S6 Fig - | ORKG Ask

Additional file 1 of Folate regulates RNA m5C modification and translation in neural stem cells

Xiguang Xu (4989533)
Zachary Johnson (571094)
Amanda Wang (673947)
Rachel L. Padget (14176512)
James W. Smyth (9977294)
Hehuang Xie (14176515)

November 2022

Additional file 1: Figure S1. Quality control of total mRNA-seq datasets. (a, b, c) Scatter plot sho...

PCA and NMF analysis on the gene-expression data of MSC, MSC-like (MSC-, mClone-3), MAPC-1 (M-1), MAPC-2 (M-2) and ESC

Fernando Ulloa-Montoya (47233)
Benjamin L Kidder (47234)
Karen A Pauwelyn (47235)
Lucas G Chase (47236)
Aernout Luttun (47237)
Annelies Crabbe (47238)
Martine Geraerts (20224)
Alexei A Sharov (2374)
Yulan Piao (2375)
Minoru SH Ko (47239)
Wei-Shou Hu (33182)
Catherine M Verfaillie (47240)

December 2011

PCA on all differentially expressed genes with samples plotted in the first two components' space. C...

Additional file3: of Increased insulin-like growth factor 1 production by polyploid adipose stem cells promotes growth of breast cancer cells

Roberta Fajka-Boja (148923)
Annamária Marton (2551180)
Anna Tóth (509449)
Péter Blazsó (148906)
Vilmos Tubak (455817)
Balázs Bálint (2447605)
István Nagy (147904)
Zoltán Hegedűs (455815)
Csaba Vizler (31416)
Robert Katona (5722379)

September 2018

Figure S3. Volcano plot displays the fold change (FC) and statistical significance (FDR) values of g...

S5 Fig -

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) PCA plot of replicate nsRNA-seq experiments performed in Med15/16-AID and Med15-AID cells treate...

S1 Fig -

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Spot assays assessing growth of parental, Med14-AID, and Med16-AID strains on YPD plates contain...

Transcription overactivation by Med16 removal is partially dependent on the tail triad.

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blots showing the kinetics of Med15-AID and Med16-AID depletion upon 3-IAA treatment of ...

Mot1 removal partially restores wild-type transcription in Med16-AID cells.

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blots showing the kinetics of Mot1-AID and Med16-AID upon 3-IAA treatment of double-degr...

S7 Fig -

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blots showing the kinetics of Med16-AID depletion and stability of TBP-3xFLAG-MNase upon...

Med16 deficiency primarily overactivates TFIID-dependent genes.

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blot showing the kinetics of Med16-AID depletion upon 3-IAA treatment of cells. (B) Spot...

HAPLN1-PTR1 induces transcriptional changes, including an NF-κB transcriptional program.

Mailee Huynh (14237438)
Hae Yeun Chang (14237441)
Dominique N. Lisiero (14237444)
Irene M. Ong (8353449)
Trinayan Kashyap (603697)
Natalie S. Callander (8859872)
Shigeki Miyamoto (87670)

December 2022

(A) Heatmap summarized all the differentially expressed genes of two-fold. Each row is a gene, each ...

High levels of MMSET lead to altered gene expression.

Relja Popovic (626043)
Eva Martinez-Garcia (626044)
Eugenia G. Giannopoulou (626045)
Quanwei Zhang (626046)
Qingyang Zhang (626047)
Teresa Ezponda (626048)
Mrinal Y. Shah (626049)
Yupeng Zheng (626050)
Christine M. Will (626051)
Eliza C. Small (626052)
Youjia Hua (199186)
Marinka Bulic (626053)
Yanwen Jiang (103833)
Matteo Carrara (165331)
Raffaele A. Calogero (184115)
William L. Kath (626054)
Neil L. Kelleher (548328)
Ji-Ping Wang (82379)
Olivier Elemento (7617)
Jonathan D. Licht (118676)

September 2014

(A) Dot plot representing differentially expressed genes in NTKO and TKO cells from the microarra...

Heatmap of differentially expressed genes identified through RNA-seq analysis (log2 fold change>2, and adjusted P<0.05).

Yixian Wu (6421511)
Songhe Guo (6828152)
Fangfang Chen (302428)
Yiqiu Li (4734129)
Yuying Huang (1817206)
Wanli Liu (384073)
Ge Zhang (112487)

January 2023

Heatmap showing RNA-seq data from RAW264.7 cells after Fn-Dps (A) or Fn (B) treatment. (PDF)</p

Table S6. List of genes differentially regulated by NAA+NF compared to NAA

Herrbach, Violaine
Chirinos, Ximena
Rengel, David
Agbevenou, Kokoévi
Vincent, Rémy
Pateyron, Stephanie
Huguet, Stéphanie
Balzergue, Sandrine
Pasha, Asher
Provart, Nicholas
Gough, Clare
Bensmihen, Sandra

January 2017

List of genes differently expressed in the NF+NAA treatment compared to NAA condition. The first col...

