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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2023 |
| Title |
Control gingival group1 |
| Sample type |
SRA |
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| Source name |
Gingival tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Gingival tissue
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution. For plant and fungi samples, we use NanoDropTMto identify the purity of the RNA samples.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
C1
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Read alignment software,software HISAT,version2.0
perform expression level for mRNAs by calculating FPKM. stimate the expression leveles of all transcripts.software StringTie,version1.3.0,parameters-bdta-q phred33-quals.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
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| Submission date |
Dec 09, 2020 |
| Last update date |
Dec 01, 2023 |
| Contact name |
chen bin |
| E-mail(s) |
a18585337725@126.com, 18585337725@sohu.com
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| Phone |
18585337725
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| Organization name |
Zunyi Medical University
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| Street address |
Xuefu West street num 6
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| City |
Zunyi |
| ZIP/Postal code |
563000 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE162912 |
Transcriptome sequencing of gingival tissues from impacted third molars patients reveals the alterations of gene expression |
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| Relations |
| BioSample |
SAMN17038008 |
| SRA |
SRX9656828 |
| 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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