EMBO/SourceData huggingface dataset:
Figure legend: "D. Immunofluorescent staining with anti-GTP-CDC42 in DSS treated colons from Gsdmd+/+ (WT) and Gsdmd-/-(GSDMD KO), IQGAP1+/+ and IQGAP1-/- mice."
NCBI gene IDs:
"Gsdmd: 69146
GSDMD: 69146
IQGAP1: 29875"
Figure legend: "Analysis of BrdU incorporation by BrdU-IP-chip 45 minutes after release into S phase in cells treated with 0.1% MMS as described in (A). A representative region on chromosome VII is shown. The position of replication origins is indicated above the map. Asterisks: late origins firing in mrc1∆ cells."
NCBI gene IDs:
"mrc1: 850297"
Figure legend: "Quantification of the BrdU incorporation (signal log ratio) at 384 early and late replication origins in wild type, rad9∆ and mrc1∆ strains exposed to 0.1 or 0.033% MMS. Red lines indicate median values. Median replication times (Trep) are indicated for bins of 96 origins."
NCBI gene IDs:
"mrc1: 850297
rad9: 851803"
Figure legend: "Wild type, mrc1∆ and rad9∆ cells were released into S phase in the presence of BrdU and 0.033% MMS, as described in Fig. 1A. DNA combing analysis was performed for samples collected 45 and 60 min after release into S phase. Representative DNA fibers are shown. Red: DNA, green: BrdU. Bar is 20 kb."
NCBI gene IDs:
"mrc1: 850297
rad9: 851803"
Figure legend: "Wild type, mrc1∆ and rad9∆ cells were synchronized in G1 with α-factor prior to release with pronase in the presence of 0.033% MMS. Cells were collected at the indicated times and Rad53 phosphorylation was monitored by western blot The asterisk indicates a non-specific band detected by the anti-Rad53 antibody."
NCBI gene IDs:
"mrc1: 850297
rad9: 851803"
Figure legend: "Wild type, mrc1∆ and rad9∆ cells were synchronized in G1 with α-factor prior to release with pronase in the presence of 0.033% MMS. Cells were collected at the indicated times and Rad53 phosphorylation was monitored with an in situ phosphorylation assay - ISA (F)."
NCBI gene IDs:
"mrc1: 850297
rad9: 851803"
Figure legend: "2D gel analysis of initiation and elongation in wild type and rad9∆ cells at the early origin ARS719 (probe 1) and at a locus 7 kb away of the origin (probe 2). Time in Zeocin after the HU wash is indicated. Arrows point to Y arcs (fork signals) with the strongest intensity."
NCBI gene IDs:
"rad9: 851803"
Figure legend: "2D gel analysis of fork progression in wild type and rad9∆ cells through a 70-kb region of chromosome VI for which all active origins downstream of ARS607 have been deleted. The position of probes and the time after release from HU are indicated. Arrows point to Y arcs (fork signals) with the strongest intensity."
NCBI gene IDs:
"rad9: 851803"
Figure legend: "Distribution of BrdU tracks length in wild type, mrc1∆ and mrc1AQ cells. DNA fibers are fully labeled in the case of rad9∆ cells. Median values are indicated in red and correspond to the analysis of at least 150 tracks from two biological replicates. ns: non-significant Mann-Whitney rank sum test."
NCBI gene IDs:
"mrc1: 850297
rad9: 851803"
Figure legend: "Analysis of chromosome mobility by Pulse Field Gel Electrophoresis (PFGE) after staining of DNA with ethidium bromide. In G1, the chromosomes are linear and are sorted according to their length. Upon entry into S phase (30 min), they cannot enter the gel due to the presence of replication intermediates. Quantitation of chromosomes re-entering the gel shows completion of DNA replication in 40% of rad9∆, rad53-11 and rad9∆ rad53-11 mutants, but not in wild type cells and mrc1 mutants as determined for a representative experiment. Error bars indicate SD between the signal intensity determined for the three larger chromosomes (arrowheads)."
