Additional file 2: Figure S1 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Additional file 1: of The constitutive differential transcriptome of a brain circuit for vocal learning

Peter Lovell (5055401)
Nicole Huizinga (5055398)
Samantha Friedrich (5055404)
Morgan Wirthlin (5055395)
Claudio Mello (5055392)

April 2018

Table S1. Summary of the numbers of oligos and cDNAs analyzed for each nucleus. Table S2. Summary of...

Additional file 2: Table S1. of Transcriptional maturation of the mouse auditory forebrain

Troy Hackett (3489725)
Yan Guo (83742)
Amanda Clause (3489713)
Nicholas Hackett (3489722)
Krassimira Garbett (3489716)
Pan Zhang (206408)
Daniel Polley (3489719)
Karoly Mirnics (1399432)

August 2015

Population and quality control data for all A1 and MG samples obtained for total RNA sequencing. For...

Additional file 1: of Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans

Aleksandra Kornienko (3460565)
Christoph Dotter (3460553)
Philipp Guenzl (196932)
Heinz Gisslinger (471239)
Bettina Gisslinger (471226)
Ciara Cleary (3460562)
Robert Kralovics (180148)
Florian Pauler (3460559)
Denise Barlow (3460556)

January 2016

Supplemental Figures (S1-S35) with legends and Supplemental Methods. (PDF 8255 kb

Additional file 3: Figure S2 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Visualization of the results of differential expression analysis for four pairs of brain regions wit...

Additional file 1: of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Table S1. Sequencing and mapping statistics. Listed are the sequencing details and mapping statistic...

Additional file 5: Figure S4 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Plot of AEI ratio versus read depth across SNP. Displays the average magnitude of the allelic expres...

Additional file 7: Figure S6 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Comparison of NRXN3 isoform representation between OSU and GTEx brains. The ratio of the blue and or...

Additional file 6: Figure S5 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Confirmation of expression levels by qRTPCR. qRTPCR was performed to correlate the FPKM of 3 invaria...

Additional file 1: Figures S1–S15. of Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis

Dejian Zhao (552133)
Mingyan Lin (139065)
Erika Pedrosa (139072)
Herbert Lachman (3505484)
Deyou Zheng (7943)

November 2017

Figure S1. SNP calling result using mouse embryonic scRNA-seq data. Figure S2. A cartoon illustratin...

Additional file 15: Figure S8. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

Siyuan Liu (696701)
Tomasz Nowakowski (3477926)
Alex Pollen (3477911)
Jan Lui (3477923)
Max Horlbeck (3477914)
Frank Attenello (3477929)
Daniel He (3477920)
Jonathan Weissman (3477932)
Arnold Kriegstein (3477917)
Aaron Diaz (177561)
Daniel Lim (155222)

April 2016

Abundant expression of cell type-specific lncRNAs in single cells. A Distributions of expression lev...

RESEARCH ARTICLE Open Access RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb
A Curtis
Leslie C. Newman
Maciej Pietrzak
Michal Seweryn
Samuel K. H
Grzegorz A. Rempala
Daqing Wang
Erica Graziosa
Rachel F. Tyndale
Caryn Lerman
John R. Kelsoe
Deborah C. Mash
Wolfgang Sadee

August 2016

Background: We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ...

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 12: Figure S6. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

Siyuan Liu (696701)
Tomasz Nowakowski (3477926)
Alex Pollen (3477911)
Jan Lui (3477923)
Max Horlbeck (3477914)
Frank Attenello (3477929)
Daniel He (3477920)
Jonathan Weissman (3477932)
Arnold Kriegstein (3477917)
Aaron Diaz (177561)
Daniel Lim (155222)

April 2016

Single cell transcriptomics of lncRNA expression in K562 cell cultures. A Distributions of median ln...

Additional file 1: 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 S1 KEGG analysis of metabolic networks. KEGG analysis identified the most enriched metabolic ...

Additional file 1: Table S1. of Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development

Martin Johansson (211193)
Elin Lundin (3428459)
Xiaoyan Qian (1572298)
Mohammadreza Mirzazadeh (3428456)
Jonatan Halvardson (3428462)
Elisabeth Darj (736066)
Lars Feuk (60288)
Mats Nilsson (7964)
Elena Jazin (31066)

January 2016

RNA sequencing results for all genes belonging to protocadherin and neuroligin families. The table s...

Additional file 1: of The constitutive differential transcriptome of a brain circuit for vocal learning

Peter Lovell (5055401)
Nicole Huizinga (5055398)
Samantha Friedrich (5055404)
Morgan Wirthlin (5055395)
Claudio Mello (5055392)

April 2018

Table S1. Summary of the numbers of oligos and cDNAs analyzed for each nucleus. Table S2. Summary of...

Additional file 2: Table S1. of Transcriptional maturation of the mouse auditory forebrain

Troy Hackett (3489725)
Yan Guo (83742)
Amanda Clause (3489713)
Nicholas Hackett (3489722)
Krassimira Garbett (3489716)
Pan Zhang (206408)
Daniel Polley (3489719)
Karoly Mirnics (1399432)

August 2015

Population and quality control data for all A1 and MG samples obtained for total RNA sequencing. For...

