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Status |
Public on Mar 01, 2024 |
Title |
BM mRNA-Seq DbhVLM-mCherry replicate 4 |
Sample type |
SRA |
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Source name |
bone marrow CD45+ cells
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Organism |
Mus musculus |
Characteristics |
cell type: bone marrow CD45+ cells strain: C57BL/6J genotype: DbhVLM-mCherry growth phase: 12 week treatment: CNO injections
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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.
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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.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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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.
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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 |
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Platform ID |
GPL21273 |
Series (1) |
GSE170737 |
Increased homing of immune cells by orexigenic catecholaminergic neurons alleviates autoimmune disorder |
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Relations |
BioSample |
SAMN18520182 |
SRA |
SRX10460918 |