|
| Status |
Public on Aug 06, 2023 |
| Title |
Replicate4_CtrlV |
| Sample type |
SRA |
| |
|
| Source name |
Co-cultures of human induced neurons grown on mouse glia feeder layer
|
| 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: Vehicle (0.5% DMSO), day in vitro 10-40
|
| 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).
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Human induced neurons on mouse glia, day 40, vehicle-treated control
40M total reads (20M paired)
|
| 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)
|
| |
|
| 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 |
SAMN29043482 |
| SRA |
SRX15700932 |
