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| Status |
Public on Mar 06, 2024 |
| Title |
JHU_AD_02 |
| Sample type |
SRA |
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| Source name |
hiPSC derived excitatory neurons
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC derived excitatory neurons
disease state: Alzheimers
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| Growth protocol |
Neural maturation medium (Neurobasal medium A (Gibco, Grand Island, NY, USA),
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Quick-RNA MiniPrep Kit (Zymo Research #R1054)
250~300 bp insert , strand-specific libraries with rRNA removal.
Fragmentation, Reverse Transcription, Second strand cDNA synthesis, End repair and A-tailing, , adapter ligation, Size selection, PCR amplification
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Hisat2 (version 2.2.1)
SAMtools (version 1.1.4)
stringtie (version 2.1.7)
Bioconductor package DESeq2
Assembly: hg38
Supplementary files format and content: csv format, gene expression levels (normalized reaad counts from the DEseq2 package) for each sample
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| Submission date |
Mar 05, 2024 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Dimitrios Avramopoulos |
| E-mail(s) |
adimitr1@jhmi.edu
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| Organization name |
Johns Hopkins University
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| Department |
Genetic Medicine
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| Street address |
733 North Broadway
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE260873 |
Excitatory Neurons Derived from Human-Induced Pluripotent Stem Cells Show Transcriptomic Differences in Alzheimer’s Patients from Controls |
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| Relations |
| BioSample |
SAMN40265824 |
| SRA |
SRX23841102 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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