Additional file 8: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

Quesada, V.
Conde, L.
Villamor, N.
Ordonez, G.
Jares, P.
Bassaganyas, L.
Ramsay, A.
Bea, S.
Pinyol, M.
Martinez-Trillos, A.
Lopez-Guerra, M.
Colomer, D.
Navarro, A.
Baumann, T.
Aymerich, M.
Rozman, M.
Delgado, J.
Gine, E.
Hernandez, J.
Gonzalez-Diaz, M.
Puente, D.
Velasco, G.
Freije, J.
Tubio, J.
Royo, R.
Gelpi, J.
Orozco, M.
Pisano, D.
Zamora, J.
Vazquez, M.
Valencia, A.
Himmelbauer, H.
Bayes, M.
Heath, S.
Gut, M.
Gut, I.
Estivill, X.
Lopez-Guillermo, A.
Puente, X.
Campo, E.
Lopez-Otin, C.

January 2012

Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leuk...

Additional file 2: of TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data

Readman Chiu (41422)
Ka Nip (5514428)
Justin Chu (732152)
Inanc Birol (277074)

September 2018

Table S4. AML-relevant structural variants detected by TAP in Leucegene. Table S5. Aberrant splicing...

Additional file 1: of Hypoxia leads to significant changes in alternative splicing and elevated expression of CLK splice factor kinases in PC3 prostate cancer cells

Elizabeth Bowler (700255)
Sean Porazinski (5045756)
Simon Uzor (5045753)
Philippe Thibault (28505)
Mathieu Durand (628572)
Elvy Lapointe (3383)
Kasper Rouschop (5045750)
John Hancock (1461232)
Ian Wilson (57185)
Michael Ladomery (255415)

April 2018

Table S1. Forward (F) and reverse (R) primer sequences for all human genes amplified using standard ...

Additional file 7: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

List of alternative spliced genes from MATS analysis, comparing CLL and B cell data. (XLSX 45Â kb

Additional file 3: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

Differentially expressed genes in CLL relative to B cells based on FPKM analysis. (XLSX 214Â kb

Additional file 4: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

IPA functional annotation of differentially expressed genes in CLL specimens. (DOCX 19Â kb

Additional file 2: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

Number of transcripts and genes in B cells, U-CLL and M-CLL. Pair wise scatter plot matrix. (DOCX 14...

Additional file 1: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

Alignment statistic summary of all 15 samples signal-end reads mapped to UCSC H. sapiens reference g...

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Liao, Wei
Jordaan, Gwen
Nham, Phillipp
Phan, Ryan T
Pelegrini, Matteo
Sharma, Sanjai

December 2015

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic l...

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

Liao, Wei
Jordaan, Gwen
Nham, Phillipp
Phan, Ryan T
Pelegrini, Matteo
Sharma, Sanjai

October 2015

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic l...

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

Liao, Wei
Jordaan, Gwen
Nham, Phillipp
Phan, Ryan T
Pelegrini, Matteo
Sharma, Sanjai

October 2015

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic l...

Additional file 1: of Genomic characterization of chronic lymphocytic leukemia (CLL) in radiation-exposed Chornobyl cleanup workers

Juhi Ojha (355965)
Iryna Dyagil (5167895)
Stuart Finch (5167916)
Robert Reiss (5167904)
Adam de Smith (5167886)
Semira Gonseth (665194)
Mi Zhou (9884)
Helen Hansen (449559)
Amy Sherborne (5167901)
Jean Nakamura (5167913)
Paige Bracci (709480)
Nataliya Gudzenko (5167898)
Maureen Hatch (18343)
Nataliya Babkina (5167907)
Mark Little (649058)
Vadim Chumak (5167892)
Kyle Walsh (5167889)
Dimitry Bazyka (5167910)
Joseph Wiemels (243305)
Lydia Zablotska (5167919)

May 2018

Table S1. List of target genes sequenced by targeted deep sequencing. Table S2. Mutations in Exposed...

Additional file 1: of The clonal evolution of two distinct T315I-positive BCR-ABL1 subclones in a Philadelphia-positive acute lymphoblastic leukemia failing multiple lines of therapy: a case report

Caterina De Benedittis (765725)
Cristina Papayannidis (148445)
Claudia Venturi (3512696)
Maria Abbenante (3512687)
Stefania Paolini (196601)
Sarah Parisi (4334455)
Chiara Sartor (4334452)
Michele Cavo (463532)
Giovanni Martinelli (148520)
Simona Soverini (148501)

August 2017

Comparison between mutations detected by conventional Sanger sequencing and Deep sequencing and esti...

