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| Status |
Public on Dec 01, 2019 |
| Title |
Control 3 |
| Sample type |
SRA |
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| Source name |
INS-1 beta cell
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| Organism |
Rattus norvegicus |
| Characteristics |
cell type: rat insulinoma cell line
tissue: pancreatic islet
strain: Wistar
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was determined using an Agilent 2100 system and an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
Paired-end strand-specific libraries were prepared using the VAHTS Total RNA-Seq Library PrepKit for Illumina (Vazyme, China) following the manufacturer’s instructions.
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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 |
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads using Seqtk
Hisat2（version:2.0.4）was used to map the cleaned reads to the mouse Rnor_6.0 reference genome with two mismatches.
Stringtie（version:1.3.0）was run with a reference annotation to generate FPKM values （Fragments Per Kilobase of exon model per Million mapped reads）for known gene models.
Stringtie（version:1.3.0 was used to assemble reads into transcripts. Putative lncRNAs were defined as novel transcripts set through the following filters: length ≥200 bp; number of exons ≥2; ORF≤300 bp; have no or weak protein coding ability (CPC score <0 & CNCI score <0 & no significant similarity with Pfam database
RNA-seq derived lncRNAs with the known lncRNAs previously annotated by NONCODE v4.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values
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| Submission date |
Jan 08, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Xiang Kong |
| E-mail(s) |
wnmcyaolikx@163.com
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| Organization name |
The First Aflliated Hospital of Wannan Medical College
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| Department |
Central Laboratory of Yijishan Hospital
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| Street address |
zheshanxi road NO 2
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| City |
WUhu |
| ZIP/Postal code |
241001 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE124833 |
Insights from long non-coding RNAs profiling of beta cells undergoing high glucose/palmitate -induced glucolipotoxicity |
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| Relations |
| BioSample |
SAMN10715993 |
| SRA |
SRX5229653 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3555700_A3.txt.gz |
392.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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