|
| Status |
Public on Jul 01, 2014 |
| Title |
CD11b_DC_LPS |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: [C57Bl/6 x B10.BR]F1
timepoint: 24
group: LPS stimulated
tissue: spleen
cell type: CD11b Dendritic Cells
|
| Treatment protocol |
Mice were injected intraperitoneally with 25 μg LPS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens from LPS-stimulated and unstimulated mice were digested with Collagenase from Clostridium histolyticum (Sigma-Aldrich) and a single-cell suspension was prepared by teasing through a mesh sieve. Splenocytes were stained with CD3, Ter119, Gr1, B220, and CD19 hybridomas, and negatively selected with anti-rat IgG MicroBeads (Miltenyi Biotec).CD11c+ cells were then enriched for using CD11c MicroBeads (Miltenyi Biotec). CD8 and CD11b DC subsets were further purifed by cell sorting on a FACS Aria II. Total RNA was extracted using a RNAeasy Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols. Unique Illumina barcode indexes were attached to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using Illumina RTA 1.9.35
Raw basecall data was converted to FASTQ sequence files using Off-Line Basecaller (Ilumina) and a custom Perl script.
Reads were aligned to the mm9 mouse genome and ensembl transcripts with TopHat version 2.05 and Bowtie1 version 0.12.7 with the search for novel junctions disabled.
Genomic coordinates were then transformed into counts of chimeric protein-coding Ensembl genes with the htseq-count script in the intersection-nonempty mode
Genome_build: mm9
Supplementary_files_format_and_content: tab delimeted text files containing raw count data for each sample
|
| |
|
| Submission date |
Nov 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David Graeme Hancock |
| E-mail(s) |
davidh@centenary.org.au
|
| Organization name |
Centenary Institute
|
| Street address |
Building 93, RPAH, Missenden Road
|
| City |
Camperdown |
| State/province |
NSW |
| ZIP/Postal code |
2050 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE42573 |
In vivo LPS responses in murine splenic CD8 and CD11b DC subsets |
|
| Relations |
| SRA |
SRX206829 |
| BioSample |
SAMN01820099 |
