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Sample GSM3618030 Query DataSets for GSM3618030
Status Public on Jun 22, 2019
Title DS1-rep2
Sample type SRA
 
Source name Skin Fibroblast
Organism Homo sapiens
Characteristics condition: Trisomic
age: 5 months
gender: Male
batch: A
Growth protocol Cells were were cultured in DMEM medium (Life Technologies #11995-065) containing 10% fetal bovine serum (Life Technologies #10270), 100 mg/L sodium pyruvate, 100 units/mL Penicillin-Streptomycin (Life Technologies #15140-122) at 37°C in a 5% CO2 atmosphere. Cell passage number ranged from p7 to p12, and cells at 85–90% confluency were used.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturer’s specifications
500 ng of total RNA were prepared using TruSeq RNA Sample prep kit V2 (Ilumina Inc., San Diego, CA, USA) following manufacturers’ instructions for the samples DS-1-6 and 2N-1-6. Quality of libraries was assessed using Agilent 2200 TapeStation system. The sequencing files for samples DS-7, DS-8, 2N-7, 2N-8 and 2N-9 were retrieved from SRA: SRP039348.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description DS-2
TMM_normalized_ReadCounts.txt
Data processing Samples DS 1-6 and 2N 1-6: For base-calling CASAVA version 1.8 was used to generate FASTQ files. Samples DS-7,8 and 2N-7, 8, 9: Retrieved from SRA: SRP039348.
Samples DS 1-6 and 2N 1-6: STAR aligner (version 2.3.1z9) was used to align sequencing files with reference genome. Samples DS-7,8 and 2N-7, 8, 9: Raw read counts obtained from public repository ARCHS4 (Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A. Massive mining of publicly available RNA-seq data from human and mouse. Nature Communications 9. Article number: 1366 (2018)). Kallisto was used as aligner according to the publication.
Samples DS 1-6 and 2N 1-6: HTSeq (version 0.6.1p2) was used for quantifying aligned reads.
Genome_build: Samples DS 1-6 and 2N 1-6: hg19 (GRCh37). Samples DS-7,8 and 2N-7, 8, 9: hg38 (According to ARCHS4)
Supplementary_files_format_and_content: TMM_normalized_ReadCounts.txt is a tab delimited text file containing TMM normalized counts for features i.e. counts are normalized between libraries.
 
Submission date Feb 21, 2019
Last update date Jun 22, 2019
Contact name Sandipkumar Darji
E-mail(s) sdarji@nki.rfmh.org
Organization name Nathan Kline Institute for Psychiatric Research
Department Center for Dementia Research
Street address 140 Old Orangeburg Rd, Bldg 39
City Orangeburg
State/province NY
ZIP/Postal code 10962
Country USA
 
Platform ID GPL11154
Series (1)
GSE126910 mTOR hyperactivation in Down Syndrome mediates deficits in autophagy induction, autophagosome formation, and mitophagy
Relations
BioSample SAMN10985288
SRA SRX5406087

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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