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Biological basis of psychiatric disorders

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Dr Michael J Ziller
ziller@uni-muenster.de

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This DAC controls 12 datasets

Dataset ID	Description	Technology	Samples
EGAD50000003209	RNA-seq (single-end FASTQ) of excitatory induced neurons (iNs) differentiated by NGN2 induction from hiPSC lines. (1) RBP knockdown: iNs were transduced with lentiviral shRNA pools against PTBP2, PCBP2 or CPSF6, or a scramble shRNA control, and harvested after 10 days of knockdown (7 libraries: 3 scramble control, 2 PCBP2, 1 CPSF6, 1 PTBP2). (2) GRIA1 3'UTR editing: iNs from the parental line PSYLMUi002-A and two CRISPR-Cas9 clones (cl13, cl15) carrying a deletion of the distal GRIA1 3'UTR (3 libraries); scramble control library PSYLMUi002-A_R2_CTRL_1 also serves as control for this experiment. The dataset comprises 10 libraries from 2 donors. iNs were co-cultured with mouse astrocytes, so reads may contain a minor mouse fraction	Illumina NovaSeq 6000	10
EGAD50000003210	PTBP2-RNA interaction profiles (modified quick-irCLIP, SMARTer smRNA-Seq libraries) of excitatory induced neurons (iNs) differentiated by NGN2 induction from the healthy-control hiPSC line PSYLMUi004-A (LMU Munich cohort) and UV-crosslinked (254 nm) at day 49 of differentiation. PTBP2-RNA complexes were immunoprecipitated after partial RNase digestion; size-matched input samples were taken from the same lysates. The dataset comprises 4 libraries from 1 donor (2 PTBP2 immunoprecipitations, 2 size-matched inputs). iNs were co-cultured with mouse astrocytes, so reads may contain a minor mouse fraction.	Illumina NovaSeq 6000	4
EGAD50000003211	Chromatin accessibility profiles (ATAC-seq, paired-end FASTQ) of excitatory induced neurons (iNs) differentiated by NGN2 induction from hiPSC lines of the LMU Munich cohort and harvested at day 49 of differentiation.	Illumina HiSeq 4000	54
EGAD50000003212	Chromatin accessibility profiles (ATAC-seq, paired-end FASTQ) of excitatory induced neurons (iNs) differentiated by NGN2 induction from hiPSC lines of the LMU Munich cohort and harvested at day 49 of differentiation.	Illumina HiSeq 4000	55
EGAD50000003213	Full-length bulk RNA-seq (SMART-Seq v4/Nextera XT, paired-end FASTQ) of excitatory induced neurons (iNs) differentiated by NGN2 induction from hiPSC lines harvested at day 49 of differentiation.	Illumina HiSeq 4000	52
EGAD50000003214	Full-length bulk RNA-seq (SMART-Seq v4/Nextera XT, paired-end FASTQ) of excitatory induced neurons (iNs) differentiated by NGN2 induction from hiPSC lines harvested at day 49 of differentiation.	Illumina HiSeq 4000	62
EGAD50000003215	' mRNA-seq (QuantSeq, single-end FASTQ) of embryoid bodies and undifferentiated cells from hiPSC lines, generated to assess the three-germ-layer differentiation potential of each line.	Illumina HiSeq 4000	72
EGAD50000003216	' mRNA-seq (QuantSeq, single-end FASTQ) of embryoid bodies and undifferentiated cells from hiPSC lines generated to assess the three-germ-layer differentiation potential of each line.	Illumina HiSeq 4000	54
EGAD50000003217	RNA-seq (single-end FASTQ) of excitatory induced neurons (iNs) differentiated by NGN2 induction from two healthy-control hiPSC lines. iNs were transduced with lentiviral shRNA pools against PTBP2, PCBP2 or CPSF6, or a scramble shRNA control, and harvested after 10 days of knockdown. The dataset comprises 13 libraries from 2 donors (6 scramble control, 3 PCBP2, 2 CPSF6, 2 PTBP2). Scramble control library MPIPi013-A_R2_CTRL_1 also serves as control for the GRIA1 3'UTR deletion experiment. iNs were co-cultured with mouse astrocytes, so reads may contain a minor mouse fraction.	Illumina NovaSeq 6000	13
EGAD50000003218	PTBP2-RNA interaction profiles (modified quick-irCLIP, SMARTer smRNA-Seq libraries) of excitatory induced neurons (iNs) differentiated by NGN2 induction from the healthy-control hiPSC line MPIPi013-A (generated at the Max Planck Institute of Psychiatry) and UV-crosslinked (254 nm) at day 49 of differentiation. PTBP2-RNA complexes were immunoprecipitated after partial RNase digestion; size-matched input samples were taken from the same lysates. The dataset comprises 4 libraries from 1 donor (2 PTBP2 immunoprecipitations, 2 size-matched inputs). iNs were co-cultured with mouse astrocytes, so reads may contain a minor mouse fraction.	Illumina NovaSeq 6000	4
EGAD50000003219	Small RNA sequencing (NovaSeq 6000) of excitatory induced neurons (iNs) differentiated by NGN2 induction from hiPSC lines generated and harvested at day 49 of differentiation.	Illumina NovaSeq 6000	39
EGAD50000003220	mall RNA sequencing (NovaSeq 6000) of excitatory induced neurons (iNs) differentiated by NGN2 induction from hiPSC lines of the LMU Munich cohort and harvested at day 49 of differentiation.	Illumina NovaSeq 6000	64