GSE161092

GSE161092

Human adipose derived stromal cells (ASC) and ABCB5+ (skin stromal cells were infused intravenously and injected intraperitoneally. Additionally, ASC and ABCB5+ derived conditioned media (CM) were administrated intraperitoneally.

Sample descriptions:

• Control untreated

• CM ABCB5 + derived co-culture medium (The supernatant of a co-culture of ABCB5+ cells and THP-1-derived macrophages stimulated with IFN-γ and LPS was collected to obtain the ABCB5+-derived CoCM+)

• IV_ADSC intravenous (i.v.) ASC + ABCB5+

• IP_ADSC intraperitoneal (i.p.) ASC + ABCB5+

contrasts:

• MSC (IP_ADSC + IV_ADSC) vs Control
• CM vs Control
• Control vs. CM. vs. MSC - CM capable of eliciting same response as MSC?

## 
## FALSE  TRUE 
##    23   165

##  [1] "Cgas"    "Aim2"    "Hmgb1"   "Itgav"   "Cd36"    "Cd24a"   "Siglecg"
##  [8] "H2-D1"   "H2-K1"   "H2-T10"  "Pirb"    "Trio"    "Adam12"  "Adam8"  
## [15] "Ndnf"    "Timd4"   "Baiap3"  "Stab1"   "H2-M2"   "Mcf2"    "Adam12" 
## [22] "Adam8"   "Ndnf"

## 
## FALSE  TRUE 
##     1     9

Genes missing from Dataset

Rat Identifiers not mouse, but the gene names are analogous.

RNA-Seq experiment, plausible that these transcripts were not captured.

print("printing missing Efferocytosis genes")

## [1] "printing missing Efferocytosis genes"

eff_genes[!(eff_genes %in% rownames(counts))]

##  [1] "Cgas"    "Aim2"    "Hmgb1"   "Itgav"   "Cd36"    "Cd24a"   "Siglecg"
##  [8] "H2-D1"   "H2-K1"   "H2-T10"  "Pirb"    "Trio"    "Adam12"  "Adam8"  
## [15] "Ndnf"    "Timd4"   "Baiap3"  "Stab1"   "H2-M2"   "Mcf2"    "Adam12" 
## [22] "Adam8"   "Ndnf"    "Rab7"

print("printing missing fibrosis genes")

## [1] "printing missing fibrosis genes"

fib_genes[!(fib_genes %in% rownames(counts))]

## [1] "Mir21a"

rm(ens_to_sym)

Efferocytosis

MSC vs Control

Can CM elicit the same MSC response?

Fibrosis

MSC vs Control

MSC + CM vs Control