Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"

Chen, Yunshun
Pal, Bhupinder
Visvader, Jane E
Smyth, Gordon K

November 2017

This data set provides data files and R code to accompany the article Differential methylation analy...

Dominant functional categories of the genes whose transcript levels are enhanced in adenomas of any of the three genera—Mouse, rat, and human.

Jennifer K. Pleiman (5724686)
Amy A. Irving (1916461)
Zhishi Wang (460794)
Erik Toraason (5724689)
Linda Clipson (400806)
William F. Dove (1916458)
Dustin A. Deming (400803)
Michael A. Newton (204762)

September 2018

Dominant functional categories (rows) enriched in the large list of 5602 genes (columns) having incr...

DataforThorley_DMRMorphology

Jack Thorley (3352718)
Nathan Katlein (5224568)
Katy Goddard (5224571)
Markus Zoettl (3352733)
Tim Clutton-Brock (3193941)

May 2018

Morphology data for female Damaraland mole-rats derived from X-rays taken in captive and wild mole-r...

Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

Elise Parey
Diego Fernandez Aroca
Stephanie Frost
Camille Berthelot
Diego Villar

August 2023

Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveal...

Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

Elise Parey
Diego Fernandez Aroca
Stephanie Frost
Camille Berthelot
Diego Villar

December 2022

This archive contains the code and datasets generated in the associated manuscript: "Phylogenetic mo...

Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits

Parey, Elise
Frost, Stephanie
Uribarren, Ainhoa
Park, Thomas, J
Zoettl, Markus
Smith, Ewan, St. John
Berthelot, Camille
Villar, Diego

January 2023

International audienceABSTRACT Changes in gene regulation have long been thought to underlie most ph...

Comparing the development of cortex-wide gene expression patterns between two rodent species in a common reference frame: Dataset

Sebastian James (2768587)
Mackenzie Englund (13842891)
Riley Bottom (13842900)
Roberto Perez (13848935)
Kathleen E. Connor (13848938)
Kelly J. Huffman (13842903)
Leah A. Krubitzer (13842906)
Stuart P. Wilson (201058)

September 2022

This is the dataset for the paper "Comparing the development of cortex-wide gene expression patterns...

Data files to support "Scaling of gene transcriptional gradients with brain size across mouse development"

Fulcher, Ben
Lau, Hoi Yan Gladys

March 2021

Matlab data files to support reproduction of the analyses contained in https://github.com/DynamicsAn...

Dataset for "Reproduction promotes adaptive increases in body size in female mole-rats"

Thorley, Jack

May 2018

Morphological data derived from X-rays of Damaraland mole-rats, taken from captive and wild animals

Biological Mammalian Dataset for Mirarab et. al.

Mirarab, Siavash
Bayzid, Md Shamsuzzoha
Boussau, Bastien
Warnow, Tandy

January 2014

Mammalian dataset was provided to us by Song et al from their 2013 PNAS paper (doi: 10.1073/pnas.121...

Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease

Huebner, N.
Wallace, C.A.
Zimdahl, H.
Petretto, E.
Schulz, H.
Maciver, F.
Mueller, M.
Hummel, O.
Monti, J.
Zidek, V.
Musilova, A.
Kren, V.
Causton, H.
Game, L.
Born, G.
Schmidt, S.
Mueller, A.
Cook, S.A.
Kurtz, T.W.
Whittaker, J.
Pravenec, M.
Aitman, T.J.

March 2005

Integration of genome-wide expression profiling with linkage analysis is a new approach to identifyi...

Rat Genome Database (RGD): mapping disease onto the genome.

Twigger, S
Lu, J
Shimoyama, M
Chen, D
Pasko, D
Long, H
Ginster, J
Chen, C F
Nigam, R
Kwitek, A
Eppig, J
Maltais, L
Maglott, D
Schuler, G
Jacob, H
Tonellato, P J

January 2002

The Rat Genome Database (RGD, http://rgd.mcw.edu) is an NIH-funded project whose stated mission is \...

Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: DEEs and DEGs]

Tonatiuh Pena Centeno (2585581)
orr shomroni (2611600)
Magali Hennion (268750)
Rashi Halder (2417332)
Ramon Vidal (97422)
Raza-Ur Rahman (2619955)
Andre Fischer (2619946)
Stefan Bonn (2619949)

June 2016

This repository contains the scripts used to identify differentially expressed genes (DEGs) and diff...

Predicting developmental limb enhancers and quantifying motif sequence differences between enhancers.

Friedrich, Tara

January 2017

Gene regulation can contribute to phenotypic divergence across species and cell types. By comparing ...

Data_Sheet_1_Unusual occurrence of domestication syndrome amongst African mole-rats: Is the naked mole-rat a domestic animal?.pdf

Guillermo Serrano Nájera (14181659)
Koryu Kin (5880710)

November 2022

The Naked mole-rat (NMR) is becoming a prominent model organism due to its peculiar traits, such as ...

Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"

Chen, Yunshun
Pal, Bhupinder
Visvader, Jane E
Smyth, Gordon K

November 2017

This data set provides data files and R code to accompany the article Differential methylation analy...

Dominant functional categories of the genes whose transcript levels are enhanced in adenomas of any of the three genera—Mouse, rat, and human.

Jennifer K. Pleiman (5724686)
Amy A. Irving (1916461)
Zhishi Wang (460794)
Erik Toraason (5724689)
Linda Clipson (400806)
William F. Dove (1916458)
Dustin A. Deming (400803)
Michael A. Newton (204762)

September 2018

Dominant functional categories (rows) enriched in the large list of 5602 genes (columns) having incr...