NCBI gene IDs:
"mrc1: 850297
rad53: 855950
rad9: 851803"
Figure legend: "Length distribution of BrdU tracks measured at that time for wild type, rad9∆, rad53-11 and rad53-11 rad9∆ cells. Median lengths are indicated in red. For each sample, at least 200 tracks were measured from two biological replicates."
NCBI gene IDs:
"rad53: 855950
rad9: 851803"
Figure legend: "B Gene expression analysis by RT-qPCR for naive (KLF17, TFCP2L1, and NANOG) and trophoblast  (GATA3, GATA2, KRT7, ELF5, TP63, and TFAP2A) marker genes in naive-iPSCs  and TSC  cells derived from two different naive-iPSC  lines (HPD06  and H9)."
NCBI gene IDs:
"ELF5: 2001
GATA2: 2624
GATA3: 2625
KLF17: 128209
KRT7: 3855
NANOG: 79923
TFAP2A: 7020
TFCP2L1: 29842
TP63: 8626"
Figure legend: "F Barplots showing the absolute expression as log(CPM+1) of ADAP2, HAVCR1, SLC28A3, ARID5B, and GATA2  in the reported conditions. Data information: (F) Bars indicate the mean ± SEM of at least n=5 biological replicates from at least 2 independent studies shown with different symbols. ***P &lt; 0.001, ns no significance (Student's t-test)."
NCBI gene IDs:
"ADAP2: 55803
ARID5B: 84159
GATA2: 2624
HAVCR1: 26762
SLC28A3: 64078"
Figure legend: "D Barplots showing the absolute expression  as log(CPM+1) of general pluripotency (OCT4  and NANOG), naive (SUSD2), and TSC-specific genes (GATA2, GATA3, KRT7, and ADAP2) in the reported conditions highlighted in different colours. Data information: (D) Dots indicate biological replicates and bars indicate the mean ± SEM of n=3 biological replicates."
NCBI gene IDs:
"ADAP2: 55803
GATA2: 2624
GATA3: 2625
KRT7: 3855
NANOG: 79923
OCT4: 5460
SUSD2: 56241"
Figure legend: "(D) Enrichment of control-sgRNA (n=5) and Slf2-sgRNA (n=6) transduced HSPCs over time."
NCBI gene IDs:
"Slf2: 226151"
Figure legend: "(E) Kaplan-Meier curves of overall survival of mice transplanted with Eµ-myc;Rosa26Cas9 HSPCs transduced with control-sgRNA (n=15) or sgRNA targeting Slf2 (n=6). p &lt; 0.0001, log-rank (Mantel-Cox) test."
NCBI gene IDs:
"myc: 
Cas9: 69900935
Rosa26: 14910
Slf2: 226151"
Figure legend: "(F) Immunohistochemical analysis of Slf2-sgRNA lymphomas described in Figure 2E. Representative example of three analyzed Slf2-sgRNA lymphomas."
NCBI gene IDs:
"Slf2: 226151"
Figure legend: "(B, C) Kaplan-Meier overall survival curves of the indicated cohorts of DLBCL patients (Lenz, NEJM). DLBCL patients were classified according to SLF2 or SLF1 mRNA expression. P-value was determined by log-rank (Mantel-Cox) test."
NCBI gene IDs:
"SLF1: 84250
SLF2: 55719"
Figure legend: "(E) Mafosphamide dose-response curves of SLF2KO and control SU-DHL-5 cells. Cells were treated with mafosphamide (MAF; 0, 31.25, 62.5, 125, 250, 500, 1000, 2000, 4000 ng/ml) for 48 hours and viability was determined by DAPI staining and flow cytometry measurement. Error bars represent SD from three independent experiments."
NCBI gene IDs:
"SLF2: 55719"
Figure legend: "(A) Immunoblot analysis of U-2-OS cells following CRISPR/Cas9 mediated knockout of SLF2 upon DRB treatment (0.5 µM) for indicated times with the indicated antibodies."
