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Series GSE195877 Query DataSets for GSE195877
Status Public on Feb 04, 2022
Title Transcriptomic analysis of undifferentiated human embryonic stem cells (hESCs) and day-25 differentiated cortical neuronal progenitor cells from 5 isogenic hESC lines with low and high levels of alpha-synuclein expression
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To compare the cortical neuroonal differentiation capacity of clonal isogenic hESC lines with different levels of alpha-synuclein (aSyn) expression.
Methods 1: Shef4 hESCs was used as a parental line to create an allelic series of clonal transgenic hESC lines expressing a human SNCA (encoding aSyn) contruct. Clonal transgenic lines with high (S8, S37) and low (S9, S34) aSyn expression were established and characterized.
Methods 2: hESCs were cultured on Laminin-521 (BioLamina) in StemMACS iPS-Brew XF self-renewal media (Miltenyi) prior to lifting for isolation of total RNA.
Methods 3: Cortical neuronal progenitor cells were differentiated from hESCs on Laminin-111 coated (Biolamina) 24-well plates at an initial plating density of 80,000 cells/cm2. Differentiation commenced in neural induction media (NIM) consisting of 50% DMEM/F12 (ThermoFisher Scientific), 50% Neurobasal Media (ThermoFisher Scientific), B27 supplement with Retinoic Acid (ThermoFisher Scientific), N2 supplement (ThermoFisher Scientific) and 2 mM L-Glutamine (ThermoFisher Scientific), 10μM SB431542 (Tocris) and 100 nM LDN-193189 (Miltenyl Biotec). From day 4 onwards, the base media was changed to 50% NIM, 25% DMEM/F12 and 25% Neurobasal Media. SB431542 (10 μM) and LDN-193189 (100 nM) were present for the first 12 days of differentiation. Cells were lifted and re-plated at day 12 and day 17 with Collagenase Type IV (Life Technologies). At day 25, differentiated cells were lifted for total RNA isolation.
 
Overall design Total RNA was isolated from self-renewing hESCs with low aSyn (Shef4, S9, S34) and high aSyn (S8, S37) expression, and from the same cell lines at Day 25 of cortical neuronal differentiation using the dual-Smad inhibition protocol
 
Contributor(s) Natalwala A, Behbehani R, Kunath T
Citation(s) 35712660
Submission date Feb 01, 2022
Last update date Jun 21, 2022
Contact name Tilo Kunath
E-mail(s) tilo.kunath@ed.ac.uk
Phone +44 (0) 131 651 9500
Organization name University of Edinburgh
Department Centre for Regenerative Medicine
Street address 5 LIttle France Drive
City Edinburgh
ZIP/Postal code EH16 4UU
Country United Kingdom
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (17)
GSM5855550 AN4-S9-d0-1
GSM5855551 AN4-S34-d0-2
GSM5855552 AN5-S9-d0-1
Relations
BioProject PRJNA802544

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE195877_Normalised_counts_1066.xlsx 5.5 Mb (ftp)(http) XLSX
GSE195877_Raw_counts_1066.xlsx 3.3 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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