| Biological sample (Homo-sapiens) |
Prenatal cortical tissue |
UCLA Gene and Cell Therapy Core |
|
|
| Commercial assay or kit |
miRNeasy-mini |
QIAGEN |
217004 |
|
| Commercial assay or kit |
TruSeq Small RNA Library Prep Kits |
Illumina |
RS-200 |
|
| Commercial assay or kit |
TruSeq Stranded RNA Library Prep Kits |
Illumina |
20020597 |
|
| Software, algorithm |
miRge 2.0 |
DOI https://doi.org/10.1186/s12859-018-2287-y
|
|
|
| Software, algorithm |
miRDeep2 |
DOI https://doi.org/10.1093/nar/gkr688
|
|
|
| Software, algorithm |
Bowtie |
DOI https://doi.org/10.1038/nmeth.1923
|
v1.2.2 |
|
| Software, algorithm |
featureCounts |
DOI https://doi.org/10.1093/bioinformatics/btt656
|
|
|
| Software, algorithm |
STAR |
DOI https://doi.org/10.1093/bioinformatics/bts635
|
v2.5.4b |
|
| Software, algorithm |
PLINK |
DOI https://doi.org/10.1186/s13742-015-0047-8
|
v1.9 |
|
| Software, algorithm |
McCarthy Group’s HRC-1000G imputation preparation tool |
https://www.well.ox.ac.uk/~wrayner/tools/
|
|
|
| Software, algorithm |
Michigan Imputation Server |
DOI https://doi.org/10.1038/ng.3656
|
|
|
| Software, algorithm |
VerifyBamID |
DOI https://doi.org/10.1016/j.ajhg.2012.09.004
|
v1.1.3 |
|
| Software, algorithm |
DESeq2 |
DOI https://doi.org/doi:10.18129/B9.bioc.DESeq2 |
|
|
| Software, algorithm |
limma |
DOI https://doi.org/doi:10.18129/B9.bioc.limma |
|
|
| Software, algorithm |
EMMAX |
DOI https://doi.org/10.1038/ng.548
|
|
|
| Software, algorithm |
eigenMT |
DOI https://doi.org/10.1016/j.ajhg.2015.11.021
|
|
|
| Software, algorithm |
Summary-data-based Mendelian Randomization |
DOI https://doi.org/10.1038/ng.3538
|
|
|
| Software, algorithm |
GARFIELD |
DOI https://doi.org/10.1038/s41588-018-0322-6
|
v2 |
|
| Software, algorithm |
qvalue |
DOI https://doi.org/doi:10.18129/B9.bioc.qvalue |
|
|
| Software, algorithm |
RMA |
DOI https://doi.org/10.1093/bioinformatics/btq431
|
|
|
| Software, algorithm |
topGO |
DOI https://doi.org/doi:10.18129/B9.bioc.topGO |
|
|
| Recombinant DNA reagent |
pTRIPZ (plasmid) |
ThermoFisher |
RHS4750 |
|
| Recombinant DNA reagent |
pTRIPZ-EGFP (plasmid) |
This paper |
|
RFP of original pTRIPZ replaced with EGFP |
| Recombinant DNA reagent |
pTRIPZ-mir-4707-EGFP (plasmid) |
This paper |
|
mir-4707 primary sequence cloned into pTRIPZ-EGFP |
| Recombinant DNA reagent |
PAX2 (plasmid) |
Addgene |
12260 |
|
| Recombinant DNA reagent |
pMD2.G |
Addgene |
12259 |
|
| Commercial assay or kit |
qPCR Lentivirus Titration Kit |
Applied Biological Materials |
LV900 |
|
| Commercial assay or kit |
FUGENE HD |
Promega |
E2311 |
|
| Cell line (Homo-sapiens) |
HEK293T |
ATCC |
CRL-11268 |
|
| Cell line (Homo-sapiens) |
Donor 54 |
This paper |
D54 |
primary human neural progenitor cells (male) |
| Cell line (Homo-sapiens) |
Donor 88 |
This paper |
D88 |