NCBI gene IDs:
"CRISPR: 
Cas9: 69900935
SLF2: 55719"
Figure legend: "(E) Immunoblot analysis of human SU-DHL-5 control and SLF2KO cell lines upon DRB treatment (0.5 µM) for indicated time points with the indicated antibodies."
NCBI gene IDs:
"SLF2: 55719"
Figure legend: "(A) TMT-based MS results of chromatin fractions from SU-DHL-5 control and SU-DHL-5 SLF2KO cells. Volcano plot depicting depleted chromatin-associated proteins. Significant hits are shown by red dots (depleted in SLF2KO cells). Proteins belonging to the DDR and cell cycle regulation are labeled. Experiments were performed in triplicates."
NCBI gene IDs:
"SLF2: 55719"
Figure legend: "(E) Immunoblot analysis of human SU-DHL-5 control and SLF2KO whole cell fractions with the indicated antibodies. (F) Immunoblot analysis of human chromatin fractions of SU-DHL-5 control and SLF2KO cell lines with the indicated antibodies."
NCBI gene IDs:
"SLF2: 55719"
Figure legend: "(E) SUMO inhibitor (SUMOi (ML-093); 0, 6.25, 12.5, 25, 50, 100, 200, 400, 800 nM) dose response curves of SLF2KO and control SU-DHL-5 cells. Cells were treated with increasing concentrations of SUMOi for 72 hours and viability was determined by negative DAPI staining and flow cytometry measurement. Error bars represent SD from three independent experiments."
NCBI gene IDs:
"SLF2: 55719"
Figure legend: "(F) Quantification of flow cytometry results for DAPI and Annexin V staining in human SLF2KO and control SU-DHL-5 cells after 12.5 nM of SUMOi treatment for 72 hours. P-value determined by unpaired t-test. Error bars represent SD from three independent experiments."
NCBI gene IDs:
"SLF2: 55719"
Figure legend: "(B) Immunoblot analysis of human SU-DHL-5 control and CLSPNKO cell lines upon DRB treatment (0.5µM) for indicated time points with the indicated antibodies."
NCBI gene IDs:
"CLSPN: 63967"
Figure legend: "(F) SUMO inhibitor (SUMOi, TAK981; 0, 6.25, 12.5, 25, 50, 100, 200, 400, 800 nM) dose-response curves of CLSPNKO and control SU-DHL-5 cells. Cells were treated with increasing concentrations of SUMOi for 72 hours and viability was determined by negative of DAPI staining and flow cytometry measurement. Error bars represent SD from three independent experiments. (G) Mafosphamide dose-response curves of CLSPNKO and control SU-DHL-5 cells. Cells were treated with mafosphamide (MAF; 0, 31.25, 62.5, 125, 250, 500, 1000, 2000, 4000 ng/ml) for 48 hours and viability was determined by negative of DAPI staining and flow cytometry measurement. Error bars represent SD from three independent experiments."
NCBI gene IDs:
"CLSPN: 63967"
Figure legend: "(G) Quantification of cell viability measured by celltiterGlo from primary murine Eµ-Myc lymphoma derived cells co-treated with indicated concentrations of SUMOi and Rabusertib for 72 hours. Bar plots represent cell viability relative to the DMSO treated control cells. Error bars represent SD from three independent experiments. P-value was determined by ANOVA test; Tukey's post hoc test."
NCBI gene IDs:
"Myc: "
Figure legend: "(A) Pearson correlation between ZEB1 and MITF mRNA expression in 61 melanomacell lines available through the CCLE."
NCBI gene IDs:
"MITF: 4286
ZEB1: 6935"
Figure legend: "(B) ZEB1, ZEB2, TWIST1 and MITF expression in a panel of BRAFV600-mutated melanomacells assessed by Western blot. GLO and C-09.10cells are patient-derived short-term cultures. Actin was used as a loading control."
