Additional file 2: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Additional file 1 of Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection

Chase E. Hawes (13922250)
Sonny R. Elizaldi (9684796)
Danielle Beckman (3696877)
Giovanne B. Diniz (6663395)
Yashavanth Shaan Lakshmanappa (13922253)
Sean Ott (13922256)
Blythe P. Durbin-Johnson (9576344)
Ashok R. Dinasarapu (9427665)
Andrea Gompers (10721824)
John H. Morrison (9688341)
Smita S. Iyer (8702931)

October 2022

Additional file 1: Fig. S1. Ranked genes by median normalized read counts in units of Log2 counts pe...

Additional file 2: of Clustering the autisms using glutamate synapse protein interaction networks from cortical and hippocampal tissue of seven mouse models

Emily Brown (194826)
Jonathan Lautz (5751308)
Tessa Davis (5751311)
Edward Gniffke (5751314)
Alison VanSchoiack (5751317)
Steven Neier (5751320)
Noah Tashbook (5751323)
Chiara Nicolini (2678902)
Margaret Fahnestock (5751326)
Adam Schrum (5751329)
Stephen Smith (117894)

September 2018

Figure S1. AKT phosphorylation is reduced in VPA mice but normal in all other models examined. Relat...

Additional file 2: of Expression analysis of RNA sequencing data from human neural and glial cell lines depends on technical replication and normalization methods

V. Knight (3507599)
Elba Serrano (3488279)

November 2018

Figure S2 KEGG analysis of metabolic networks. KEGG analysis identified the most enriched metabolic ...

Additional file 3: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this file we list the genome-wide in vivo NEUROD2 peak coordinates. (XLSX 3195 kb

Additional file 1: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this file we provide raw data for characterization of antibodies used for NEUROD2 ChIP-Seq experi...

Additional file 6: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this file we provide the list of most significantly represented pathways among NEUROD2 target gen...

Additional file 7: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this table we provide the NEUROD2 target genes that are differentially expressed in the SVZ-IZ re...

Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Bayam, Efil

June 2016

Background: Cellular differentiation programs are controlled, to a large extent, by the combinatoria...

Additional file 11: of Establishment of high reciprocal connectivity between clonal cortical neurons is regulated by the Dnmt3b DNA methyltransferase and clustered protocadherins

Etsuko Tarusawa (3449000)
Makoto Sanbo (213657)
Atsushi Okayama (3449009)
Toshio Miyashita (3092721)
Takashi Kitsukawa (3449012)
Teruyoshi Hirayama (3449003)
Takahiro Hirabayashi (267887)
Sonoko Hasegawa (3449006)
Ryosuke Kaneko (2795341)
Shunsuke Toyoda (3448997)
Toshihiro Kobayashi (150445)
Megumi Kato-Itoh (150434)
Hiromitsu Nakauchi (150454)
Masumi Hirabayashi (213659)
Takeshi Yagi (267888)
Yumiko Yoshimura (3449015)

December 2016

Table S2. Alignment scores for the DNA sequence of each PcdhÎł gene versus the probes used for in si...

Additional file 2: of The atypical RhoGTPase RhoE/Rnd3 is a key molecule to acquire a neuroprotective phenotype in microglia

Veronika Neubrand (6088628)
Irene Forte-Lago (6088631)
Marta Caro (238964)
Mario Delgado (35544)

December 2018

Table S1. List of siRNA targets resulting in positive differential circularity. Primary microglia we...

Additional file 2: of RNA sequencing analysis reveals quiescent microglia isolation methods from postnatal mouse brains and limitations of BV2 cells

Yingbo He (2886041)
Xiang Yao (499265)
Natalie Taylor (227095)
Yuchen Bai (238875)
Timothy Lovenberg (654883)
Anindya Bhattacharya (127895)

May 2018

Sequencing depth of all the RNA-Seq samples. a Read count of all samples. b Mapping percentage of al...

Additional file 1 of Proteo-genomics of soluble TREM2 in cerebrospinal fluid provides novel insights and identifies novel modulators for Alzheimer’s disease

Lihua Wang (14548)
Niko-Petteri Nykänen (578481)
Daniel Western (15363291)
Priyanka Gorijala (12449887)
Jigyasha Timsina (6085454)
Fuhai Li (203913)
Zhaohua Wang (529179)
Muhammad Ali (266260)
Chengran Yang (9666011)
Menghan Liu (3413381)
William Brock (3595931)
Marta Marquié (5906372)
Mercè Boada (3429242)
Ignacio Alvarez (17732181)
Miquel Aguilar (646325)
Pau Pastor (314894)
Agustín Ruiz (166769)
Raquel Puerta (14667257)
Adelina Orellana (2143609)
Jarod Rutledge (17732184)
Hamilton Oh (10026239)
Michael D Greicius (17732187)
Yann Le Guen (10103346)
Richard J. Perrin (9313430)
Tony Wyss-Coray (247349)
Angela Jefferson (17732190)
Timothy J. Hohman (8356254)
Neill Graff-Radford (337955)
Hiroshi Mori (341642)
Alison Goate (48756)
Johannes Levin (312804)
Yun Ju Sung (12647002)
Carlos Cruchaga (15233365)

January 2024

Additional file 1: Fig. S1. Principal component plots of C2 vs C1 using HapMap Phase II as reference...

