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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 04, 2021 |
| Title |
APP rep2 |
| Sample type |
SRA |
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| Source name |
iPSC-derived neurons
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| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: APP duplication (APP)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The transcript-level expression analysis was performed as previously described (Pertea et al, Nat Protoc 11, 1650-1667, 2016). Briefly, quality control was first accomplished using FastQC and RSeQC. The FASTQ files were aligned to human GRCh38.91 reference genome using HISAT2 alignment program. The aligned files were assembled into potential transcripts using StringTie assembler program. Next, the potential transcripts were passed to the prepDE program to generate read counts. Minimal pre-filtering with row counts greater than 10 reads was performed. Differential gene expression analysis was performed using DESeq2 from Bioconductor version 3.10
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Oct 27, 2020 |
| Last update date |
Feb 04, 2021 |
| Contact name |
Nancy Y. Ip |
| Organization name |
Hong Kong University of Science and Technology
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| Street address |
Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
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| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE160224 |
Efficient manipulation of gene dosage in human iPSCs using CRISPR/Cas9 nickases |
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| Relations |
| BioSample |
SAMN16571289 |
| SRA |
SRX9373678 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4869295_APP_2.csv.gz |
249.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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