NCBI gene IDs:
"BRAF: 673"
Figure legend: "(C) Quantitative PCR analyses of ZEB1, ZEB2, TWIST1and MITF in the same panel of cell lines. mRNA expression levels are represented relatively to C-09.10 cells, in which the levels were arbitrarily fixed at 1 (n=3, mean ± SD). The dotted line separates ZEB1high (left) and ZEB1low (right) cell lines."
NCBI gene IDs:
"MITF: 4286
ZEB1: 6935"
Figure legend: "(D) Tukey box plot of ZEB1, ZEB2, TWIST1, and MITF mRNA expression according to the IC50 of the drug (µM) administered (BRAFi/MEKi), in melanoma cell lines from the CCLE (n=28) (Student's t-Test). High ZEB1, low ZEB2, and low MITF expression levels were correlated with BRAFi (PLX4720) and MEKi (AZD6244) resistance. PLX4720 is an analog of PLX4032."
NCBI gene IDs:
"MITF: 4286
TWIST1: 7291
ZEB1: 6935
ZEB2: 9839"
Figure legend: "(E) IC50 values of PLX4032 (µM) in the panel of BRAFV600 melanoma cells as determined by ATP assay (n=3, mean ± SD). For SKMEL24 and WM793, IC50 was &gt;8µM."
NCBI gene IDs:
"BRAF: 673"
Figure legend: "(A) Pearson correlation between ZEB1 and MITF mRNA expression levels in 467 melanomatumors from TCGA data set."
NCBI gene IDs:
"MITF: 4286
ZEB1: 6935"
Figure legend: "(C) Representative pictures of ZEB1 immunostaining in BRAFV600 tumors from patients, classified in ZEB1 high, int and low subgroups, based on the intensity of ZEB1 staining and on the percentage of cells positive for ZEB1. Scale bar = 80 µm. (D) Pie charts representing the distribution of ZEB1 alone (upper part), or ZEB1 and TWIST1 (lower part) immunohistochemistry staining in tumors according to their initial response to vemurafenib +/- cobimetinib treatment. ZEB1 +/- TWIST1 levels are higher in MAPKi primary resistant melanomas (initial non-responders) compared to tumors that initially respond to treatment (n=70, Fisher's exact test)."
NCBI gene IDs:
"BRAF: 673"
Figure legend: "(C) Quantitative PCR analyses of ZEB1and MITF in A375-R and SKMEL5-Rversus the parental naive cells, and in GOKA and ESP cells. mRNA expression levels are represented as arbitrary units (a.u). Statistical difference relative to sensitive A375 cells is shown (n=3, mean ± SD, Student's t-test)."
NCBI gene IDs:
"MITF: 4286
ZEB1: 6935"
Figure legend: "(A) A375 cells were infected with retroviruses expressing ZEB1. Western blot analyses of ZEB1 and p75. GAPDH was used as a loading control."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(B) Quantitative PCR analyses of MITF, p75, ABCB5 and JARID1B upon ZEB1 expression. mRNA expression levels are represented relatively to control cells, in which the levels were fixed at 1 (mean ± SD, n=3, Student's t-test)."
NCBI gene IDs:
"ABCB5: 340273
JARID1B: 10765
MITF: 4286
p75: 4804
ZEB1: 6935"
Figure legend: "(C) Soft agar colony formation assay upon ZEB1 expression. Scale bar = 200 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(D) 2 x 106 Control or ZEB1-overexpressing A375 cells were injected subcutaneously into nude mice. The mean tumor volume for 5 mice is represented ± SEM (Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(E) Western blot analyses of ZEB1, MITF, P-ERK, and TWIST1 levels in control or ZEB1-expressing cells +/- 150 nM PLX4032 treatment for 24 h. GAPDH was used as a loading control."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(F) FACS analyses of p75 cell surface expression upon ZEB1 overexpression, after 10 days treatment with or without 150 nM PLX4032. Bar chart representing the mean percentage of p75-high, int and low cells from 2 independent experiments (Fisher's Exact Test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(G) Control or ZEB1-overexpressing A375 cells were transfected with control or p75-siRNA. p75 and MITF expression levels were was analyzed by quantitative PCR after 48 h. mRNA expression levels are represented relatively to control cells transfected with siRNA Control, in which the levels were fixed at 1 (mean ± SD, n=2)."
