Growth Protocol:	iPSCs were cultured on matrigel coated plated using mTeSR(Stem Cell Technologies) media with mTeSR supplement at 37C incubator with 5% CO2.
Treatment Protocol:	Neuron progenitor cells were differentiated from iPSCs. Briefly, iPSCs were cultured in Matrigel coated plates and dislodged by dispase. To form embryonic bodies, the dislodged colonies were cultured in DMEM/F12(invitrogen) with GlutaMax and N2 supplement in non-adhere petri dish. Media were replaced every other day for 7 days. EBs were then placed onto matrigel coated plate to allow rosette formation. Clean rosette were picked manually and maintained in EB media for 7 days and subsequently dissociated with accutase and cultured in NPC media (DMEM/F12, GlutaMax, N2 and B27 with 2ug/ml FGF) to allow neuron progenitor cell differentiation. NPCs were maintained in NPC media.
Extract Protocol:	Motor neurons were directly differentiated from iPSCs as previous described (Chambers S, Nature Biotechnology, 2009). Briefly, iPSCs were cultured on matrigel coated plates until fully confluent in mTeSR then switch to knock-out serum replacement media (KSR) containing Dorsomorphin(1uM) and SB431542(10uM). Upon day 4 of differentiation, increasing amounts of N2 media (25%, 50%) was added to the KSR. From day 7 of differentiation, 1.5uM retinoic acid and 200nM Smoothened Agonist (SAG, EMD Millipore) were added to induce patterning. Cells were dissociated on day 17 of differentiation and replated in poly-D-lysine and laminin coated plates. Maturation was performed using BDGF(2ng/ml), GDNF(2ng/ml), CNTF(2ng/ml), ascorbid acid, sonic hedgehog and retinoic acid in N2 and B27 media up until 35 days of differentiation.
Library Construction Protocol:	Single cells were captured on C1 auto prep platform (Fluidigm, CA) according to manufacturer's instructions. C1 auto prep chips were visually inspected with a light microscopy at 20X to ensure singularity of captured cells. All non-single cells were discarded from analysis. SMARTer Ultra Low RNA cDNA Synthesis Kit (Clontech) was used to reverse transcribe polyA-tailed RNA. cDNA was amplified using Advantage 2 Polumerase Mix by PCR at 95¡C for 1 minutes, followed by 21 cylcles of 15 secondes at 95¡C, 30 seconds at 65¡C and 6 minutes at 68¡C, followed by another 10 minutes at 72¡C as a final extension. cDNAs were inspected using Agilent Bioanalyzer High Sensitivity DNA chips and quantitated by PicoGreen dsDNA Assay kit (ThermoFisher). cDNAs were diluted to 1ng to generate libraries using the Nextera XT DNA kit(Illumina, CA). Libraries were multiplexed and sequenced on Illumina HiSeq200 to generate 100bp PE reads.

Molecule Type:	poly(A)+ RNA
Library Source:
Library Layout:	paired; single
Library Strand:	-
Platform:	Illumina
Instrument Model:	Illumina HiSeq 2000
Strand-Specific:	Unspecific

Data Resource	GEN Sample ID	GEN Dataset ID	Project ID	BioProject ID	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Case Detail	Control Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate