|
| Status |
Public on Jan 04, 2020 |
| Title |
B6_IL4c_sample_0004 |
| Sample type |
SRA |
| |
|
| Source name |
Peritoneal macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
macrophage phenotype: Tissue resident, F4/80hi CD206-
|
| Treatment protocol |
-
4 days prior to peritoneal cells harvest, all mice were treated with intra-peritoneal injection of IL-4 complexes (i.e. 5μg of IL-4 and 25μg of anti-IL4) every other day, in addition to the group-specific treatment as detailed in the Samples Section above.
|
| Growth protocol |
C57BL/6 and BALB/c mice used to compare strain effects on accessible chromatin landscape were purchased directly from Jackson laboratory and used immediately for experiments.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (QIAgen) based on manufacturer’s protocol, with an additional DNase digestion step using the RNase-free DNase set (QIAgen).
RNA from each sample was uniquely barcoded and libraries were constructed using the CELSeq2 protocol as described in Hashimshony et al (Genome Biology 2016).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
CEL-seq2 reads were first demultiplexed using the bc_demultiplex script from https://github.com/yanailab/CEL-Seq-pipeline
Demultiplexed reads were aligned to the mm10 mouse reference genome using bowtie2 (version 2.2.9).
Aligned reads were counted for each gene using a modified htseq-count script (from https://github.com/yanailab/CEL-Seq-pipeline) adapted for CEL-seq2 reads with unique molecular identified (UMI). We included only reads with MAPQ score > 30.
Finally, singleton genes (genes counted only once) were removed and a count matrix were generated, where each row is a unique gene and each column a unique sample.
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix, where each row is a unique gene and each column is a unique sample.
|
| |
|
| Submission date |
Jun 21, 2018 |
| Last update date |
Jan 04, 2020 |
| Contact name |
Mei San Tang |
| Organization name |
Washington University in St Louis
|
| Department |
Pathology & Immunology
|
| Street address |
660 S Euclid, Campus Box 8118
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE116105 |
Transcriptional profiles of IL-4 stimulated mouse peritoneal macrophages derived from different cellular lineages and of different genetics backgrounds |
| GSE116108 |
Profiles of IL-4 stimulated mouse peritoneal macrophages |
|
| Relations |
| BioSample |
SAMN09464574 |
| SRA |
SRX4277460 |
