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Sample GSM4869296 Query DataSets for GSM4869296
Status Public on Feb 04, 2021
Title APP rep3
Sample type SRA
Source name iPSC-derived neurons
Organism Homo sapiens
Characteristics genotype/variation: APP duplication (APP)
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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
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
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
Street address Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
City Hong Kong
ZIP/Postal code 000000
Country China
Platform ID GPL11154
Series (1)
GSE160224 Efficient manipulation of gene dosage in human iPSCs using CRISPR/Cas9 nickases
BioSample SAMN16571287
SRA SRX9373679

Supplementary file Size Download File type/resource
GSM4869296_APP_3.csv.gz 249.8 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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