Additional file 3: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Ksenia Anufrieva (5461703)
Victoria Shender (5461709)
Georgij Arapidi (3606356)
Marat Pavlyukov (5461700)
Michail Shakhparonov (5461706)
Polina Shnaider (5461697)
Ivan Butenko (3455030)
Maria Lagarkova (3547298)
Vadim Govorun (2131033)

June 2018

(A) Description of all alternative splicing events in cancer cell lines after therapy. (B) Identific...

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

Quesada, V.
Conde, L.
Villamor, N.
Ordonez, G.
Jares, P.
Bassaganyas, L.
Ramsay, A.
Bea, S.
Pinyol, M.
Martinez-Trillos, A.
Lopez-Guerra, M.
Colomer, D.
Navarro, A.
Baumann, T.
Aymerich, M.
Rozman, M.
Delgado, J.
Gine, E.
Hernandez, J.
Gonzalez-Diaz, M.
Puente, D.
Velasco, G.
Freije, J.
Tubio, J.
Royo, R.
Gelpi, J.
Orozco, M.
Pisano, D.
Zamora, J.
Vazquez, M.
Valencia, A.
Himmelbauer, H.
Bayes, M.
Heath, S.
Gut, M.
Gut, I.
Estivill, X.
Lopez-Guillermo, A.
Puente, X.
Campo, E.
Lopez-Otin, C.

January 2012

Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leuk...

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

Quesada, V.
Conde, L.
Villamor, N.
Ordonez, G.
Jares, P.
Bassaganyas, L.
Ramsay, A.
Bea, S.
Pinyol, M.
Martinez-Trillos, A.
Lopez-Guerra, M.
Colomer, D.
Navarro, A.
Baumann, T.
Aymerich, M.
Rozman, M.
Delgado, J.
Gine, E.
Hernandez, J.
Gonzalez-Diaz, M.
Puente, D.
Velasco, G.
Freije, J.
Tubio, J.
Royo, R.
Gelpi, J.
Orozco, M.
Pisano, D.
Zamora, J.
Vazquez, M.
Valencia, A.
Himmelbauer, H.
Bayes, M.
Heath, S.
Gut, M.
Gut, I.
Estivill, X.
Lopez-Guillermo, A.
Puente, X.
Campo, E.
Lopez-Otin, C.

January 2012

Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leuk...

Additional file 2: of TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data

Readman Chiu (41422)
Ka Nip (5514428)
Justin Chu (732152)
Inanc Birol (277074)

September 2018

Table S4. AML-relevant structural variants detected by TAP in Leucegene. Table S5. Aberrant splicing...

Additional file 1: of Hypoxia leads to significant changes in alternative splicing and elevated expression of CLK splice factor kinases in PC3 prostate cancer cells

Elizabeth Bowler (700255)
Sean Porazinski (5045756)
Simon Uzor (5045753)
Philippe Thibault (28505)
Mathieu Durand (628572)
Elvy Lapointe (3383)
Kasper Rouschop (5045750)
John Hancock (1461232)
Ian Wilson (57185)
Michael Ladomery (255415)

April 2018

Table S1. Forward (F) and reverse (R) primer sequences for all human genes amplified using standard ...

Additional file 7: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

List of alternative spliced genes from MATS analysis, comparing CLL and B cell data. (XLSX 45Â kb

Additional file 3: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

Differentially expressed genes in CLL relative to B cells based on FPKM analysis. (XLSX 214Â kb

Additional file 4: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

IPA functional annotation of differentially expressed genes in CLL specimens. (DOCX 19Â kb

Additional file 2: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

Number of transcripts and genes in B cells, U-CLL and M-CLL. Pair wise scatter plot matrix. (DOCX 14...

Additional file 1: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Wei Liao (166135)
Gwen Jordaan (3487397)
Phillipp Nham (3487400)
Ryan Phan (453462)
Matteo Pelegrini (3487394)
Sanjai Sharma (453459)

October 2015

Alignment statistic summary of all 15 samples signal-end reads mapped to UCSC H. sapiens reference g...

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Liao, Wei
Jordaan, Gwen
Nham, Phillipp
Phan, Ryan T
Pelegrini, Matteo
Sharma, Sanjai

December 2015

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic l...

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

Liao, Wei
Jordaan, Gwen
Nham, Phillipp
Phan, Ryan T
Pelegrini, Matteo
Sharma, Sanjai

October 2015

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic l...

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

Liao, Wei
Jordaan, Gwen
Nham, Phillipp
Phan, Ryan T
Pelegrini, Matteo
Sharma, Sanjai

October 2015

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic l...

