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| Status |
Public on Dec 23, 2017 |
| Title |
NL84Opt |
| Sample type |
SRA |
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| Source name |
Optic chiasm
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| Organism |
Homo sapiens |
| Characteristics |
tissue: optic chiasm
disease state: healthy control
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
hg19.gene_NL_Opt.txt
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| 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 files include count values for each Sample
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| Submission date |
Jun 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuichiro Itoh |
| E-mail(s) |
yitoh@ucla.edu
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| Phone |
3102068999
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| Organization name |
UCLA
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| Department |
Neurology
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| Street address |
635 Charles E. Young Drive South
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE100297 |
Human optic chiasm from healthy controls and multiple sclerosis patients |
| GSE100330 |
Multiple sclerosis and EAE |
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| Relations |
| BioSample |
SAMN07260405 |
| SRA |
SRX2940967 |
| 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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