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Sample GSM3168333 Query DataSets for GSM3168333
Status Public on May 21, 2024
Title L1C1: Spinal cord
Sample type SRA
Source name Spinal cord
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
tissue: Upper spinal cord
group: without spinal cord injury
Extracted molecule total RNA
Extraction protocol Spinal cords were removed, flash frozen in liquid nitrogen, and RNA was harvested.
Library were constructed in accordance with the CEL-Seq2 protocol and prepared on the Illumina HiSeq1500 platform.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing The raw sequence reads were aligned to the rat reference genome (Rnor_6.0) using HISAT2 (version 2.0.4).
Read counting was performed with HTSeq (version 0.6.0) so that UMI duplicates were removed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The txt file contains UMI count matrix.
Submission date May 31, 2018
Last update date May 21, 2024
Contact name Yasuyuki Ohkawa
Organization name Medical Institute of Bioregulation
Lab Division of Transcriptomics
Street address 3-1-1 Maidashi
City Fukuoka
ZIP/Postal code 8128582
Country Japan
Platform ID GPL18404
Series (1)
GSE115230 Genome wide analysis of the upper lumbar spinal cord at 4 days after T9 hemisection injury
BioSample SAMN09288686
SRA SRX4167865

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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