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Sample GSM2677515 Query DataSets for GSM2677515
Status Public on Dec 23, 2017
Title NL78Opt
Sample type SRA
Source name Optic chiasm
Organism Homo sapiens
Characteristics tissue: optic chiasm
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
Description hg19.gene_NL_Opt.txt
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 (, 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 files include count values for each Sample
Submission date Jun 21, 2017
Last update date May 15, 2019
Contact name Yuichiro Itoh
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 (2)
GSE100297 Human optic chiasm from healthy controls and multiple sclerosis patients
GSE100330 Multiple sclerosis and EAE
BioSample SAMN07260406
SRA SRX2940966

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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