primary human neural progenitor cells (male) |
| Chemical compound, drug |
DMEM |
Life Technologies |
11995081 |
|
| Chemical compound, drug |
FBS |
Sigma-Aldrich |
F2442 |
|
| Chemical compound, drug |
Antibiotic-Antimycotic |
Life Technologies |
15240096 |
|
| Chemical compound, drug |
Growth Factor Reduced Matrigel |
Corning |
354230 |
|
| Chemical compound, drug |
Neurobasal A |
Life Technologies |
10888–022 |
|
| Chemical compound, drug |
Primocin |
Invivogen |
ant-pm-2 |
|
| Chemical compound, drug |
BIT 9500 |
Stemcell Technologies |
9500 |
|
| Chemical compound, drug |
Glutamax |
Life Technologies |
PHG0313 |
|
| Chemical compound, drug |
Heparin |
Sigma-Aldrich |
H3393-10KU |
|
| Chemical compound, drug |
EGF |
Life Technologies |
PHG0313 |
|
| Chemical compound, drug |
FGF |
Life Technologies |
PHG0023 |
|
| Chemical compound, drug |
LIF |
Life Technologies |
PHC9481 |
|
| Chemical compound, drug |
PDGF |
Life Technologies |
PHG1034 |
|
| Chemical compound, drug |
Trypsin-EDTA |
Life Technologies |
25300062 |
|
| Chemical compound, drug |
Doxycycline |
Sigma-Aldrich |
D9891 |
|
| Chemical compound, drug |
B27 |
Life Technologies |
17504–044 |
|
| Chemical compound, drug |
NT-3 |
Life Technologies |
PHC7036 |
|
| Chemical compound, drug |
BDNF |
Life Technologies |
PHC7074 |
|
| Commercial assay or kit |
Dnase |
QIAGEN |
79254 |
|
| Commercial assay or kit |
iScript cDNA Synthesis Kit |
Bio-Rad |
1708891 |
|
| Commercial assay or kit |
TaqMan Advanced miRNA cDNA Synthesis Kit |
ThermoFisher |
A28007 |
|
| Commercial assay or kit |
SsoAdvanced Universal SYBR Green Supermix |
Bio-Rad |
1725271 |
|
| Commercial assay or kit |
TaqMan Advanced miRNA Assays |
ThermoFisher |
A25576 |
|
| Commercial assay or kit |
TaqMan Fast Advanced Master Mix |
ThermoFisher |
4444557 |
|
| Commercial assay or kit |
Clariom S Pico Assay |
ThermoFisher |
902963 |
|
| Commercial assay or kit |
Click-iT EdU Imaging Kit (AF647) |
Invitrogen |
C10340 |
|
| Chemical compound, drug |
Paraformaldehyde in PBS |
FisherScientific |
50-980-487 |
|
| Chemical compound, drug |
Triton X-100 |
Sigma-Aldrich |
T8787 |
|
| Chemical compound, drug |
Goat serum |
MP Biomedicals |
219135680 |
|
| Chemical compound, drug |
Tween-20 |
FisherScientific |
BP337500 |
|
| Antibody |
anti-GFP (chicken polyclonal) |
FisherScientific |
AB16901 |
(1:500) |
| Antibody |
anti-chicken-AF488 (goat polyclonal) |
ThermoFisher |
A11011 |
(1:1000) |
| Antibody |
anti-NESTIN (rabbit polyclonal) |
Millipore |
ABD69 |
(1:500) |
| Antibody |
anti-TUJ1 (mouse monoclonal) |
BioLegend |
801202 |
(1:1000) |
| Antibody |
anti-rabbit-AF568 (goat polyclonal) |
ThermoFisher |
A11036 |
(1:1000) |
| Antibody |
anti-mouse-AF750 (goat polyclonal) |
ThermoFisher |
A21037 |
(1:1000) |
| Chemical compound, drug |
DAPI |
ThermoFisher |
62248 |
|
