon entropy (H(codon)), amino-acid entropy (H(a.a.)), and conditional synonymous entropy (H(codon|a.a.)) are shown; the motifs are outlined. (F) Violin plots showing the distribution of Δ median entropy (ROI − rest of window) from circular-shift permutation tests for H(codon), H(a.a.), and H(codon|a.a.). P values are indicated; n.s. denotes not significant. (G) Los Alamos National Laboratory (LANL) genome alignments of HIV-1 strains using the HXB2 genome as a reference. Transcriptional activity predicted using CREST is shown in shades of green. (H) Scatter plot showing the activity predicted using CREST for the two CREs in HIV-1 env . Dots are colored by clade. The top diagram shows the location of the CREs within the env protein coding sequence. C1-5 = conserved regions, V1-5 = variable regions, FP = fusion peptide. (I) TF motif profiles determined using CREST-based saturation mutagenesis across HIV-1 isolates from LANL. Regions were aligned to the HXB2 genome. (J-K) Baseline activity in Jurkat cells for two PWH predicted using CREST corresponding to HXB2 regions 7432-7632 (J) and 7712-7912 (K). Isolates are shown within their respective evolutionary trees. The color of the nodes represents activity levels. The size of the nodes indicate the day post infection of the corresponding sample. Square nodes represent predicted ancestral sequences.

Journal: bioRxiv

Article Title: Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

doi: 10.64898/2026.04.03.716403

Figure Lengend Snippet: (A) MPRA activity map across the genome of HIV-1 clade B REJO strain in unstimulated Jurkat cells. The genome organization is shown below. (B) Saturation mutagenesis MPRA experiments in unstimulated Jurkat cells for HIV-1 intragenic CREs at HXB2:1330-1530 and HXB2:7784-7984. TF motifs that contribute to activity are outlined. (C-D) Violin plots showing the distribution of activity across isolates for intragenic CREs from HIV-1 across clades: HXB2:1330-1530 (C) and HXB2:7784-7984 (D). The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. (E) Entropy decomposition across the ETS–bZIP region in HIV-1 Gag aligned to HXB2 coordinates (codon start positions). Codon entropy (H(codon)), amino-acid entropy (H(a.a.)), and conditional synonymous entropy (H(codon|a.a.)) are shown; the motifs are outlined. (F) Violin plots showing the distribution of Δ median entropy (ROI − rest of window) from circular-shift permutation tests for H(codon), H(a.a.), and H(codon|a.a.). P values are indicated; n.s. denotes not significant. (G) Los Alamos National Laboratory (LANL) genome alignments of HIV-1 strains using the HXB2 genome as a reference. Transcriptional activity predicted using CREST is shown in shades of green. (H) Scatter plot showing the activity predicted using CREST for the two CREs in HIV-1 env . Dots are colored by clade. The top diagram shows the location of the CREs within the env protein coding sequence. C1-5 = conserved regions, V1-5 = variable regions, FP = fusion peptide. (I) TF motif profiles determined using CREST-based saturation mutagenesis across HIV-1 isolates from LANL. Regions were aligned to the HXB2 genome. (J-K) Baseline activity in Jurkat cells for two PWH predicted using CREST corresponding to HXB2 regions 7432-7632 (J) and 7712-7912 (K). Isolates are shown within their respective evolutionary trees. The color of the nodes represents activity levels. The size of the nodes indicate the day post infection of the corresponding sample. Square nodes represent predicted ancestral sequences.

Article Snippet: Jurkat cells (ATCC-TIB-15) were cultured in RPMI media (Fisher Scientific, Catalogue # A1049101) with 10% Fetal Bovine Serum (R&D Systems, Catalog # S12450H) and 1% Antibiotic-antimicotic (Thermofisher Scientific, Catalogue #15240062) up to a density of 1 million cells per mL prior to transfection.

Techniques: Activity Assay, Mutagenesis, Sequencing, Infection

(A) MPRA activity in Jurkat cells tiling through the LTRs of HIV-1 and HIV-2. (B, G) Saturation mutagenesis MPRA experiments in unstimulated Jurkat cells for tiles in the LTR (B), gag/env (G) regions of HIV-2 ROD strain that show transcriptional activity. Region coordinates are provided using standardized SIVmac239 genomic coordinates. TF motifs that contribute to activity are outlined. (C) Saturation mutagenesis MPRA experiments in unstimulated and stimulated Jurkat cells for tile SIVmac239:379-571 in the HIV-2 LTR. (D) Violin plots showing the distribution of LTR activity in unstimulated Jurkat cells across 41 HIV-2 isolates with full-length sequences in NCBI. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. The dots heatmaps below indicate the fold activation by stimulation of Jurkat cells with αCD3+PMA, TNFα, or IFNγ. The color indicates the median fold activation across isolates, whereas the size of the dots reflects the fold activity differences between the 5th and 95th percentiles. (E) CASCADE-derived motifs for different cofactors in the LTR and gag regions of HIV-2 ROD strain. (F) MPRA activity map across the genome of HIV-2 ROD strain in unstimulated Jurkat cells. The genome organization is shown below. (H-I) Los Alamos National Laboratory (LANL) genome alignments of HIV-2 strains using the SIVmac239 genome as a reference. (H) Transcriptional activity predicted using CREST is shown in shades of green. (I) Transcription start sites predicted using Puffin trained on FANTOM CAGE data are shown in shades of red.

