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Sample GSM3505521 Query DataSets for GSM3505521
Status Public on Apr 29, 2019
Title NL73CC
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
Department Neurology
Street address 635 Charles E. Young Drive South
City Los Angeles
State/province California
ZIP/Postal code 90095
Country USA
 
Platform ID GPL21290
Series (1)
GSE123496 Human brain tissues from healthy controls and multiple sclerosis patients
Relations
BioSample SAMN10533322
SRA SRX5122465

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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