NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4256680 Query DataSets for GSM4256680
Status Public on Apr 07, 2021
Title Ak4 shRNA KD M1 rep1
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: M1 macrophages
genotype: Ak4 shRNA
Treatment protocol Lentiviral transduction was conducted in serum free medium containing 20% L929 supernatant with 8 μg/ml polybrene at day 3 (MOI = 30). For BMDMs were stimulated with 1000 ng/ml LPS and 20 ng/ml IFNγfor 6 hours.
Growth protocol BMDMs were cultured in complete DMEM containing 20%L929 supernatant for 7 days
Extracted molecule total RNA
Extraction protocol cell lyses RNA was harvested using Trizol reagent. Direct-zol RNA miniPrep (Zymo Research) was used for total RNA isolation for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Total RNA extracted from M1 cells was digested to 180 bp fragments after removing rRNAs with a Ribo-Zero Gold kit (Illumina, San Diego, USA). A sequencing library was created by reverse-transcribing RNA fragments to cDNA, and ligating specific adapters at both ends of these cDNA fragments.
The sequencing libraries were loaded to the surface of flow cells, and amplified into clonal clusters through bridge amplification. All of the clusters on the flow cell were sequenced by NextSeq 500 (Illumina).
The FastQC (v0.11.8) program (http://www.bioinformatics. babraham.ac.uk/projects/fastqc/) was used to examine the quality of sequencing reads, and HISAT2 (v2.1.0) was used to align sequencing reads to mouse genome references (GRCm38).
The output SAM files were normalized and quantified with R packages Rsubread (v 2.0.0)and edgeR (v 3.28.0) from Bioconductor. A robust normalization approach, the trimmed mean of M value, was applied and log2-transformation was used to obtain the final expression values.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts
 
Submission date Jan 08, 2020
Last update date Apr 07, 2021
Contact name Shi-Chuen Miaw
E-mail(s) smiaw@ntu.edu.tw
Phone 0939676785
Organization name National Taiwan University, College of Medicine
Department Immunology
Street address No.1 Jen Ai road section 1
City Taipei
ZIP/Postal code 100
Country Taiwan
 
Platform ID GPL19057
Series (1)
GSE143302 Adenylate kinase 4 Promotes the expression of Inflammatory Genes in Macrophages via Hif-1a
Relations
BioSample SAMN13762627
SRA SRX7521429

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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