NCBI gene IDs:
"MITF: 4286
p75: 4804
ZEB1: 6935"
Figure legend: "(H) Clonogenic assay +/- PLX4032 (150 nM), +/- GDC-0973 (5 nM) treatment for 10 days. The graphs represent the mean number of colonies (± SD) in 3 independent experiments (Student's t-test). (I) Number of weeks of chronic exposure to PLX4032 before emergence of resistance in control or ZEB1-expressing cells (n=3, Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(A) C-09.10 short-term culture cells were infected with retroviruses expressing ZEB1. Western blot analyses of ZEB1 and p75. GAPDH was used as a loading control."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(B) Quantitative PCR analyses of MITF and p75 upon ZEB1 expression. mRNA expression levels are represented relatively to control cells (mean ± SD, n=3, Student's t-test)."
NCBI gene IDs:
"MITF: 4286
p75: 4804
ZEB1: 6935"
Figure legend: "(C) Soft agar colony formation assay following ZEB1 expression. Scale bar = 200 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(D) FACS analyses of p75 cell surface expression upon ZEB1 overexpression. Bar chart representing the mean percentage of p75-high, int, low and negative cells from 2 independent experiments (Fisher's exact test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(A) A375 cells were infected with retroviruses expressing a control or ZEB1-shRNA. Western blot analyses of ZEB1 and p75 upon ZEB1 knock-down. GAPDH was used as a loading control. High and low exposures (exp) for p75 are shown."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(B) Quantitative PCR analyses of MITF, p75, ABCB5 and JARID1B upon ZEB1 knock-down. mRNA expression levels are represented relatively to shRNA control cells (mean ± SD, n=3, Student's t-test)."
NCBI gene IDs:
"ABCB5: 340273
JARID1B: 10765
MITF: 4286
p75: 4804
ZEB1: 6935"
Figure legend: "(C) FACS analyses of p75 expression upon ZEB1 knock-down. Bar chart representing the mean percentage of p75-high, int and low cells from 2 independent experiments (Fisher's exact test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(D) Soft agar colony formation assay upon ZEB1 knock-down. Scale bar = 200 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(E) 2 x 106 Control or ZEB1-shRNA A375 cells were injected subcutaneously into nude mice. The mean tumor volume for 5 mice is represented (± SEM). (Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(F) A375 cells were infected with an IPTG-inducible ZEB1-shRNA. Left panel: Western blot analyses of ZEB1 expression ± IPTG (100µM) treatment for 6 days. Actin was used as a loading control. Right panel: 2 x 106 IPTG-inducible shRNA-Control or shRNA-ZEB1A375 cells were injected subcutaneously into nude mice. When the tumor reached 5 mm in diameter, ZEB1 expression was silenced by adding IPTG (10 mM) into the drinking water for 20 days. The mean tumor volume for 5 mice is represented (± SEM). (Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(G) SKMEL5 cells expressing an IPTG-inducible ZEB1-shRNA were treated with IPTG (100µM) for 10 days (+IPTG), then IPTG was removed (-IPTG) and ZEB1, MITF and p75 expression levels were analyzed by Western blot and/or quantitative PCR analyses. GAPDH was used as a protein loading control, mRNA expression levels are represented relatively to untreated cells, in which the levels were fixed at 1 (mean ± SD, n=2)."
