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| Status |
Public on Jan 22, 2020 |
| Title |
Late neuritis rep1 |
| Sample type |
SRA |
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| Source name |
Sciatic nerves
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Sciatic nerves
strain: Lewis
gender: female
group: Late neuritis
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| Treatment protocol |
EAN rats were subcutaneously injected at the base of the tail with 200 μL of an emulsion containing 230 μg myelin P2 peptide (amino acids 53–78; TESPFKNTEISFKLGQEFEETTADNR; GL Biochem, Shanghai, China), 2 mg Mycobacterium tuberculosis H37RA (Difco, Detroit, MI, USA), 100 μL Freund’s incomplete adjuvant (Sigma, St. Louis, MO, USA), and 100 μL saline. Control animals (sham) were injected with an inoculum containing 100 µL saline and 100 µL Freund’s incomplete adjuvant.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the sciatic nerve tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA degradation and contamination were assessed by 1% agarose gel electrophoresis. RNA integrity and concentration were evaluated on a Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA) using an RNA Nano 6000 Assay Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
L1
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| Data processing |
Basecalls performed using bcl2fastq.
The useful Perl script was used to filter the original data (raw reads) to guarantee the data quality. The contaminated reads for adapters (read bases containing more than 5 base pairs of adapter sequences), low-quality reads (number of read bases whose phred quality value was ≤19 accounting for more than 15%), and reads whose N base value was >5% of the total bases in raw reads were removed. The contents of Q30 of clean reads were calculated. All subsequent analysis was based on clean reads.
Reference gene and genome annotation files were downloaded from the ENSEMBL website (http://www.ensembl.org/index.html). Bowtie v1.0.1 was used to build the reference genome library, and then clean reads were compared to the reference genome using HISAT2 v2.1.0. The fragments per kilobase per million mapped fragments value was calculated to estimate the expression level of genes in each sample.
Genome_build: ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
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| Submission date |
Jul 03, 2019 |
| Last update date |
Jan 22, 2020 |
| Contact name |
Yang Xue |
| E-mail(s) |
xueyanghyd@163.com
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| Organization name |
The First Affiliated Hospital of Harbin Medical University
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| Street address |
23 You Zheng Street
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| City |
Harbin |
| ZIP/Postal code |
150001 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (1) |
| GSE133750 |
Transcriptomes in the Sciatic Nerves of Lewis Rats with Experimental Autoimmune Neuritis |
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| Relations |
| BioSample |
SAMN12207092 |
| SRA |
SRX6401711 |
| 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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