EMBO/SourceData huggingface dataset:
Figure legend: "E: (Left) Luciferase activity of human NF-kB promoter was measured in Kms27 MM  cells transiently transfected with siChe-1A  or siControl oligonucleotides or with empty vector or p65/RelA   protein expressing vector. Error bars represent the standard error of three different biological experiments performed in duplicate (Two Tailed T test ***P&lt;0.005, ****P&lt;0.001). (Right) WB  analysis of total extracts of Kms27 MM  cells transiently transfected as described in E and incubated with the indicated antibodies."
NCBI gene IDs:
"Che-1A: 26574
NF-kB: 4791///4790
p65: 5970
RelA: 5970"
Figure legend: "RT-qPCR  analysis of the levels of the indicated genes in Kms27 MM  cells transiently transfected with siChe-1A or siControl. Values were normalized to Actin  expression. Error bars represent the standard error of three different experiments in duplicate (Two Tailed T test ***P&lt;0.001, ****P&lt;0.001)."
NCBI gene IDs:
"Che-1A: 26574
Actin: 60"
Figure legend: "G: RT-qPCR analysis of the levels of the indicated genes in Kms27 MM cells transiently transfected with siChe-1A or siControl. Values were normalized to Actin  expression. Error bars represent the standard error of three different experiments in duplicate (Two Tailed T test ***P&lt;0.001, ****P&lt;0.001)."
NCBI gene IDs:
"Che-1A: 26574
Actin: 60"
Figure legend: "H: WB  analysis for the indicated antibodies of total extracts from Kms27 MM  cells with siChe-1A or siControl and where indicated with GFP-tagged RNaseH  expression vectors."
NCBI gene IDs:
"GFP: 
Che-1A: 26574
RNaseH: 6050"
Figure legend: "I: RT-qPCR analysis of IFNB  and IFNG  levels in Kms27 MM  cells transiently transfected as in H. Values were normalized to Actin  expression. Error bars represent the standard error of three different biological experiments performed in duplicate (Two Tailed T test **P&lt;0.01, ***P&lt;0.005.)"
NCBI gene IDs:
"Actin: 60
IFNB: 3456
IFNG: 3458"
Figure legend: "C: Different expression   of IFNG  and IFNB  in Kms27  and U266 MM  cells was assessed by RT-qPCR. Values were normalized to Actin  expression. Error bars represent the standard error of three different biological experiments performed in duplicate (Two Tailed T test ***P&lt;0.005)."
NCBI gene IDs:
"Actin: 60
IFNB: 3456
IFNG: 3458"
Figure legend: "F: RT-qPCR analysis of IFNG  and IFNB  in U266 MM  cells treated or not with THAP. Values were normalized to Actin  expression. Error bars represent the standard error of three different biological experiments performed in duplicate (Two Tailed T test ***P&lt;0.005, ****P&lt;0.001) I:  RT-qPCR  analysis of IFNG  and IFNB  levels in Kms27 MM  cells treated as in G. Values were normalized to Actin  expression. Error bars represent the standard error of three different biological experiments performed in duplicate (Two Tailed T test ****P&lt;0.001)."
NCBI gene IDs:
"Actin: 60
IFNB: 3456
IFNG: 3458"
Figure legend: "(C) Dose-dependent antiviral activity of nirmatrelvir in HEK293T-hACE2 cells infected with SARS-CoV-2 D614G (purple symbols), B.1.617.2 (green symbols) or B.1.1.529 (blue symbols). Antiviral activity was determined as percent inhibition of the virus-induced cytopathic effect."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "A Tissue distribution of RIPK2 determined by anti-FLAG immunoprecipitation. Organ homogenates from WT (wild-type) and KI (homozygous FLAG-RIPK2) mice were subjected to anti-FLAG immunoprecipitation and immunoblotting."
NCBI gene IDs:
"FLAG: 
RIPK2: 192656"
Figure legend: "B Inflammatory signaling in wild-type (WT/WT), RIPK2 CRISPR KO (KO/KO) and FLAG-RIPK2 heterozygous (WT/KI) and homozygous (KI/KI) BMDMs. BMDMs were primed with IFNy, stimulated with MDP for indicated times and analysed by immunoblotting."
