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Sample GSM4083813 Query DataSets for GSM4083813
Status Public on Dec 16, 2019
Title Alveolar macrophages, WTCS_IIa1
Sample type SRA
 
Source name FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+)
Organism Mus musculus
Characteristics cell type: FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+)
treatment protocol: cigarette smoke
genotype: wild-type
strain: C57BL/6
Treatment protocol wild-type and miR-155 knock-out mice to four weeks of air or cigarette smoke
Extracted molecule polyA RNA
Extraction protocol RNA extraction of FACS sorted alveolar macrophages was performed with the miRNeasy Mini Kit (Qiagen).
libraries were prepared using the TruSeq mRNA library prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. A total of 25 ng of RNA was used as input for polyA selection, followed by fragmentation, reverse transcription and PCR amplification
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing sequencing reads were mapped to the murine reference genome (GRCm38.p6) using STAR v2.6.0c and GENCODE release M18 as guidance
read counts were quantified using the "--quantMode GeneCounts" option
genomic features with a zero read count across all samples and without read count greater or equal than four in at least sixty percent of the samples from one group were discarded
raw counts were transformed into log2-counts per million using limma-voom
Genome_build: GRCm38.p6 + GENCODE release M18
Supplementary_files_format_and_content: tab-delimited text file including log-CPM transformed values
 
Submission date Sep 18, 2019
Last update date Dec 16, 2019
Contact name Ken R Bracke
Organization name Ghent University
Department Department of Respiratory Medicine
Street address Corneel Heymanslaan 10
City Ghent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL19057
Series (1)
GSE137653 polyA+ RNA sequencing on FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+) from air and cigarette-smoke exposed wild type and miR-155 KO mice
Relations
BioSample SAMN12781396
SRA SRX6865447

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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