NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5356118 Query DataSets for GSM5356118
Status Public on Dec 22, 2021
Title Suz12-AM-ind3
Sample type SRA
 
Source name Alveolar macrophage
Organism Mus musculus
Characteristics background strain: C57BL/6
tissue: Lung
transgenic mouse genotype: Suz12 cKO
Extracted molecule polyA RNA
Extraction protocol RNA was isolated with the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome using the align function of RSubread 2.1.1.
Read counts were summarized by Entrez Gene ID using the featureCounts function of Rsubread 2.4.3 and Rsubread's built-in NCBI annotation. The supplementary file GenewiseCounts.tsv.gz provides the gene-level counts for all the samples.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length and the number of reads mapping to that gene.
 
Submission date Jun 03, 2021
Last update date Dec 22, 2021
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL19057
Series (2)
GSE176111 RNA-seq profiling of bone marrow-derived alveolar macrophages from wildtype and Suz12 knockout mice
GSE176117 RNA-seq profiling of bone marrow-derived alveolar macrophages, foetal-derived alveolar macrophages and foetal-derived Langerhans cells from the lungs of wildtype and Suz12 knockout mice
Relations
BioSample SAMN19549914
SRA SRX11055258

Supplementary file Size Download File type/resource
GSM5356118_Suz12-AM-ind3.tsv.gz 175.1 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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