NCBI gene IDs:
"FLAG: 
RIPK2: 192656"
Figure legend: "C Cytokine production of RIPK2 CRISPR KO (KO), wild-type (WT) and FLAG-RIPK2 heterozygous (WT/KI) and homozygous (KI/KI) BMDMs in response to MDP. BMDMs were left untreated or treated with IFNy or IFNy and MDP over-night and cytokines were measured by ELISA. N = 5-8 mice. Shown is average ± SEM. ns = P &gt; 0.05; ** = P ≤ 0.01; **** = P ≤ 0.0001; two-way ANOVA."
NCBI gene IDs:
"FLAG: 
RIPK2: 192656"
Figure legend: "D Serum cytokines in RIPK2 CRISPR KO (KO), wild-type (WT) and FLAG-RIPK2 heterozygous (WT/KI) or homozygous (KI/KI) mice after i.p. MDP administration. Mice were injected i.p. with PBS or MDP, sacrificed after 4h and serum cytokines were measured by ELISA. N = 3-6 mice. Shown is average ± SEM. ns = P &gt; 0.05; ** = P ≤ 0.01; two-way ANOVA."
NCBI gene IDs:
"FLAG: 
RIPK2: 192656"
Figure legend: "A Two step enrichment to isolate ubiquitinated RIPK2 from BMDMs. Protein lysates from FLAG-RIPK2 BMDMs (A) were sequentially subjected to ubiquitin enrichment (UBA, B) and FLAG pulldown (C) prior to protein elution and subsequent mass spectrometry analysis."
NCBI gene IDs:
"FLAG: 
RIPK2: 192656"
Figure legend: "A Activation of the NF-κB pathway by RIPK2 Lysine- and phosphosite mutants. RIPK2-deficient THP-1 cells reconstituted with wild-type RIPK2 or RIPK2 mutants were stimulated with L18-MDP, harvested at indicated time points and activation of the NF-κB pathway was analyzed by immunoblotting."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "B IL-8 production of wild-type THP-1 and RIPK2-deficient THP-1 cells reconstituted with wild-type RIPK2 or RIPK2 mutants and stimulated with L18-MDP was assessed by ELISA. N = 4-8 experiments. Shown is average ± SEM. * = P ≤ 0.05; two-way ANOVA."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "C) RIPK2 ubiquitination determined by UBA pulldown in RIPK2-deficient cells reconstituted with wild-type or mutant RIPK2 after stimulation with L18-MDP."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "D) Detection of K63- and M1-linked ubiquitin chains by UBA pulldown or pulldown with ubiquitin chain type-specific antibodies in RIPK2-deficient cells reconstituted with RIPK2 K209R after stimulation with L18-MDP."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "C Activation of the NF-κB pathway by RIPK2 pocket mutants. RIPK2-deficient THP-1 cells were reconstituted with wild-type RIPK2 or RIPK2 mutants, stimulated with L18-MDP, harvested at indicated time points and analyzed by immunoblotting. ­"
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "D IL-8 production of RIPK2-deficient THP-1cells reconstituted with wild-type RIPK2 or RIPK2 mutants and stimulated with L18-MDP was assessed by ELISA. N = 3-8 experiments. Shown is average ± SEM. ns = P &gt; 0.05; * = P ≤ 0.05; *** = P ≤ 0.001; **** = P ≤ 0.0001; two-way ANOVA."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "E Ubiquitination of RIPK2 pocket mutants. RIPK2-deficient THP-1 cells were reconstituted with wild-type or mutant RIPK2, left unstimulated or stimulated with L18-MDP and subjected to UBA pulldown and immunoblotting."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "A: Thermal stability assay using selected RIPK2 mutants. THP-1 cells expressing RIPK2 were subjected to heat treatment and the non-denatured fraction was analysed by immunoblotting."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "B: Binding of RIPK2 to XIAP-BIR2. Lysates from RIPK2-deficient THP-1 cells reconstituted with WT or mutant RIPK2 were subjected to pulldown experiments with recombinantly expressed XIAP-BIR2 and analysed by immunoblotting."