Additional file 2: Figure S1. of A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues

Isha Sethi (3454058)
Rose-Anne Romano (263720)
Christian Gluck (3453233)
Kirsten Smalley (263723)
Borivoj Vojtesek (394471)
Michael Buck (3454055)
Satrajit Sinha (28564)

August 2015

Expression estimates of genes are consistent across two independent analysis pipelines. RNA-Seq expr...

Volcano plots of differentially regulated genes detected by RNA-Seq analysis of N2a cells treated with RG3039 or its 7-methyl analog PF-06802336 with summary of number of genes significantly (P<0.05) changed.

Jonathan J. Cherry (501180)
Christine J. DiDonato (358186)
Elliot J. Androphy (24737)
Alessandro Calo (4458832)
Kyle Potter (4458823)
Sara K. Custer (3219273)
Sarah Du (3549542)
Timothy L. Foley (1307850)
Ariamala Gopalsamy (1616713)
Emily J. Reedich (4458841)
Susana M. Gordo (4458838)
William Gordon (150154)
Natalie Hosea (4458835)
Lyn H. Jones (465244)
Daniel K. Krizay (4458826)
Gregory LaRosa (2641600)
Hongxia Li (493545)
Sachin Mathur (3401684)
Carol A. Menard (1616707)
Paraj Patel (4458829)
Rebeca Ramos-Zayas (281706)
Anne Rietz (501181)
Haojing Rong (2138929)
Baohong Zhang (108942)
Michael A. Tones (1616704)

September 2017

Plates of cells (in quadruplicate) were treated with 1 μM of either compound or DMSO (1 μM) for 2...

Additional file 1 of Folate regulates RNA m5C modification and translation in neural stem cells

Xiguang Xu (4989533)
Zachary Johnson (571094)
Amanda Wang (673947)
Rachel L. Padget (14176512)
James W. Smyth (9977294)
Hehuang Xie (14176515)

November 2022

Additional file 1: Figure S1. Quality control of total mRNA-seq datasets. (a, b, c) Scatter plot sho...

PCA and NMF analysis on the gene-expression data of MSC, MSC-like (MSC-, mClone-3), MAPC-1 (M-1), MAPC-2 (M-2) and ESC

Fernando Ulloa-Montoya (47233)
Benjamin L Kidder (47234)
Karen A Pauwelyn (47235)
Lucas G Chase (47236)
Aernout Luttun (47237)
Annelies Crabbe (47238)
Martine Geraerts (20224)
Alexei A Sharov (2374)
Yulan Piao (2375)
Minoru SH Ko (47239)
Wei-Shou Hu (33182)
Catherine M Verfaillie (47240)

December 2011

PCA on all differentially expressed genes with samples plotted in the first two components' space. C...

Additional file3: of Increased insulin-like growth factor 1 production by polyploid adipose stem cells promotes growth of breast cancer cells

Roberta Fajka-Boja (148923)
Annamária Marton (2551180)
Anna Tóth (509449)
Péter Blazsó (148906)
Vilmos Tubak (455817)
Balázs Bálint (2447605)
István Nagy (147904)
Zoltán Hegedűs (455815)
Csaba Vizler (31416)
Robert Katona (5722379)

September 2018

Figure S3. Volcano plot displays the fold change (FC) and statistical significance (FDR) values of g...

S5 Fig -

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) PCA plot of replicate nsRNA-seq experiments performed in Med15/16-AID and Med15-AID cells treate...

S1 Fig -

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Spot assays assessing growth of parental, Med14-AID, and Med16-AID strains on YPD plates contain...

Transcription overactivation by Med16 removal is partially dependent on the tail triad.

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blots showing the kinetics of Med15-AID and Med16-AID depletion upon 3-IAA treatment of ...

Mot1 removal partially restores wild-type transcription in Med16-AID cells.

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blots showing the kinetics of Mot1-AID and Med16-AID upon 3-IAA treatment of double-degr...

S7 Fig -

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blots showing the kinetics of Med16-AID depletion and stability of TBP-3xFLAG-MNase upon...

Med16 deficiency primarily overactivates TFIID-dependent genes.

Moustafa M. Saleh (9864299)
Célia Jeronimo (11269206)
François Robert (60350)
Gabriel E. Zentner (11269209)

August 2021

(A) Western blot showing the kinetics of Med16-AID depletion upon 3-IAA treatment of cells. (B) Spot...

HAPLN1-PTR1 induces transcriptional changes, including an NF-κB transcriptional program.

Mailee Huynh (14237438)
Hae Yeun Chang (14237441)
Dominique N. Lisiero (14237444)
Irene M. Ong (8353449)
Trinayan Kashyap (603697)
Natalie S. Callander (8859872)
Shigeki Miyamoto (87670)

December 2022

(A) Heatmap summarized all the differentially expressed genes of two-fold. Each row is a gene, each ...

High levels of MMSET lead to altered gene expression.

