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Status |
Public on Aug 06, 2023 |
Title |
Replicate6_DAPT |
Sample type |
SRA |
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|
Source name |
Co-cultures of human induced neurons grown on mouse glia feeder layer
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Organisms |
Homo sapiens; Mus musculus |
Characteristics |
tissue: Co-cultures of human induced neurons grown on mouse glia feeder layer cell line: Human Induced Neurons from H1 ESC (WA01) cell type: Human induced neurons, day 40 / mouse primary glia genotype: Wild-type human induced neurons / CD1 mouse glia treatment: DAPT (40 uM), day in vitro 10-40
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Treatment protocol |
Gamma-secretase inhibition was performed starting day 10 until day 40 in vitro (30 days total). Treatment groups were vehicle (0.5% DMSO), DAPT (40 µM) or LY411575 (2.5 µM).
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Growth protocol |
Human induced neurons (trans-differentiated from human H1 ESC cell line using Ngn2 overexpression) were grown on mouse glia to day 40 in vitro in growth media (MEM, B27, Glutamax, transferrin, 5% FBS) at 37˚C and 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA from 6 biological replicates was harvested using TRIzol for lysis, choloroform extraction, and column purification with the Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared for stranded mRNA using Illumina TruSeq Library Prep Kit following manufacturer's protocols. Bulk RNA-seq
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
Human induced neurons on mouse glia, day 40, DAPT-treated 40M total reads (20M paired)
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Data processing |
Kallisto (V0.44.0) was used for pseudoalignment to human / mouse transcriptome DESeq2 package in R Studio was used to analyze differential gene expression (FDR alpha < 0.1; p-value < 0.05; log2 fold change > 0.25 or < -0.25) Batch effects were controlled for and log2 fold change shrinkage was applied P-values were corrected for using the Benjamini-Hochberg correction Assembly: hg38, mm10 Supplementary files format and content: Kallisto output files for human transcripts include raw counts (abundance) Supplementary files format and content: Kallisto output files for mouse transcripts include raw counts (abundance)
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Submission date |
Jun 14, 2022 |
Last update date |
Aug 07, 2023 |
Contact name |
Sofia Essayan-Perez |
E-mail(s) |
sofia.essayan-perez@stanford.edu
|
Organization name |
Stanford University
|
Department |
Molecular and Cellular Physiology
|
Lab |
Sudhof Lab
|
Street address |
265 Campus Drive
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL25526 |
Series (1) |
GSE206102 |
Neuronal γ-secretase regulates lipid metabolism, linking cholesterol to synaptic dysfunction in Alzheimer's disease |
|
Relations |
BioSample |
SAMN29043475 |
SRA |
SRX15700939 |