DataforThorley_DMRMorphology

Jack Thorley (3352718)
Nathan Katlein (5224568)
Katy Goddard (5224571)
Markus Zoettl (3352733)
Tim Clutton-Brock (3193941)

May 2018

Morphology data for female Damaraland mole-rats derived from X-rays taken in captive and wild mole-r...

Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

Elise Parey
Diego Fernandez Aroca
Stephanie Frost
Camille Berthelot
Diego Villar

August 2023

Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveal...

Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

Elise Parey
Diego Fernandez Aroca
Stephanie Frost
Camille Berthelot
Diego Villar

December 2022

This archive contains the code and datasets generated in the associated manuscript: "Phylogenetic mo...

Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits

Parey, Elise
Frost, Stephanie
Uribarren, Ainhoa
Park, Thomas, J
Zoettl, Markus
Smith, Ewan, St. John
Berthelot, Camille
Villar, Diego

January 2023

International audienceABSTRACT Changes in gene regulation have long been thought to underlie most ph...

Comparing the development of cortex-wide gene expression patterns between two rodent species in a common reference frame: Dataset

Sebastian James (2768587)
Mackenzie Englund (13842891)
Riley Bottom (13842900)
Roberto Perez (13848935)
Kathleen E. Connor (13848938)
Kelly J. Huffman (13842903)
Leah A. Krubitzer (13842906)
Stuart P. Wilson (201058)

September 2022

This is the dataset for the paper "Comparing the development of cortex-wide gene expression patterns...

Data files to support "Scaling of gene transcriptional gradients with brain size across mouse development"

Fulcher, Ben
Lau, Hoi Yan Gladys

March 2021

Matlab data files to support reproduction of the analyses contained in https://github.com/DynamicsAn...

Dataset for "Reproduction promotes adaptive increases in body size in female mole-rats"

Thorley, Jack

May 2018

Morphological data derived from X-rays of Damaraland mole-rats, taken from captive and wild animals

Biological Mammalian Dataset for Mirarab et. al.

Mirarab, Siavash
Bayzid, Md Shamsuzzoha
Boussau, Bastien
Warnow, Tandy

January 2014

Mammalian dataset was provided to us by Song et al from their 2013 PNAS paper (doi: 10.1073/pnas.121...

Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease

Huebner, N.
Wallace, C.A.
Zimdahl, H.
Petretto, E.
Schulz, H.
Maciver, F.
Mueller, M.
Hummel, O.
Monti, J.
Zidek, V.
Musilova, A.
Kren, V.
Causton, H.
Game, L.
Born, G.
Schmidt, S.
Mueller, A.
Cook, S.A.
Kurtz, T.W.
Whittaker, J.
Pravenec, M.
Aitman, T.J.

March 2005

Integration of genome-wide expression profiling with linkage analysis is a new approach to identifyi...

Rat Genome Database (RGD): mapping disease onto the genome.

Twigger, S
Lu, J
Shimoyama, M
Chen, D
Pasko, D
Long, H
Ginster, J
Chen, C F
Nigam, R
Kwitek, A
Eppig, J
Maltais, L
Maglott, D
Schuler, G
Jacob, H
Tonellato, P J

January 2002

The Rat Genome Database (RGD, http://rgd.mcw.edu) is an NIH-funded project whose stated mission is \...

Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: DEEs and DEGs]

Tonatiuh Pena Centeno (2585581)
orr shomroni (2611600)
Magali Hennion (268750)
Rashi Halder (2417332)
Ramon Vidal (97422)
Raza-Ur Rahman (2619955)
Andre Fischer (2619946)
Stefan Bonn (2619949)

June 2016

This repository contains the scripts used to identify differentially expressed genes (DEGs) and diff...

Predicting developmental limb enhancers and quantifying motif sequence differences between enhancers.

Friedrich, Tara

January 2017

Gene regulation can contribute to phenotypic divergence across species and cell types. By comparing ...

Data_Sheet_1_Unusual occurrence of domestication syndrome amongst African mole-rats: Is the naked mole-rat a domestic animal?.pdf

Guillermo Serrano Nájera (14181659)
Koryu Kin (5880710)

November 2022

The Naked mole-rat (NMR) is becoming a prominent model organism due to its peculiar traits, such as ...

Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"

Chen, Yunshun
Pal, Bhupinder
Visvader, Jane E
Smyth, Gordon K

November 2017

This data set provides data files and R code to accompany the article Differential methylation analy...

Dominant functional categories of the genes whose transcript levels are enhanced in adenomas of any of the three genera—Mouse, rat, and human.

Jennifer K. Pleiman (5724686)
Amy A. Irving (1916461)
Zhishi Wang (460794)
Erik Toraason (5724689)
Linda Clipson (400806)
William F. Dove (1916458)
Dustin A. Deming (400803)
Michael A. Newton (204762)

September 2018

Dominant functional categories (rows) enriched in the large list of 5602 genes (columns) having incr...

DataforThorley_DMRMorphology

Jack Thorley (3352718)
Nathan Katlein (5224568)
Katy Goddard (5224571)
Markus Zoettl (3352733)
Tim Clutton-Brock (3193941)

May 2018

Morphology data for female Damaraland mole-rats derived from X-rays taken in captive and wild mole-r...

Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

Abstract

Extracted data

Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"

Abstract

Extracted data

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