NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5215324 Query DataSets for GSM5215324
Status Public on Mar 01, 2024
Title BM mRNA-Seq DbhVLM-mCherry replicate 4
Sample type SRA
 
Source name bone marrow CD45+ cells
Organism Mus musculus
Characteristics cell type: bone marrow CD45+ cells
strain: C57BL/6J
genotype: DbhVLM-mCherry
growth phase: 12 week
treatment: CNO injections
Treatment protocol AAV-DIO-hM3Dq-mCherry or the same volume of AAV-DIO-mCherry was bilaterally injected into the VLM of Dbh-Cre mice. CD45+ cells were obtained from the spleen and bone marrow 4 hour after CNO injections.
Growth protocol Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 7 am to 7 pm), and ad libitum access to water and a standard chow diet.
Extracted molecule polyA RNA
Extraction protocol Total RNA of CD45+ cells was extracted using a Takara MiniBest Universal RNA Extraction kit (code no. 9767) according to the manufacturer’s instructions. Poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB,E7490L).
poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB,E7490L).First-strand cDNA was synthesized with the SuperScript II Reverse Transcriptase (Invitrogen,18064014) and Second Strand cDNA was synthesized using Second Strand cDNA Synthesis Kit (Invitrogen,A48570). Libraries were subsequently constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB,E7645L).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
 
Submission date Mar 27, 2021
Last update date Mar 01, 2024
Contact name Liang Wang
E-mail(s) wangliang@ustc.edu.cn
Organization name University of Science and Technology of China
Street address 96 Jinzhai Road
City Hefei
State/province Anhui
ZIP/Postal code 230001
Country China
 
Platform ID GPL21273
Series (1)
GSE170737 Increased homing of immune cells by orexigenic catecholaminergic neurons alleviates autoimmune disorder
Relations
BioSample SAMN18520182
SRA SRX10460918

Supplementary file Size Download File type/resource
GSM5215324_BM-mCherry-4.txt.gz 329.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap