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Sample GSM5956541 Query DataSets for GSM5956541
Status Public on Apr 03, 2022
Title c2h
Sample type SRA
 
Source name BAL AM (CD45+ Ly6G-SIglecF + CD11c+)
Organism Mus musculus
Characteristics age: 12wks
genotype: CGD/CYBB KO (C57BL/6)
cell type: Pooled BAL cells
group: CD45+ Ly6G-SIglecF + CD11c+ CD11bhigh
Extracted molecule total RNA
Extraction protocol Qiagen RNAeasy micro plus
Clontech SMRTr
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description CGD 12wks CD11bhigh
Naive
CGD_12W_CD11bhigh AM
Data processing The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount.
Sailfish was used to produce isoform estimated counts.
Assembly: Mus musculus Ensemble R76
Supplementary files format and content: Tab-delimited text files include read count values for each Sample
 
Submission date Mar 16, 2022
Last update date Apr 03, 2022
Contact name Mary C Dinauer
E-mail(s) mdinauer@wustl.edu
Organization name Washington University In St Louis
Department Pathology & Immunology
Street address 660 South Euclid Ave
City St Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21493
Series (2)
GSE198769 Bronchoalveolar lavage alveolar macrophage subset transcriptomes in WT and NOX2-knockout mice
GSE198778 The leukocyte NADPH oxidase 2 (NOX2) plays a key role in pathogen killing and immunoregulation
Relations
BioSample SAMN26724458
SRA SRX14474404

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

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