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Sample GSM5356122 Query DataSets for GSM5356122
Status Public on Dec 22, 2021
Title WT-AM-ind4
Sample type SRA
Source name Alveolar macrophage
Organism Mus musculus
Characteristics background strain: C57BL/6
tissue: Lung
transgenic mouse genotype: Wild type
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
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
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
BioSample SAMN19549910
SRA SRX11055262

Supplementary file Size Download File type/resource
GSM5356122_WT-AM-ind4.tsv.gz 172.8 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

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