Additional file 1: of Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans

Aleksandra Kornienko (3460565)
Christoph Dotter (3460553)
Philipp Guenzl (196932)
Heinz Gisslinger (471239)
Bettina Gisslinger (471226)
Ciara Cleary (3460562)
Robert Kralovics (180148)
Florian Pauler (3460559)
Denise Barlow (3460556)

January 2016

Supplemental Figures (S1-S35) with legends and Supplemental Methods. (PDF 8255 kb

Additional file 3: Figure S2 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Visualization of the results of differential expression analysis for four pairs of brain regions wit...

Additional file 1: of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Table S1. Sequencing and mapping statistics. Listed are the sequencing details and mapping statistic...

Additional file 5: Figure S4 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Plot of AEI ratio versus read depth across SNP. Displays the average magnitude of the allelic expres...

Additional file 7: Figure S6 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Comparison of NRXN3 isoform representation between OSU and GTEx brains. The ratio of the blue and or...

Additional file 6: Figure S5 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Confirmation of expression levels by qRTPCR. qRTPCR was performed to correlate the FPKM of 3 invaria...

Additional file 1: Figures S1–S15. of Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis

Dejian Zhao (552133)
Mingyan Lin (139065)
Erika Pedrosa (139072)
Herbert Lachman (3505484)
Deyou Zheng (7943)

November 2017

Figure S1. SNP calling result using mouse embryonic scRNA-seq data. Figure S2. A cartoon illustratin...

Additional file 15: Figure S8. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

Siyuan Liu (696701)
Tomasz Nowakowski (3477926)
Alex Pollen (3477911)
Jan Lui (3477923)
Max Horlbeck (3477914)
Frank Attenello (3477929)
Daniel He (3477920)
Jonathan Weissman (3477932)
Arnold Kriegstein (3477917)
Aaron Diaz (177561)
Daniel Lim (155222)

April 2016

Abundant expression of cell type-specific lncRNAs in single cells. A Distributions of expression lev...

RESEARCH ARTICLE Open Access RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb
A Curtis
Leslie C. Newman
Maciej Pietrzak
Michal Seweryn
Samuel K. H
Grzegorz A. Rempala
Daqing Wang
Erica Graziosa
Rachel F. Tyndale
Caryn Lerman
John R. Kelsoe
Deborah C. Mash
Wolfgang Sadee

August 2016

Background: We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ...

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 12: Figure S6. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

Siyuan Liu (696701)
Tomasz Nowakowski (3477926)
Alex Pollen (3477911)
Jan Lui (3477923)
Max Horlbeck (3477914)
Frank Attenello (3477929)
Daniel He (3477920)
Jonathan Weissman (3477932)
Arnold Kriegstein (3477917)
Aaron Diaz (177561)
Daniel Lim (155222)

April 2016

Single cell transcriptomics of lncRNA expression in K562 cell cultures. A Distributions of median ln...

Additional file 1: 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 S1 KEGG analysis of metabolic networks. KEGG analysis identified the most enriched metabolic ...

Additional file 1: Table S1. of Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development

Martin Johansson (211193)
Elin Lundin (3428459)
Xiaoyan Qian (1572298)
Mohammadreza Mirzazadeh (3428456)
Jonatan Halvardson (3428462)
Elisabeth Darj (736066)
Lars Feuk (60288)
Mats Nilsson (7964)
Elena Jazin (31066)

January 2016

RNA sequencing results for all genes belonging to protocadherin and neuroligin families. The table s...

Additional file 1: of The constitutive differential transcriptome of a brain circuit for vocal learning

Peter Lovell (5055401)
Nicole Huizinga (5055398)
Samantha Friedrich (5055404)
Morgan Wirthlin (5055395)
Claudio Mello (5055392)

April 2018

Table S1. Summary of the numbers of oligos and cDNAs analyzed for each nucleus. Table S2. Summary of...

Additional file 2: Table S1. of Transcriptional maturation of the mouse auditory forebrain

Troy Hackett (3489725)
Yan Guo (83742)
Amanda Clause (3489713)
Nicholas Hackett (3489722)
Krassimira Garbett (3489716)
Pan Zhang (206408)
Daniel Polley (3489719)
Karoly Mirnics (1399432)

August 2015

Population and quality control data for all A1 and MG samples obtained for total RNA sequencing. For...

Additional file 1: of Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans

Aleksandra Kornienko (3460565)
Christoph Dotter (3460553)
Philipp Guenzl (196932)
Heinz Gisslinger (471239)
Bettina Gisslinger (471226)
Ciara Cleary (3460562)
Robert Kralovics (180148)
Florian Pauler (3460559)
Denise Barlow (3460556)

January 2016

Supplemental Figures (S1-S35) with legends and Supplemental Methods. (PDF 8255 kb

Additional file 2: Figure S1 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Abstract

Extracted data

Additional file 2: Figure S1 of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Abstract

Extracted data

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