NCBI gene IDs:
"MITF: 4286
p75: 4804
ZEB1: 6935"
Figure legend: "(A) Western blot analyses of ZEB1 and P-ERK in shRNA-control or shRNA-ZEB1-expressing A375 cells +/- 150 nM PLX4032 treatment for 24 h. GAPDH was used as a loading control."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(B) Soft agar colony formation assay in A375 cells in the presence or absence of PLX4032 (150 nM). Scale bar = 100 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student's t-test). (C) Number of weeks of chronic exposure to PLX4032 before emergence of resistance in control or shRNA-ZEB1-expressing cells (n=3, Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(D) RPMI7951, A375-R and SKMEL5-R were infected with a retrovirus encoding a constitutive shRNA-ZEB1. Short-term cultures of GOKA and ESP cells, derived from vemurafenib-resistant patients, were infected with a lentivirus encoding an IPTG-inducible shRNA-ZEB1. Western blot analyses showing efficient ZEB1 knock-down in the different models, ±IPTG (200µM), ±PLX4032 (3µM) as indicated. Induction of cell death was assessed by PARP cleavage. GAPDH or actin were used as loading control."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(F) Western blot analyses of ZEB1, p75 and quantitative PCR analyses of MITF in shRNA-Control or shRNA-ZEB1ESPvemurafenib-resistant patient-derived short-term culture cells. Actin was used as a loading control. mRNA expression levels are represented relatively to control cells (mean ± SD, n=3, Student's t-test)."
NCBI gene IDs:
"MITF: 4286
ZEB1: 6935"
Figure legend: "(G) 2,5 x 106 shRNA-Control or shRNA-ZEB1ESPvemurafenib-resistant cells were injected subcutaneously in nude mice. When the tumor reached 5 mm in diameter, ZEB1 expression was silenced by providing mice with IPTG (10 mM) in their drinking water and orally administering vemurafenib (50 mg/kg) daily for 4 weeks. The mean tumor volume for 5 mice is represented (± SEM). (Student's t-test)."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "(H) Upper part: Western blot analyses of ZEB1 in shRNA-Control (1 to 4) or shRNA-ZEB1 (5 to 8) ESPxenografttumors, showing efficient ZEB1 knock-down directly in the tumors, after IPTG ±PLX4032 treatment in vivo. Lower part: Representative pictures of ZEB1 immunostaining in shRNA-Control or shRNA-ZEB1tumors, after IPTG treatment in vivo. Scale bar = 40µm."
NCBI gene IDs:
"ZEB1: 6935"
Figure legend: "UCSC genome browser tracks with examples of IL-2 pDHSs within the Locus Control Region (LCR) within the Rad50 gene which controls the Th2 cytokines Il13, Il4 and Il5, plus IL-2 pDHSs within the Tnfrsf9 and Cish loci. IL-2 pDHSs are highlighted with blue boxes."
NCBI gene IDs:
"Cish: 12700
Il13: 16163
Il4: 16189
Il5: 16191
Rad50: 19360
Tnfrsf9: 21942"
Figure legend: "Jund mRNA levels in TB IL-2 and TB IL-2nil. Standard deviation is shown from the mean of 3 samples. P-values were calculated from the RNA-seq data using Limma with Benjamini-Hochberg correction for multiple testing."
NCBI gene IDs:
"Jund: 16478"
Figure legend: "UCSC genome browser tracks at the Il13/Il4/Il5 Th2 cytokine locus LCR (indicated by the grey box within the Rad50 gene), Gzmb and Il24 showing DNase-Seq and ChIP-Seq for STAT5 and JUND in TB IL-2 and TB IL-2nil. Replicate JUND and STAT5 ChIP-Seq tracks are shown for TB IL-2."
NCBI gene IDs:
"Gzmb: 14939
Il13: 16163
Il24: 93672
Il4: 16189
Il5: 16191
Rad50: 19360"
Figure legend: "Examples of IL-2 iDHSs which are proximal to IL-2 pDHSs at the Csf2/Il2 and Il10 loci. IL-2 iDHSs are highlighted in red and IL-2 pDHSs in blue."
NCBI gene IDs:
"Csf2: 1437
Il10: 16153
Il2: 16183"
Figure legend: "UCSC genome browser tracks showing DNase-seq and RNA-seq at the Socs1 (E) and Sell loci (F)."
