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Sample GSM3505526

Query DataSets for GSM3505526

Status

Public on Apr 29, 2019

Title

NL79CC

Sample type

SRA

Source name

corpus callosum

Organism

Homo sapiens

Characteristics

tissue: corpus callosum
disease state: healthy control

Extracted molecule

total RNA

Extraction protocol

Tissues were homogenized into Trizol Reagent (Thermo Fisher Scientific), and aqueous phase was collected after phase separation by adding chloroform. Further RNA purification was performed using Direct-zol™ RNA MiniPrep Plus (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 3000

Data processing

Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic was used for cleaning.
R package “QuasR” was used for the read alignment to human genome (hg19) followed by the counting at gene level.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

Submission date

Dec 07, 2018

Last update date

Apr 29, 2019

Contact name

Yuichiro Itoh

E-mail(s)

yitoh@ucla.edu

Phone

3102068999

Organization name

UCLA