Additional file 2: Figure S2. of RAB18, a protein associated with Warburg Micro syndrome, controls neuronal migration in the developing cerebral cortex

Qinwei Wu (3442847)
Xiaqin Sun (3442844)
Weihua Yue (102491)
Tianlan Lu (102474)
Yanyan Ruan (102468)
Tianda Chen (3442841)
Dai Zhang (102500)

February 2016

Overexpression of DN-RAB18 (S22N) mildly impairs the neuronal migration at E18.5. A Representative c...

Additional file 3: of The atypical RhoGTPase RhoE/Rnd3 is a key molecule to acquire a neuroprotective phenotype in microglia

Veronika Neubrand (6088628)
Irene Forte-Lago (6088631)
Marta Caro (238964)
Mario Delgado (35544)

December 2018

Table S2. List of siRNA targets resulting in negative differential circularity. Primary microglia we...

Supplementary files for integrated spatial genomics in mouse brain cortex

Yodai Takei
Long Cai

April 2021

Supplementary raw and processed data. The raw microscopy data are not uploaded owing to their large ...

Additional file 1 of Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection

Chase E. Hawes (13922250)
Sonny R. Elizaldi (9684796)
Danielle Beckman (3696877)
Giovanne B. Diniz (6663395)
Yashavanth Shaan Lakshmanappa (13922253)
Sean Ott (13922256)
Blythe P. Durbin-Johnson (9576344)
Ashok R. Dinasarapu (9427665)
Andrea Gompers (10721824)
John H. Morrison (9688341)
Smita S. Iyer (8702931)

October 2022

Additional file 1: Fig. S1. Ranked genes by median normalized read counts in units of Log2 counts pe...

Additional file 2: of Clustering the autisms using glutamate synapse protein interaction networks from cortical and hippocampal tissue of seven mouse models

Emily Brown (194826)
Jonathan Lautz (5751308)
Tessa Davis (5751311)
Edward Gniffke (5751314)
Alison VanSchoiack (5751317)
Steven Neier (5751320)
Noah Tashbook (5751323)
Chiara Nicolini (2678902)
Margaret Fahnestock (5751326)
Adam Schrum (5751329)
Stephen Smith (117894)

September 2018

Figure S1. AKT phosphorylation is reduced in VPA mice but normal in all other models examined. Relat...

Additional file 2: of Expression analysis of RNA sequencing data from human neural and glial cell lines depends on technical replication and normalization methods

V. Knight (3507599)
Elba Serrano (3488279)

November 2018

Figure S2 KEGG analysis of metabolic networks. KEGG analysis identified the most enriched metabolic ...

Additional file 3: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this file we list the genome-wide in vivo NEUROD2 peak coordinates. (XLSX 3195 kb

Additional file 1: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this file we provide raw data for characterization of antibodies used for NEUROD2 ChIP-Seq experi...

Additional file 6: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this file we provide the list of most significantly represented pathways among NEUROD2 target gen...

Additional file 7: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Efil Bayam (3519806)
Gulcan Sahin (3519818)
Gizem Guzelsoy (3519809)
Gokhan Guner (3519812)
Alkan Kabakcioglu (3519815)
Gulayse Ince-Dunn (3519821)

September 2015

In this table we provide the NEUROD2 target genes that are differentially expressed in the SVZ-IZ re...

Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Bayam, Efil

June 2016

Background: Cellular differentiation programs are controlled, to a large extent, by the combinatoria...

Additional file 11: of Establishment of high reciprocal connectivity between clonal cortical neurons is regulated by the Dnmt3b DNA methyltransferase and clustered protocadherins

Etsuko Tarusawa (3449000)
Makoto Sanbo (213657)
Atsushi Okayama (3449009)
Toshio Miyashita (3092721)
Takashi Kitsukawa (3449012)
Teruyoshi Hirayama (3449003)
Takahiro Hirabayashi (267887)
Sonoko Hasegawa (3449006)
Ryosuke Kaneko (2795341)
Shunsuke Toyoda (3448997)
Toshihiro Kobayashi (150445)
Megumi Kato-Itoh (150434)
Hiromitsu Nakauchi (150454)
Masumi Hirabayashi (213659)
Takeshi Yagi (267888)
Yumiko Yoshimura (3449015)

December 2016

Table S2. Alignment scores for the DNA sequence of each PcdhÎł gene versus the probes used for in si...

