cell-to-cell variability in expression across cells and species shapes adaptive immunity
Gene expression variability across cells and
Using bulk and single-cell transcriptomics in LCLs
Cell-to-cell transcriptional variability adaptive immunity
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Gene expression variability across cells and species shapes innate immunity
Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
For the PCA analysis, cell-cycle genes were defined from
GO:0007049 and from Cyclebase
24. Specifically, we took genes from
GO:0007049 that showed strong evidence of cell-cycle association by having a rank within the top 400 Cyclebase genes (giving a total of 578 genes). For the S versus G2/M DE analysis, we sampled 50 cells from the S phase and 50 cells from the G2/M phase to match on cellular detection rate (CDR). For the S condition, the 25th, 50th, and 75thpercentiles of CDR were 0.62, 0.63, and 0.64, respectively; for the G2/M condition they were 0.61, 0.63, and 0.64, respectively.
Cell cycle specific co-expression network
scRNA-seq + pacbio alternative splicing
Variable genes
Antigen binding
GHM - immunoglobulin heavy constant mu
SIRPA - signal-regulatory protein alpha
ITGA4 - integrin, alpha 4 (antigen cd49d, alpha 4 subunit of vla-4 receptor)
IGKC - immunoglobulin kappa constant
CD1C - cd1c molecule
IGKV3-20 - immunoglobulin kappa variable 3-20
DHCR24 - 24-dehydrocholesterol reductase
HLA-DRB1 - major histocompatibility complex, class ii, dr beta 1
HLA-DRA - major histocompatibility complex, class ii, dr alpha
HLA-DQB1 - major histocompatibility complex, class ii, dq beta 1
IGLC3 - immunoglobulin lambda constant 3 (kern-oz+ marker)
IGLC2 - immunoglobulin lambda constant 2 (kern-oz- marker)
IGKV4-1 - immunoglobulin kappa variable 4-1
HLA-DQA1 - major histocompatibility complex, class ii, dq alpha 1
IGLV1-47 - immunoglobulin lambda variable 1-47
SLAMF1 - signaling lymphocytic activation molecule family member 1
IGLL5 - immunoglobulin lambda-like polypeptide 5
TGFB1 - transforming growth factor, beta 1
HLA-DPA1 - major histocompatibility complex, class ii, dp alpha 1
CD48 - cd48 molecule
IGLV2-23 - immunoglobulin lambda variable 2-23
HLA-DPB1 - major histocompatibility complex, class ii, dp beta 1
CD40 - cd40 molecule, tnf receptor superfamily member 5
IGHA1 - immunoglobulin heavy constant alpha 1
TRBC2 - t cell receptor beta constant 2
IGLV6-57 - immunoglobulin lambda variable 6-57
IGHD - immunoglobulin heavy constant delta
IGHA2 - immunoglobulin heavy constant alpha 2 (a2m marker)
PLG - plasminogen
IGHG1 - immunoglobulin heavy constant gamma 1 (g1m marker)
IGHV1-24 - immunoglobulin heavy variable 1-24
IGHG4 - immunoglobulin heavy constant gamma 4 (g4m marker)
IGHG3 - immunoglobulin heavy constant gamma 3
cytokine activity
LTB - lymphotoxin beta (tnf superfamily, member 3)
IL16 - interleukin 16
LTA - lymphotoxin alpha
EBI3 - epstein-barr virus induced 3
MIF - macrophage migration inhibitory factor (glycosylation-inhibiting factor)
HMGB1 - high mobility group box 1
CD70 - cd70 molecule
TNFSF4 - tumor necrosis factor (ligand) superfamily, member 4
TNFSF13B - tumor necrosis factor (ligand) superfamily, member 13b
TNFSF14 - tumor necrosis factor (ligand) superfamily, member 14
TNFSF10 - tumor necrosis factor (ligand) superfamily, member 10
CCL4L2 - chemokine (c-c motif) ligand 4-like 2
CCL17 - chemokine (c-c motif) ligand 17
CSF1 - colony stimulating factor 1 (macrophage)
C10orf99 - chromosome 10 open reading frame 99
TGFB1 - transforming growth factor, beta 1
CCL5 - chemokine (c-c motif) ligand 5
CCL4 - chemokine (c-c motif) ligand 4
CXCL10 - chemokine (c-x-c motif) ligand 10
CCL3 - chemokine (c-c motif) ligand 3
TNF - tumor necrosis factor
IL10 - interleukin 10
EDN1 - endothelin 1
BMP4 - bone morphogenetic protein 4
IL32 - interleukin 32
CCL22 - chemokine (c-c motif) ligand 22