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| Status |
Public on Apr 05, 2022 |
| Title |
29-CCI14d |
| Sample type |
SRA |
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| Source name |
Anterior Cingulate Cortex
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: brain
age: 8 weeks
treatment: CCI 14d
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set(Cat#79254, QIAGEN, GmBH, Germany).
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 |
Illumina HiSeq 2500 |
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| Data processing |
Using seqtk to filter raw reads, we can get clean reads that can be used for data analysis. The main steps are as follows: remove the junction sequence contained in the reads; remove the base with 3 'end quality Q less than 20, that is, the base error rate is less than 0.01, where Q= - 10logerror_ Ratio; remove the reads less than 25 in length; remove the ribosome RNA reads of the species.
Using splited mapping algorithm of Hisat2（ version:2.0.4 ）to do genome mapping for clean reads,
Counting fragments of every gene by Stringtie（version:1.3.0). TMM (trimmed mean of m values) method was used to normalize, and then Fragments Per Kilobase of exon model per Million mapped reads (FPKM) value of each gene was calculated by Perl script.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Apr 15, 2021 |
| Last update date |
Apr 05, 2022 |
| Contact name |
Changsheng Huang |
| E-mail(s) |
docthuang2005@hotmail.com
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| Organization name |
Xiangya Hospital, Central South University
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| Department |
Department of Anesthesiology
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| Street address |
87 Xiangya Road
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410008 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE172133 |
A Transcriptomic Analysis of Neuropathic Pain in the Anterior Cingulate Cortex after Nerve Injury |
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| Relations |
| BioSample |
SAMN18747284 |
| SRA |
SRX10606118 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5242561_gene_expression_29_CCI14d.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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