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Sample GSM6506766 Query DataSets for GSM6506766
Status Public on Jan 01, 2024
Title WT-B-1
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics tissue: brain
genotype: wildtype C57BL6/J
treatment: water
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCm38.p6 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
 
Submission date Aug 24, 2022
Last update date Jan 01, 2024
Contact name Bo Meng
E-mail(s) bmeng2019@gmail.com
Organization name East China Normal Univeristy
Street address 3663 Zhongshan Rd(N.)
City Shanghai
ZIP/Postal code 200062
Country China
 
Platform ID GPL24247
Series (1)
GSE211983 Chronic oral administration of nicotine affects transcriptomic profiling in conditional Presenilin 1/2 knockout mice and wild type mice
Relations
BioSample SAMN30480410
SRA SRX17198930

Supplementary file Size Download File type/resource
GSM6506766_WT-B-1.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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