Additional file 2: of The atypical RhoGTPase RhoE/Rnd3 is a key molecule to acquire a neuroprotective phenotype in microglia

Veronika Neubrand (6088628)
Irene Forte-Lago (6088631)
Marta Caro (238964)
Mario Delgado (35544)

December 2018

Table S1. List of siRNA targets resulting in positive differential circularity. Primary microglia we...

Additional file 2: of RNA sequencing analysis reveals quiescent microglia isolation methods from postnatal mouse brains and limitations of BV2 cells

Yingbo He (2886041)
Xiang Yao (499265)
Natalie Taylor (227095)
Yuchen Bai (238875)
Timothy Lovenberg (654883)
Anindya Bhattacharya (127895)

May 2018

Sequencing depth of all the RNA-Seq samples. a Read count of all samples. b Mapping percentage of al...

Additional file 1 of Proteo-genomics of soluble TREM2 in cerebrospinal fluid provides novel insights and identifies novel modulators for Alzheimer’s disease

Lihua Wang (14548)
Niko-Petteri Nykänen (578481)
Daniel Western (15363291)
Priyanka Gorijala (12449887)
Jigyasha Timsina (6085454)
Fuhai Li (203913)
Zhaohua Wang (529179)
Muhammad Ali (266260)
Chengran Yang (9666011)
Menghan Liu (3413381)
William Brock (3595931)
Marta Marquié (5906372)
Mercè Boada (3429242)
Ignacio Alvarez (17732181)
Miquel Aguilar (646325)
Pau Pastor (314894)
Agustín Ruiz (166769)
Raquel Puerta (14667257)
Adelina Orellana (2143609)
Jarod Rutledge (17732184)
Hamilton Oh (10026239)
Michael D Greicius (17732187)
Yann Le Guen (10103346)
Richard J. Perrin (9313430)
Tony Wyss-Coray (247349)
Angela Jefferson (17732190)
Timothy J. Hohman (8356254)
Neill Graff-Radford (337955)
Hiroshi Mori (341642)
Alison Goate (48756)
Johannes Levin (312804)
Yun Ju Sung (12647002)
Carlos Cruchaga (15233365)

January 2024

Additional file 1: Fig. S1. Principal component plots of C2 vs C1 using HapMap Phase II as reference...

Additional file 2: Figure S2. of RAB18, a protein associated with Warburg Micro syndrome, controls neuronal migration in the developing cerebral cortex

Qinwei Wu (3442847)
Xiaqin Sun (3442844)
Weihua Yue (102491)
Tianlan Lu (102474)
Yanyan Ruan (102468)
Tianda Chen (3442841)
Dai Zhang (102500)

February 2016

Overexpression of DN-RAB18 (S22N) mildly impairs the neuronal migration at E18.5. A Representative c...

Additional file 3: of The atypical RhoGTPase RhoE/Rnd3 is a key molecule to acquire a neuroprotective phenotype in microglia

Veronika Neubrand (6088628)
Irene Forte-Lago (6088631)
Marta Caro (238964)
Mario Delgado (35544)

December 2018

Table S2. List of siRNA targets resulting in negative differential circularity. Primary microglia we...

Supplementary files for integrated spatial genomics in mouse brain cortex

Yodai Takei
Long Cai

April 2021

Supplementary raw and processed data. The raw microscopy data are not uploaded owing to their large ...

Additional file 1 of Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection

Chase E. Hawes (13922250)
Sonny R. Elizaldi (9684796)
Danielle Beckman (3696877)
Giovanne B. Diniz (6663395)
Yashavanth Shaan Lakshmanappa (13922253)
Sean Ott (13922256)
Blythe P. Durbin-Johnson (9576344)
Ashok R. Dinasarapu (9427665)
Andrea Gompers (10721824)
John H. Morrison (9688341)
Smita S. Iyer (8702931)

October 2022

Additional file 1: Fig. S1. Ranked genes by median normalized read counts in units of Log2 counts pe...

Additional file 2: of Clustering the autisms using glutamate synapse protein interaction networks from cortical and hippocampal tissue of seven mouse models

Emily Brown (194826)
Jonathan Lautz (5751308)
Tessa Davis (5751311)
Edward Gniffke (5751314)
Alison VanSchoiack (5751317)
Steven Neier (5751320)
Noah Tashbook (5751323)
Chiara Nicolini (2678902)
Margaret Fahnestock (5751326)
Adam Schrum (5751329)
Stephen Smith (117894)

September 2018

Figure S1. AKT phosphorylation is reduced in VPA mice but normal in all other models examined. Relat...

Additional file 2: of Expression analysis of RNA sequencing data from human neural and glial cell lines depends on technical replication and normalization methods

V. Knight (3507599)
Elba Serrano (3488279)

November 2018

Figure S2 KEGG analysis of metabolic networks. KEGG analysis identified the most enriched metabolic ...

Additional file 2: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Abstract

Extracted data

Additional file 2: of Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Abstract

Extracted data

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