Journal: bioRxiv

Article Title: Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

doi: 10.64898/2026.04.03.716403

Figure Lengend Snippet: (A) MPRA activity in Jurkat cells tiling through the LTRs of HIV-1 and HIV-2. (B, G) Saturation mutagenesis MPRA experiments in unstimulated Jurkat cells for tiles in the LTR (B), gag/env (G) regions of HIV-2 ROD strain that show transcriptional activity. Region coordinates are provided using standardized SIVmac239 genomic coordinates. TF motifs that contribute to activity are outlined. (C) Saturation mutagenesis MPRA experiments in unstimulated and stimulated Jurkat cells for tile SIVmac239:379-571 in the HIV-2 LTR. (D) Violin plots showing the distribution of LTR activity in unstimulated Jurkat cells across 41 HIV-2 isolates with full-length sequences in NCBI. The thick black line indicates the median, and the dotted lines indicate the first and third quartiles. The dots heatmaps below indicate the fold activation by stimulation of Jurkat cells with αCD3+PMA, TNFα, or IFNγ. The color indicates the median fold activation across isolates, whereas the size of the dots reflects the fold activity differences between the 5th and 95th percentiles. (E) CASCADE-derived motifs for different cofactors in the LTR and gag regions of HIV-2 ROD strain. (F) MPRA activity map across the genome of HIV-2 ROD strain in unstimulated Jurkat cells. The genome organization is shown below. (H-I) Los Alamos National Laboratory (LANL) genome alignments of HIV-2 strains using the SIVmac239 genome as a reference. (H) Transcriptional activity predicted using CREST is shown in shades of green. (I) Transcription start sites predicted using Puffin trained on FANTOM CAGE data are shown in shades of red.

Article Snippet: Jurkat cells (ATCC-TIB-15) were cultured in RPMI media (Fisher Scientific, Catalogue # A1049101) with 10% Fetal Bovine Serum (R&D Systems, Catalog # S12450H) and 1% Antibiotic-antimicotic (Thermofisher Scientific, Catalogue #15240062) up to a density of 1 million cells per mL prior to transfection.

Techniques: Activity Assay, Mutagenesis, Activation Assay, Derivative Assay

The cell lines MPC11, L363 and KMS12-BM were seeded at 10,000 cells/well in a 96-well plate. The cells were stimulated with control medium or Met(-)- medium. For the positive control (death), the cells were stimulated with 1 µM staurosporine. After 24 h, 48 h and 72 h, measurements were performed with the EarlyTox Live/Dead Assay Kit (Molecular Devices). The staining solution (5 µg/mL Hoechst 33342 (Thermo Fisher, Darmstadt, Germany), 6 µM EthD-III, and 6 µM calcein AM (CAM) in DMEM (Gibco, Life Technologies; Darmstadt, Germany)) was added, and after 30 min of incubation, measurements were made with the ImageXpress Pico Automated Cell Imaging System. The number of cells was determined via Hoechst 33342. Living cells were stained with the nonfluorescent calcein AM, which permeates the intact cell membrane and is converted into calcein, the fluorescent form, by intracellular esterases (cells are shown in green). If compromised cell membrane integrity is associated with cell death, EthD-III enters cells and binds to nucleic acids (cells are shown in red). A representative area for cell viability is shown for each cell line. The cell numbers are not representative of every case. The white bar, representing 52.44 µm, is used for size classification.

Journal: bioRxiv

Article Title: Metabolic silencing via methionine-based amino acid restriction in multiple myeloma cell lines reveals a potential new strategy for cancer therapy

doi: 10.1101/2025.08.17.670755

Figure Lengend Snippet: The cell lines MPC11, L363 and KMS12-BM were seeded at 10,000 cells/well in a 96-well plate. The cells were stimulated with control medium or Met(-)- medium. For the positive control (death), the cells were stimulated with 1 µM staurosporine. After 24 h, 48 h and 72 h, measurements were performed with the EarlyTox Live/Dead Assay Kit (Molecular Devices). The staining solution (5 µg/mL Hoechst 33342 (Thermo Fisher, Darmstadt, Germany), 6 µM EthD-III, and 6 µM calcein AM (CAM) in DMEM (Gibco, Life Technologies; Darmstadt, Germany)) was added, and after 30 min of incubation, measurements were made with the ImageXpress Pico Automated Cell Imaging System. The number of cells was determined via Hoechst 33342. Living cells were stained with the nonfluorescent calcein AM, which permeates the intact cell membrane and is converted into calcein, the fluorescent form, by intracellular esterases (cells are shown in green). If compromised cell membrane integrity is associated with cell death, EthD-III enters cells and binds to nucleic acids (cells are shown in red). A representative area for cell viability is shown for each cell line. The cell numbers are not representative of every case. The white bar, representing 52.44 µm, is used for size classification.

Article Snippet: The MPC11 murine MM cell line was purchased from the American Type Culture Collection (ATCC), and the KMS12-BM and L363 human MM cell lines were purchased from the Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH (Braunschweig, Germany).

Techniques: Control, Positive Control, Live Dead Assay, Staining, Incubation, Imaging, Membrane