Additional file 1: of Genomic characterization of chronic lymphocytic leukemia (CLL) in radiation-exposed Chornobyl cleanup workers

Juhi Ojha (355965)
Iryna Dyagil (5167895)
Stuart Finch (5167916)
Robert Reiss (5167904)
Adam de Smith (5167886)
Semira Gonseth (665194)
Mi Zhou (9884)
Helen Hansen (449559)
Amy Sherborne (5167901)
Jean Nakamura (5167913)
Paige Bracci (709480)
Nataliya Gudzenko (5167898)
Maureen Hatch (18343)
Nataliya Babkina (5167907)
Mark Little (649058)
Vadim Chumak (5167892)
Kyle Walsh (5167889)
Dimitry Bazyka (5167910)
Joseph Wiemels (243305)
Lydia Zablotska (5167919)

May 2018

Table S1. List of target genes sequenced by targeted deep sequencing. Table S2. Mutations in Exposed...

Additional file 1: of The clonal evolution of two distinct T315I-positive BCR-ABL1 subclones in a Philadelphia-positive acute lymphoblastic leukemia failing multiple lines of therapy: a case report

Caterina De Benedittis (765725)
Cristina Papayannidis (148445)
Claudia Venturi (3512696)
Maria Abbenante (3512687)
Stefania Paolini (196601)
Sarah Parisi (4334455)
Chiara Sartor (4334452)
Michele Cavo (463532)
Giovanni Martinelli (148520)
Simona Soverini (148501)

August 2017

Comparison between mutations detected by conventional Sanger sequencing and Deep sequencing and esti...

Additional file 3: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Ksenia Anufrieva (5461703)
Victoria Shender (5461709)
Georgij Arapidi (3606356)
Marat Pavlyukov (5461700)
Michail Shakhparonov (5461706)
Polina Shnaider (5461697)
Ivan Butenko (3455030)
Maria Lagarkova (3547298)
Vadim Govorun (2131033)

June 2018

(A) Description of all alternative splicing events in cancer cell lines after therapy. (B) Identific...

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

Quesada, V.
Conde, L.
Villamor, N.
Ordonez, G.
Jares, P.
Bassaganyas, L.
Ramsay, A.
Bea, S.
Pinyol, M.
Martinez-Trillos, A.
Lopez-Guerra, M.
Colomer, D.
Navarro, A.
Baumann, T.
Aymerich, M.
Rozman, M.
Delgado, J.
Gine, E.
Hernandez, J.
Gonzalez-Diaz, M.
Puente, D.
Velasco, G.
Freije, J.
Tubio, J.
Royo, R.
Gelpi, J.
Orozco, M.
Pisano, D.
Zamora, J.
Vazquez, M.
Valencia, A.
Himmelbauer, H.
Bayes, M.
Heath, S.
Gut, M.
Gut, I.
Estivill, X.
Lopez-Guillermo, A.
Puente, X.
Campo, E.
Lopez-Otin, C.

January 2012

Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leuk...

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

Quesada, V.
Conde, L.
Villamor, N.
Ordonez, G.
Jares, P.
Bassaganyas, L.
Ramsay, A.
Bea, S.
Pinyol, M.
Martinez-Trillos, A.
Lopez-Guerra, M.
Colomer, D.
Navarro, A.
Baumann, T.
Aymerich, M.
Rozman, M.
Delgado, J.
Gine, E.
Hernandez, J.
Gonzalez-Diaz, M.
Puente, D.
Velasco, G.
Freije, J.
Tubio, J.
Royo, R.
Gelpi, J.
Orozco, M.
Pisano, D.
Zamora, J.
Vazquez, M.
Valencia, A.
Himmelbauer, H.
Bayes, M.
Heath, S.
Gut, M.
Gut, I.
Estivill, X.
Lopez-Guillermo, A.
Puente, X.
Campo, E.
Lopez-Otin, C.

January 2012

Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leuk...

Additional file 2: of TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data

Readman Chiu (41422)
Ka Nip (5514428)
Justin Chu (732152)
Inanc Birol (277074)

September 2018

Table S4. AML-relevant structural variants detected by TAP in Leucegene. Table S5. Aberrant splicing...

Additional file 1: of Hypoxia leads to significant changes in alternative splicing and elevated expression of CLK splice factor kinases in PC3 prostate cancer cells

Elizabeth Bowler (700255)
Sean Porazinski (5045756)
Simon Uzor (5045753)
Philippe Thibault (28505)
Mathieu Durand (628572)
Elvy Lapointe (3383)
Kasper Rouschop (5045750)
John Hancock (1461232)
Ian Wilson (57185)
Michael Ladomery (255415)

April 2018

Table S1. Forward (F) and reverse (R) primer sequences for all human genes amplified using standard ...

Additional file 8: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Abstract

Extracted data

Additional file 8: of Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

Abstract

Extracted data

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