NCBI gene IDs:
"RIPK2: 8767
XIAP: 331"
Figure legend: "(A,B) Representative immunofluorescence microscopy images of the distribution of septin 7 (red), Cdc42 (red) and tubulin (green) in LT-HSCs from borg4fl/fl or borg4∆/∆ mice. Nuclei were stained with DAPI (blue), scale bar= 5 µm. (C) Percentage of cells with a polar distribution of septin 7, Cdc42 or tubulin in borg4fl/fl or borg4∆/∆ LT-HSCs. At least 3 biological repeats, at least 50 cells were scored per sample. Error bars indicate mean±SEM, Two-way ANOVA analysis, ***P&lt;0.001, **P&lt;0.01, *P&lt;0.05. "
NCBI gene IDs:
"borg4: 56699"
Figure legend: "(D,E) Representative immunofluorescence microscopy images of the distribution of borg4 (red), Cdc42 (red) or tubulin (green) in LT-HSCs from septin 7fl/fl or septin 7∆/∆ mice. Nuclei were stained with DAPI (blue). scale bar= 5 µm. (F) Percentage of cells with a polar distribution of borg4, Cdc42 or tubulin in septin 7fl/fl or septin 7∆/∆ LT-HSCs. At least 3 biological repeats, at least 30 to 50 cells were scored per sample. Error bars indicate mean±SEM, Two-way ANOVA analysis, **P&lt;0.01, *P&lt;0.05. "
NCBI gene IDs:
"septin 7: 235072"
Figure legend: "(J-O) Percentage of donor derived (borg4fl/fl or borg4∆/∆ or septin 7fl/fl or septin 7∆/∆) B-cells (B220 positive cells), T-cells (CD3 positive cells) and myeloid cells (Mac-1+ or Gr+ positive cells) among BM cells, percentage of donor derived LT-HSCs, ST-HSCs and LMPPs in LSK cells and percentage of donor derived CLPs in lin-Sca1C-kit low cells in animals at post- transplantation (n=12). Error bars indicate mean±SD, ****P&lt;0.0001, **P&lt;0.01 and *P&lt;0.05, Two-way ANOVA analysis and 2 tailed unpaired t-test."
NCBI gene IDs:
"borg4: 56699
septin 7: 235072"
Figure legend: "(A) Percentage of single LT-HSCs from septin 7fl/fl of septin 7∆/∆ mice that completed first and second division up to 48 hours post initiation of culture. (192 sorted HSCs cells were analysed, error bars indicate mean±SD)."
NCBI gene IDs:
"septin 7: 235072"
Figure legend: "B Analysis of cell differentiation  (left) and proliferation  (right) in the intestine  after CDK8  deletion as in (A). Olfm4, Lysozyme, PAS  and Dclk1 staining  was used to reveal, respectively, stem, Paneth, goblet  and tuft cells. β-Catenin staining  allows detection of cancer cells (cytoplasmic  vs nuclear localisation). Cell proliferation was assessed by PCNA, Ki-67 and BrdU  (2h pulse) staining. Scatter plots represent the percentage of the area stained  by each antibody (relative to the area occupied by hematoxylin). For Paneth  cells, BrdU, PCNA   and Ki67, only crypts  were analysed. For  goblet  cells, crypts  and villi  were analysed. For Tuft cell quantification, Dclk1-positive cells were counted in 50 villi. Colour code depicts small intestine (green), proximal colon  (blue), and distant colon  (red). Mean ± SEM is shown. P-value of unpaired two-tailed t-test is indicated (ns, not significant; p &gt; 0.05). Scale bars, 25μm (Olfm4, Lysozyme, Dclk1  and  β-Catenin) and 50μm (PAS, BrdU,  Ki-67 and PCNA). (n=9 biological replicates)"
NCBI gene IDs:
"CDK8: 264064"
Figure legend: "C Analysis of mouse colon  after AOM/DSS  treatment. Quantification of the number of neoplastic lesions  (n = 10 for Cdk8+/+, and n = 7 for Cdk8 -/- mice). P-value of unpaired t-test is indicated: ns, not significant (p &gt; 0.05). Mean ± SD is shown."
NCBI gene IDs:
"Cdk8: 264064"
Figure legend: "A Genotyping  confirms the loss of Cdk8  exon 2 in Cdk8 -/- and Cdk8 -/-/Cdk19 -/- organoids after 7 days of OH-tamoxifen  treatment."
