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GEO help: Mouse over screen elements for information. |
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Status |
Public on Nov 07, 2019 |
Title |
Islets, NCD mice 1 (lncRNA-seq) |
Sample type |
SRA |
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Source name |
islet
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: islet treatment: post 8-week normal chow diet
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Extracted molecule |
total RNA |
Extraction protocol |
islet were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
HiSeq X Ten |
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Data processing |
Illumina software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, The reads mapped to the mouse genome (GRCM38/mm10) were analyzed using GEM software. Reads Per Kilobase of exon per Megabase of library size (RPKM) 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. Genome_build: mm10 Supplementary_files_format_and_content: sample.txt: tab-delimited text file includes FPKM values for each Sample
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Submission date |
Nov 06, 2019 |
Last update date |
Nov 07, 2019 |
Contact name |
fangfang zhang |
E-mail(s) |
1170563131@qq.com
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Organization name |
China Pharmaceutical University
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Street address |
24 Tongjiaxiang, Nanjing, Jiangsu province, People's republic of China
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City |
nnajing |
ZIP/Postal code |
210009 |
Country |
China |
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Platform ID |
GPL21273 |
Series (1) |
GSE139991 |
high-throughput sequencing analysis of NCD mice, HFD mice and db/db mice |
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Relations |
SRA |
SRX5801949 |
BioSample |
SAMN08730473 |
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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