|
Status |
Public on Jan 04, 2020 |
Title |
Balbc_IL4c_sample_0006 |
Sample type |
SRA |
|
|
Source name |
Peritoneal macrophages
|
Organism |
Mus musculus |
Characteristics |
strain: BALB/c 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).
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|
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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.
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|
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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 |
SAMN09464561 |
SRA |
SRX4277473 |