SRX5246695 GSM3561317 SRP179024 SRS4248957 GSM3561317 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561317 GSM3561317 GEO Accession GSM3561317 SRX5246696 GSM3561318 SRP179024 SRS4248958 GSM3561318 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561318 GSM3561318 GEO Accession GSM3561318 SRX5246697 GSM3561319 SRP179024 SRS4248959 GSM3561319 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561319 GSM3561319 GEO Accession GSM3561319 SRX5246698 GSM3561320 SRP179024 SRS4248960 GSM3561320 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561320 GSM3561320 GEO Accession GSM3561320 SRX5246699 GSM3561321 SRP179024 SRS4248961 GSM3561321 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561321 GSM3561321 GEO Accession GSM3561321 SRX5246700 GSM3561322 SRP179024 SRS4248962 GSM3561322 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561322 GSM3561322 GEO Accession GSM3561322 SRX5246701 GSM3561323 SRP179024 SRS4248963 GSM3561323 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561323 GSM3561323 GEO Accession GSM3561323 SRX5246702 GSM3561324 SRP179024 SRS4248964 GSM3561324 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561324 GSM3561324 GEO Accession GSM3561324 SRX5246703 GSM3561325 SRP179024 SRS4248965 GSM3561325 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561325 GSM3561325 GEO Accession GSM3561325 SRX5246704 GSM3561326 SRP179024 SRS4248967 GSM3561326 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561326 GSM3561326 GEO Accession GSM3561326 SRX5246705 GSM3561327 SRP179024 SRS4248966 GSM3561327 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561327 GSM3561327 GEO Accession GSM3561327 SRX5246706 GSM3561328 SRP179024 SRS4248968 GSM3561328 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561328 GSM3561328 GEO Accession GSM3561328 SRX5246707 GSM3561329 SRP179024 SRS4248969 GSM3561329 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561329 GSM3561329 GEO Accession GSM3561329 SRX5246708 GSM3561330 SRP179024 SRS4248970 GSM3561330 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561330 GSM3561330 GEO Accession GSM3561330 SRX5246709 GSM3561331 SRP179024 SRS4248971 GSM3561331 RNA-Seq TRANSCRIPTOMIC cDNA At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer's instructions. RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average. Illumina HiSeq 2000 gds 303561331 GSM3561331 GEO Accession GSM3561331