|
| Status |
Public on Dec 22, 2021 |
| Title |
suz12 KO5 |
| 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 |
| |
|
| Description |
suz12-KO5_S5
|
| 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 2.4.3.
Read counts were summarized by Entrez Gene ID using the featureCounts function of Rsubread 2.6.0 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) |
| GSE176115 |
RNA-seq profiling of foetal-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 |
SAMN19550289 |
| SRA |
SRX11055268 |
