| Antibodies |
| Rabbit anti-HA |
Abcam |
Cat#ab9110 |
| Mouse anti-Myc |
Abcam |
Cat#ab9E10 |
| Rabbit anti-Myc |
Abcam |
Cat#ab9106 |
| Rabbit anti-His |
Abcam |
Cat#ab9108 |
| Rabbit anti-NOTCH2 |
SCBT |
Cat#sc25-255 |
| Goat anti-Rabbit-HRP |
ThermoFisher |
Cat#65-6120 |
| Goat anti-Mouse-HRP |
ThermoFisher |
Cat#62-6520 |
| Rat anti-CTIP2/BCL11B |
Abcam |
Cat#ab18465 |
| Mouse anti-PAX6 |
DSHB |
Cat#Pax6 |
| Rabbit anti-TBR1 |
Millipore |
Cat#AB10554 |
| Rabbit anti-TBR2/EOMES |
Abcam |
Cat#ab23345 |
| Rabbit anti-SOX2 |
Abcam |
Cat#ab97959 |
| Rabbit anti-CTIP2 |
Abcam |
Cat#ab28448 |
| Donkey anti-Rabbit Alexa488 |
ThermoFisher |
Cat#R37118
|
| Donkey anti-Mouse Alexa488 |
ThermoFisher |
Cat#R37114
|
| Goat anti-Rabbit Cy3 |
Jackson |
Cat#111-165-144 |
| Goat anti-Rat Cy3 |
Jackson |
Cat#112-165-143 |
| Chemical, Peptides
and Recombinant Proteins |
| FGF2 |
Peprotech |
Cat#100-18B |
| Noggin |
R&D Systems |
Cat#3344-ng |
| DKK-1 |
Preprotech |
Cat#120-30 |
| SB431542 |
Sigma |
Cat#S4317-5mg |
| Cyclopamine V. californicum |
VWR |
Cat#239803-1mg |
| Dorsomorphin |
Sigma |
Cat#P5499 |
| IWR-1-Endo |
Sigma |
Cat#681669 EMD MILLIPORE |
| EGF |
R&D Systems |
Cat#236-EG-01M |
| Polyethylenimine |
Polysciences |
Cat#23966-1 |
| Dibenzazepine |
Sigma |
Cat#SML0649-5MG |
| rDLL4 |
R&D Systems |
Cat#1506-D4-050/CF |
| Deposited
Data |
| Wild type H9 hESC cortical organoid
time course RNA-Seq data |
this study |
GEO: GSE106245
|
| Week 4 human H9* WT and
NOTCH2NLΔ, and day 6 mouse 46C EV and NOTCH2NL knock in
RNA-Seq |
this study |
GEO: GSE111082
|
| Enriched linked read DNA-Seq on normal
samples and H9 |
this study |
SRA: SRP130766 |
| Microarray data from controls and
patients |
DECIPHER |
Control is GEO: GSE44300, patient data
contact http://decipher.sanger.ac.uk/
|
| Linked read DNA-Seq on two trios
(NA12878/NA12891/NA12892 and NA24385/NA21419/NA24143) |
10x Genomics / Genome in a Bottle
Consortium (NA12891 and NA12892 data are not publicly
available) |
ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/ |
| Enriched linked read DNA-Seq on Simons
VIP samples |
Simons Foundation |
SFARIbase: SFARI_SVIP_VSV_1 |
| NA12878 Sequencing Data |
Illumina Platinum Genomes |
SRA: ERR194147 |
| Vindjia Neanderthal Sequencing
Data |
doi:10.1126/science.aao1887 |
SRA: PRJEB21157 |
| Altai Neanderthal Sequencing Data |
doi:10.1038/nature12886 |
SRA: PRJEB1265 |
| Denisovan Sequencing Data |
doi:10.1126/science.1224344 |
SRA: ERP001519 |
| Chimpanzee Sequencing Data |
University of Nebraska - Non Human
Primate Genomics Center (UN-NHPGC) |
SRA: SRP012268 |
| Gorilla Sequencing Data |
doi:10.1371/journal.pone.0065066 |
SRA: PRJEB2590 |
| Orangutan Sequencing Data |
doi:10.1038/nature12228 |
SRA: SRR748005 |
| Human Fetal brain scRNA-seq data |
doi: 10.1126/science.aap8809 |
dbGAP: phs000989.v3 |
| Experimental Models:
Cell lines |
| H9 hESC |
WiCell |
Cat#WA09 |
| HEK293T |
ATCC |
Cat#CRL-3216 |
| 46C mESC |
Austin Smith |
Cat#46C |
| U2OS |
Marc Vooijs |
na |
| U2OS-JAG2 |
Marc Vooijs |
na |
| OP9 |
Bianca Blom |
na |
| OP9-DLL1 |
Bianca Blom |
