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Status |
Public on Jun 22, 2019 |
Title |
DS2-rep1 |
Sample type |
SRA |
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Source name |
Skin Fibroblast
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Organism |
Homo sapiens |
Characteristics |
condition: Trisomic age: 2 years gender: Male batch: A
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
DS-4 TMM_normalized_ReadCounts.txt
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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.
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Submission date |
Feb 21, 2019 |
Last update date |
Jun 22, 2019 |
Contact name |
Sandipkumar Darji |
E-mail(s) |
sdarji@nki.rfmh.org
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Organization name |
Nathan Kline Institute for Psychiatric Research
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Department |
Center for Dementia Research
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Street address |
140 Old Orangeburg Rd, Bldg 39
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City |
Orangeburg |
State/province |
NY |
ZIP/Postal code |
10962 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE126910 |
mTOR hyperactivation in Down Syndrome mediates deficits in autophagy induction, autophagosome formation, and mitophagy |
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Relations |
BioSample |
SAMN10985286 |
SRA |
SRX5406089 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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