NCBI gene IDs:
"Cdk19: 78334
Cdk8: 264064"
Figure legend: "C Left, IHC staining  of WT and Cdk8 -/-/Cdk19 -/- organoids  with Olfm4  (stem cells), Lysozyme  (Paneth cells), Muc2  (goblet cells), and Dclk1  (tuft cells) antibodies. Scale bars, 50μm (Olfm4, Muc2, Dclk1) and 25μm (Lysozyme). Right, quantification of Olfm4, Lysozyme  and Muc2  positive area (% of the total organoid   area as indicated by hematoxylin staining; mean ± SEM), or the number of Dclk1  positive cells per organoid. P-value, unpaired two-tailed t-test: (***) p-value ≤ 0.001; ns, not significant (p &gt; 0.05). 20 different organoids  from 2 biological replicates of each genotype were used for the analysis."
NCBI gene IDs:
"Cdk19: 78334
Cdk8: 264064"
Figure legend: "D WB  of indicated proteins extracted from Wt and Cdk8 -/-/Cdk19 -/- organoids. Included are CFTR  positive and negative control cell line samples obtained from the Cystic Fibrosis  Foundation (CFF). Amidoblack  was used as loading control."
NCBI gene IDs:
"Cdk19: 78334
Cdk8: 264064
CFTR: 12638"
Figure legend: "C Representative  phase contrast  images of organoids  at the indicated  time points  after 7 days of  OH-tamoxifen treatment are shown. Scale bar, 100 μm. D Quantification of the time  needed for mucus  release (observed as a dark staining  in the center of the organoid; mean ± SD are shown). Adjusted p-values of ordinary one-way Anova followed by Tukey's multiple comparison test are indicated: (***) p-value ≤ 0.001; ns: not significant (p &gt; 0.05); (n= 17 for Wt, 11 for Cdk8 -/-, 18 for Cdk19 -/-, and 12 for Cdk8 -/-/ Cdk19 -/- , all biological replicates)."
NCBI gene IDs:
"Cdk19: 78334
Cdk8: 264064"
Figure legend: "E Fluorescence confocal microscopy images of Calcein  green-labeled WT and Cdk8-/-/Cdk19-/- organoids  treated with forskolin. Scale bars, 100 μm. F Quantification of forskolin-induced swelling  in WT organoids  treated for 1hour or 24 hours with 0.1μM, 1μM or 10μM Senexin B  (SenB), as indicated, or double KO organoids; DMSO  vehicle was used as control. The surface area of individual organoids  at different time points relative to the area at t = 0 (100%) was measured (mean ± SD, n=8 biological replicates). Linear regression lines are shown."
NCBI gene IDs:
"Cdk19: 78334
Cdk8: 264064"
Figure legend: "H WB  of indicated proteins extracted from Senexin B-treated (10μM, 2h and 24h) organoids  (left), and WT and Cdk8 -/-/ Cdk19 -/- organoids  (right). Amidoblack  was used as loading control."
NCBI gene IDs:
"Cdk19: 78334
Cdk8: 264064"
Figure legend: "I. SRE-luciferase reporter activity analysis of GICs treated with prazosin in absence or presence of U0126 (10 μM), an inhibitor of the ERK-activating kinase MEK. U0126 prevented prazosin-induced SRE-luciferase activation in GICs."
NCBI gene IDs:
"luciferase: "
Figure legend: "G. Decreased PKCδ expression using shRNA counteracts prazosin-induced GIC death. Viability analysis of GICs transduced with scrambled or PKCδ shRNA and treated with prazosin for 72 h. *P &lt; 0.005 by two-tailed unpaired Student's t-test, n=4."
NCBI gene IDs:
"PKCδ: 5580"
Figure legend: "B. Bioluminescent in vivo images of tumors in mice grafted with GICs expressing either scrambled or PKCδ shRNA. All mice were treated with prazosin (PRZ) for 45 days.C. Quantification of the bioluminescent signals showing that decreased expression of PKC counteracts prazosin inhibition of tumor growth. Fold change in total flux represents the ratio: total flux after treatment/total flux prior treatment. *P=0.0007, n=8, two-sided Mann-Whitney U-test."
