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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 25, 2024 |
| Title |
AD2 Neurons, Control, Replicate3 |
| Sample type |
SRA |
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| Source name |
iNeurons
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| Organism |
Homo sapiens |
| Characteristics |
tissue: iNeurons
cell type: AD2 Neurons
genotype: Control
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| Growth protocol |
NPC were seeded at a density of 4.29x104/cm2 on PLO/Laminin-coated 12-well plates in Neural Progenitor medium (day in vitro (DIV)-1). On DIV0, cells were transduced with pLV-TetO-hNGN2-eGFP-Puro + FUdeltaGW-rtTA (Addgene #79823 (23), #19780 (24)) for differentiation into glutamatergic neurons (NGN2) and TetO-Ascl1-puro + DLX2-hygro + FUdeltaGW-rtTA (Addgene #97329 (25), #97330 (25), #19780) for differentiation into GABAergic neurons (AD2) in separate wells according to published protocols (23, 26). On DIV1, the medium was changed to Neural Progenitor Medium containing 1 µg/ml of Doxycycline (Sigma-Aldrich #D9891), to induce tetracycline-dependent transgene expression. After 24h (DIV2), selection of transduced cells was performed by addition of the respective antibiotics to the medium (2 µg/ml puromycine (Thermo Fisher Scientific) for NGN2-transduced cells, 2 µg/ml of puromycine + 250 µg/ml of hygromycin (Carl Roth) for AD2-transduced cells). On DIV3, NGN2 and AD2 neurons were detached with Accutase and seeded into monocultures or co-cultures at a ratio of 80:20 on PLO/Laminin-coated plates. The total seeding density was 1.25x105 neurons/cm2 for types of cultures. Neurons were cultured in Neurobasal Plus medium, supplemented with 1 x B27 Plus supplement, 1 x N2 supplement, 1 µg/ml of laminin, 20 ng/ml of GDNF (Peprotech), 20 ng/ml of BDNF (Peprotech), 35 µg/ml of L-Ascorbic Acid (Sigma-Aldrich), 1x Penicillin/Streptomycin and 1 µg/ml of Doxycycline. After neurons attached to the plate bottom, 3.125x104/cm2 primary mouse astrocytes were added to all cultures. 50 % medium changes with neuronal medium (without Doxycycline) were performed until DIV24, when the medium was again supplemented with 1 µg/ml Doxycycline to support neuronal maturation at the final stages of the differentiation process until DIV28.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were lysed with RLT Buffer and extracted with Micro Rneasy (Qiagen) kit after shredding. Eluted in 14 ul of H20
SmartSeq V4 Ultra Low Input RNA & Nextera-XT Library Prep
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Library name: Control_3_AD2
Control_3_AD2
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| Data processing |
bcl2fast2
Star Alignment
htseq-count
DESeq2 Normalisation
Assembly: GRCh38.107
Supplementary files format and content: Raw Counts
Supplementary files format and content: Normalised Counts
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| Submission date |
Nov 21, 2024 |
| Last update date |
Nov 25, 2024 |
| Contact name |
Moritz J Rossner |
| E-mail(s) |
[email protected]
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| Organization name |
Lud.-Max.-University
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| Department |
Psychiatry
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| Lab |
Molecular Neurobiology
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| Street address |
Nussbaumstr. 7
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| City |
Munich |
| ZIP/Postal code |
80336 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE282524 |
Aberrant Neuronal Connectivity and Network Activity of Neurons Derived from Patients with Idiopathic Schizophrenia |
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| Relations |
| BioSample |
SAMN44858442 |
| SRA |
SRX26804012 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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