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| Status |
Public on Nov 01, 2022 |
| Title |
Experiment_1_con_2 |
| Sample type |
SRA |
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| Source name |
human neurons differentiated from neural precursor cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC derived neurons
origin: hiPSC derived from cord bood
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| Growth protocol |
The smNPCs were grown on Matrigel (Corning, 354263) coated dishes, fed with N2/B27 medium (48% (vol/vol) DMEM/F12, 48% (vol/vol) Neurobasal, 2% (vol/vol) B27 minus AO, 0.5% (vol/vol), N2 supplement, 1% (vol/vol) Penicillin/streptomycin, and 1% (vol/vol) GlutaMAX™ Supplement) containing 3 μM CHIR 99021 (Axon Medchem, Groningen, The Netherlands), 0.5 μM purmorphamine (PMA, Alexis, Farmingdale, NY), and 150 μM L-Ascorbic acid (Sigma).The day 60 human neurons were grown on on Matrigel (Corning, 354263) coated dishes, fed with N2/B27 medium (48% (vol/vol) DMEM/F12, 48% (vol/vol) Neurobasal, 2% (vol/vol) B27 minus AO, 0.5% (vol/vol) N2 supplement, 1% (vol/vol) Penicillin/streptomycin, and 1% (vol/vol) GlutaMAX™ Supplement) containing 25, 10, 10 ng/ml of NGF, BDNF, and GDNF, respectively.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from day 60 hiNeurons and smNPCs, followed by removal of ribosomal RNA and transfer RNA using Macherey Nagel RNA isolation kit.
The RNA population containing messenger RNA (mRNA), pre-processed RNA and regulatory RNA molecules were reverse transcribed into short double-strained DNA fragments to construct the cDNA library for sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
raw reads was confirmed by FastQC
aligned to the human reference genome GRCh38 using STAR
counted per gene by employing the 'quantmode GeneCounts' option
Fold changes and FDRs for each gene were estimated with DESeq2
differentially expressed genes were selected by FDR < 0.001 and absolute log2foldChange value >= 1
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| Submission date |
Feb 09, 2021 |
| Last update date |
Nov 01, 2022 |
| Contact name |
shuyong zhu |
| E-mail(s) |
[email protected]
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| Organization name |
Hannover Medical School
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| Department |
Institute of Virology
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| Street address |
OE 5230, Carl-Neuberg-Str. 1, 30625
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| City |
Hannover |
| State/province |
Lower Saxony |
| ZIP/Postal code |
30625 |
| Country |
Germany |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE166442 |
Quantitative Analysis of Transcriptomes of small molecules generated Neural Precursor Cesll (smNPCs) and smNPCs-derived neurons by next generation sequencing |
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| Relations |
| BioSample |
SAMN17841272 |
| SRA |
SRX10058358 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5071251_experiment_1_con_2_GCCAAT_L005_R1_001_paired_GE_.xlsx |
7.6 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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