na |
| 8919 Chimp iPSC |
doi: https://doi.org/10.1101/232553
|
na |
| 00053 Gorilla iPSC |
Carol Marchetto and Fred Gage |
na |
| Software and
Algorithms |
| Bowtie2 |
doi:10.1038/nmeth.1923 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| STAR |
doi:10.1093/bioinformatics/bts635 |
https://github.com/alexdobin/STAR |
| bedtools |
doi:10.1093/bioinformatics/btq033 |
https://github.com/arq5x/bedtools2 |
| DESeq2 |
doi:10.1186/s13059-014-0550-8 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| trimmomatic |
doi:10.1093/bioinformatics/btu170 |
http://www.usadellab.org/cms/?page=trimmomatic |
| htseq-count |
na |
http://htseq.readthedocs.io/en/master/count.html |
| Panther V13.0 |
na |
http://www.pantherdb.org/panther/ontologies.jsp |
| Longranger |
doi:10.1101/230946 |
https://support.10xgenomics.com/genome-exome/software/downloads/latest |
| Microarray copy number inference |
This study |
https://bitbucket.org/adam_novak/copynumber |
| Gordian assembler downstream analysis
scripts and enriched linked read normalization |
This study |
https://github.com/vrubels/Notch2NL-Project |
| Gordian Assembler |
This study |
https://github.com/abishara/gordian_assembler |
| Critical Commercial
Assays |
| OneStep RT-PCR kit |
Qiagen |
Cat#210212 |
| RNA Clean & Concentrator |
Zymo |
Cat#R1013 |
| Dynabeads™mRNA
DIRECT™Micro Purification Kit |
ThermoFisher |
Cat#61021 |
| Ribo-Zero rRNA removal kit |
Epicentre |
MRZH11124 |
| TruSeq DNA Sample Preparation kit |
Illumina |
FC-121-1001 |
| Ion Total RNA-Seq Kit v2 |
ThermoFisher |
Cat#4475936 |
| Ion Xpress™RNA-Seq
Barcode 1–16 Kit |
ThermoFisher |
Cat#4475485 |
| Chromium WGS kit V2 |
10X Genomics |
120258 |
| Custom MyBaits-3 oligo kit |
Mycroarray |
Mybaits 3–12 |
| Kapa HiFi Library Amplification Kit
(Illumina) |
Kapa |
KK2621 |
| Xfect DNA transfection reagent |
Clontech |
631317 |
| Zymo Quick-gDNA Miniprep kit |
Zymo |
D3006 |
| Dual Luciferase Reporter assay |
Promega |
Cat#E1960 |
| system |
|
|
| Recombinant
DNA |
| pX458 |
Addgene |
#48138 |
| pX458-E2.1 |
This study |
na |
| pX4580E5.2 |
This study |
na |
| pCAG-hCas9 |
Addgene |
#51142 |
| pCAG-GFP |
Addgene |
#11150 |
| pCAG-EV |
This study |
na |
| pCAG-NOTCH2NLSh
|
This study |
na |
| pCAG-NOTCH2NLSh,T197I
|
This study |
na |
| pCAG-NOTCH2NLL
|
This study |
na |
| pCAG-NOTCH2NLL,T197I
|
This study |
na |
| pCAG-NOTCH2NLSh,+ATAA
|
This study |
na |
| pCAG-NOTCH2NLL,T197I,+ATAA
|
This study |
na |
| pCAG-NOTCH2NL-HASh
|
This study |
na |
| pCAG-NOTCH2NL-HASh,T197I
|
This study |
na |
| pCAG-NOTCH2NL-HisSh
|
This study |
na |
| pCAG-NOTCH2NL-HisSh,T197I
|
This study |
na |
| pCIG2a |
Pierre Vanderhaeghen |
na |
| pCIG2a-NOTCH2NLSh,T197I
|
This study |
na |
| pCIG2a-NOTCH2-Myc |
This study |
na |
| pCIG2a-PDGFR-Myc |
This study |
na |
| pCIG2a-EGFR-Myc |
This study |
na |
| pRL-CMV |
Promega |
E2231 |
| pGL3-UAS |
Marc Vooijs |
na |
| pcDNA5-NOTCH1-GAL4-TAD-N1 |
Marc Vooijs |
na |
| pcDNA5-NOTCH2-GAL4-TAD-N1 |
Marc Vooijs |
na |
| pLVX-NOTCH3-GAL4GV16 |
Marc Vooijs |
na |
| Oligonucleotides |
| Refer to Supplemental Table
5
|
|
|
