|
| Status |
Public on Dec 16, 2019 |
| Title |
Alveolar macrophages, KOAIR_IIIb2 |
| 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: air
genotype: mir-155-KO
strain: B6.Cg-Mir155tm1.1Rsky/J
|
| 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 |
SAMN12781389 |
| SRA |
SRX6865454 |