Relja Popovic (626043)
Eva Martinez-Garcia (626044)
Eugenia G. Giannopoulou (626045)
Quanwei Zhang (626046)
Qingyang Zhang (626047)
Teresa Ezponda (626048)
Mrinal Y. Shah (626049)
Yupeng Zheng (626050)
Christine M. Will (626051)
Eliza C. Small (626052)
Youjia Hua (199186)
Marinka Bulic (626053)
Yanwen Jiang (103833)
Matteo Carrara (165331)
Raffaele A. Calogero (184115)
William L. Kath (626054)
Neil L. Kelleher (548328)
Ji-Ping Wang (82379)
Olivier Elemento (7617)
Jonathan D. Licht (118676)

September 2014

(A) Dot plot representing differentially expressed genes in NTKO and TKO cells from the microarra...

Heatmap of differentially expressed genes identified through RNA-seq analysis (log2 fold change>2, and adjusted P<0.05).

Yixian Wu (6421511)
Songhe Guo (6828152)
Fangfang Chen (302428)
Yiqiu Li (4734129)
Yuying Huang (1817206)
Wanli Liu (384073)
Ge Zhang (112487)

January 2023

Heatmap showing RNA-seq data from RAW264.7 cells after Fn-Dps (A) or Fn (B) treatment. (PDF)</p

Table S6. List of genes differentially regulated by NAA+NF compared to NAA

Herrbach, Violaine
Chirinos, Ximena
Rengel, David
Agbevenou, Kokoévi
Vincent, Rémy
Pateyron, Stephanie
Huguet, Stéphanie
Balzergue, Sandrine
Pasha, Asher
Provart, Nicholas
Gough, Clare
Bensmihen, Sandra

January 2017

List of genes differently expressed in the NF+NAA treatment compared to NAA condition. The first col...

Additional file 2: Figure S1. of A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues

Isha Sethi (3454058)
Rose-Anne Romano (263720)
Christian Gluck (3453233)
Kirsten Smalley (263723)
Borivoj Vojtesek (394471)
Michael Buck (3454055)
Satrajit Sinha (28564)

August 2015

Expression estimates of genes are consistent across two independent analysis pipelines. RNA-Seq expr...

Volcano plots of differentially regulated genes detected by RNA-Seq analysis of N2a cells treated with RG3039 or its 7-methyl analog PF-06802336 with summary of number of genes significantly (P<0.05) changed.

Jonathan J. Cherry (501180)
Christine J. DiDonato (358186)
Elliot J. Androphy (24737)
Alessandro Calo (4458832)
Kyle Potter (4458823)
Sara K. Custer (3219273)
Sarah Du (3549542)
Timothy L. Foley (1307850)
Ariamala Gopalsamy (1616713)
Emily J. Reedich (4458841)
Susana M. Gordo (4458838)
William Gordon (150154)
Natalie Hosea (4458835)
Lyn H. Jones (465244)
Daniel K. Krizay (4458826)
Gregory LaRosa (2641600)
Hongxia Li (493545)
Sachin Mathur (3401684)
Carol A. Menard (1616707)
Paraj Patel (4458829)
Rebeca Ramos-Zayas (281706)
Anne Rietz (501181)
Haojing Rong (2138929)
Baohong Zhang (108942)
Michael A. Tones (1616704)

September 2017

Plates of cells (in quadruplicate) were treated with 1 μM of either compound or DMSO (1 μM) for 2...

Additional file 1 of Folate regulates RNA m5C modification and translation in neural stem cells

Xiguang Xu (4989533)
Zachary Johnson (571094)
Amanda Wang (673947)
Rachel L. Padget (14176512)
James W. Smyth (9977294)
Hehuang Xie (14176515)

November 2022

Additional file 1: Figure S1. Quality control of total mRNA-seq datasets. (a, b, c) Scatter plot sho...

PCA and NMF analysis on the gene-expression data of MSC, MSC-like (MSC-, mClone-3), MAPC-1 (M-1), MAPC-2 (M-2) and ESC

Fernando Ulloa-Montoya (47233)
Benjamin L Kidder (47234)
Karen A Pauwelyn (47235)
Lucas G Chase (47236)
Aernout Luttun (47237)
Annelies Crabbe (47238)
Martine Geraerts (20224)
Alexei A Sharov (2374)
Yulan Piao (2375)
Minoru SH Ko (47239)
Wei-Shou Hu (33182)
Catherine M Verfaillie (47240)

December 2011

PCA on all differentially expressed genes with samples plotted in the first two components' space. C...

Additional file3: of Increased insulin-like growth factor 1 production by polyploid adipose stem cells promotes growth of breast cancer cells

Roberta Fajka-Boja (148923)
Annamária Marton (2551180)
Anna Tóth (509449)
Péter Blazsó (148906)
Vilmos Tubak (455817)
Balázs Bálint (2447605)
István Nagy (147904)
Zoltán Hegedűs (455815)
Csaba Vizler (31416)
Robert Katona (5722379)

September 2018

Figure S3. Volcano plot displays the fold change (FC) and statistical significance (FDR) values of g...

S6 Fig -

Abstract

Extracted data

S6 Fig -

Abstract

Extracted data

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