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Status |
Public on Apr 29, 2019 |
Title |
MS47IC |
Sample type |
SRA |
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Source name |
internal capsule
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Organism |
Homo sapiens |
Characteristics |
tissue: internal capsule disease state: MS
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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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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
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Submission date |
Dec 07, 2018 |
Last update date |
Apr 29, 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 (1) |
GSE123496 |
Human brain tissues from healthy controls and multiple sclerosis patients |
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Relations |
BioSample |
SAMN10533343 |
SRA |
SRX5122444 |
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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