NCBI gene IDs:
"Sell: 20343
Socs1: 12703"
Figure legend: "UCSC genome browser tracks showing DNase-Seq and RNA-Seq at the IL-2 regulated genes Csf2/Il3 and at the LCR within the Rad50 gene (grey box) which controls the Th2 cytokines Il13, Il4 and Il5. IL-2 pDHSs are highlighted in blue and IL-2 iDHSs in red."
NCBI gene IDs:
"Csf2: 12981
Il13: 16163
Il3: 16187
Il4: 16189
Il5: 16191
Rad50: 19360"
Figure legend: "UCSC genome browser tracks with DNase-Seq data for TB IL-7 and TB IL-7nil showing examples of IL-2 pDHSs within the Locus Control Region (LCR) within the Rad50 gene which controls the Th2 cytokines Il13, Il4 and Il5, plus IL-2 pDHSs within the Tnfrsf9 and Cish loci (C) IL-2 pDHSs are highlighted with blue boxes."
NCBI gene IDs:
"Cish: 12700
Il13: 16163
IL-2: 16183
Il4: 16189
Il5: 16191
Rad50: 19360
Tnfrsf9: 21942"
Figure legend: "UCSC genome browser tracks with DNase-Seq data for TB IL-7 and TB IL-7nil showing examples of IL-2 pDHSs within the Locus Control Region (LCR) within the non-primed control regions from the CD3 gene cluster and the Tbp locus (D). IL-2 pDHSs are highlighted with blue boxes."
NCBI gene IDs:
"CD3: 12501
Tbp: 21374"
Figure legend: "Flow cytometric analysis of IL-7Rα expression by 2W1S-specific CD44hi CD4 T cells in the presence or absence of cre recombinase."
NCBI gene IDs:
"cre recombinase: 2777477"
Figure legend: "Average number of 2W1S-specific cells recovered/mouse after sorting 3 replicate samples of Il7rf/f compared to CD4creERT2 x Il7rf/f . Errors bars indicate the standard deviation."
NCBI gene IDs:
"CD4: 12504
cre: 2777477
ERT2: 2099
Il7r: 16197"
Figure legend: "UCSC genome browser tracks at loci with IL-2 pDHSs showing replicate ATAC-Seq samples for CD4creERT2 x Il7rf/f memory T cells, Il7rf/f control memory T cells, replicate DNase-Seq samples for TB IL-2 and TB IL-2nil and TB IL-2 and TB IL‑2nil STAT5 ChIP-Seq samples. The grey boxes signify IL-2 pDHSs which diminish after disruption of the Il7r gene."
NCBI gene IDs:
"CD4: 12504
cre: 2777477
ERT2: 2099
Il7r: 16197"
Figure legend: "UCSC genome browser tracks showing ChIP-Seq and DNase-Seq at the LCR within the Rad50 gene which controls the Il4/Il13/Il5 Th2 cytokine locus, and also Il17a, Il12rb2 and Tbx21. The grey boxes indicate IL-2 pDHSs which bind STAT5 in Th0 cells and other STAT proteins in other T cell lineages."
NCBI gene IDs:
"Il12rb2: 16162
Il13: 16163
Il17a: 16171
IL-2: 16183
Il4: 16189
Il5: 16191
Rad50: 19360
Tbx21: 57765"
Figure legend: "mRNA expression levels of JUN family transcription factors. Normalised TPM is shown for TB IL-2, TB IL2nil, TB+ IL-2 and TB+ IL-2nil. Standard deviation is shown for 3 replicates."
NCBI gene IDs:
"JUN: 16476"
Figure legend: "Average JUND ChIP-Seq signal at the 1000 IL-2 pDHSs in Junb+/+CD4Cre (Junb WT) and Junbf/fCD4Cre (Junb KO) Th17 cells."
NCBI gene IDs:
"CD4: 12504
Cre: 2777477
Junb: 16477"