NCBI gene IDs:
"PKCδ: 5580"
Figure legend: "D. Relative quantities of  RNA  in the RNAchIP samples, detected by  RT-qPCR  with primers aligning on the intron1 of the Fosl1 gene as depicted in B (orange arrow). n=3 independent experiments. Data information: Histograms represent mean and s.d. Dots represent individual data points. P-values indicate significantly higher difference between  IP in HP1γ  and in KO cells (***P &lt; 0.001; two-tailed Student's t-test)."
NCBI gene IDs:
"HP1γ: 12417
Fosl1: 14283"
Figure legend: "F. Percentage of RNAchIP   peaks overlapping with indicated chromatin features in  MEF  samples from ENCODE database (green bars). Overlaps was evaluated by comparison with the list of merged peaks whose genomic location was randomized among genes with one hundred permutations (random, gray bars). Data information: Histograms represent mean and s.d. Dots represent individual data points. P-values indicate significantly higher difference between IP in HP1γ and in KO cells (***P &lt; 0.001; two-tailed Student's t-test). "
NCBI gene IDs:
"HP1γ: 12417"
Figure legend: "E. Left, representative example of a locus on the Ppp3ca  gene surrounding an RNAchIP merged peak, showing the RNAchIP read density as in Fig 1B. Red and orange arrowheads correspond to oriented  CACACA and  GAGAGA  motifs, respectively. Right, sequence of the RNA surrounding a CACACA motif highlighted in red, as well as a second a neighboring imperfect motif. The sequence was used to design a CACACA-containing RNA oligonucleotide probe (CACACA), compared to a control probe (no-CA) devoid of any related motif."
NCBI gene IDs:
"Ppp3ca: 19055"
Figure legend: "C. Box plot depicting the  length of exon junctions found differentially regulated by MAJIQ between HP1γ (green) and KO (orange) in three categories as in Fig EV5A, all classified differential HP1γ/KO junctions, annotated alternative exon junctions, non-annotated de novo cryptic junctions detected in KO only; n, differential events. Box boundaries represent 25th and 75th percentiles; center line represents median; whiskers indicate ±1.5×IQR; points are values of outliers. Data information: All graphes represent mean and s.d. (** P &lt; 0.005, ***P &lt; 0.001; two-tailed Student's t-test)."
NCBI gene IDs:
"HP1γ: 12417"
Figure legend: "D. RNAchIP  read density per kb on the indicated introns for input and  IP in samples from both untreated and  PMA stimulated cells, n=6 biological replicates, or 3-times randomized intervals, n=18 samples. Dots represent individual data points. HP1γ/KO introns are all 272 intronic intervals between exon junctions  differentially detected in HP1γ  and KO. Random introns are a matching library of random intronic intervals. E.  RNAchIP read density per kb on the genes corresponding to the introns tested in (D), and analyzed as in (D), n=6 biological replicates, or 3-times randomized intervals, n=18 samples. Data information: All graphes represent mean and s.d. (** P &lt; 0.005, ***P &lt; 0.001; two-tailed Student's t-test)."
NCBI gene IDs:
"HP1γ: 12417"
Figure legend: "B. RT-PCR analysis of the RNAs produced in the  splicing assay with the Prl3 wt or Prl3 CAmut constructs as depicted in A transfected into HP1γ or KO cell lines. The top 210bp and bottom 120bp amplicons correspond to the included form (beta globin with Prl  exon, more included in lane1, blue arrow, compared to lane 2), and the skipped form (beta globin exons only) of  RNA, respectively. Orange arrowheads, position of the HBGEX-F and HBGEX-R primers used in PCR analysis. C. Histogram showing the loss of inclusion of the Prl3 exon upon depletion of  HP1γ (in KO) relative to inclusion in the presence of HP1γ with the Prl3 wt (red) or Prl3 CA mut (grey) reporters. Based on the quantitation of 4 experiments as the one depicted in B. Values represent the fold change relative to HP1γ as a reference (dashed line). Graph represents mean and s.d. (*** P &lt; 0.001; two-tailed Student's t-test; n=4). "
NCBI gene IDs:
"HP1γ: 12417
beta globin: 3043
Prl3: 24683
Prl: 58937///53950///691552///266782///24282///24283"
Figure legend: "(A-B) Spinal cord sections from 5-month-old WT and Tmem106b-/- mice were stained with anti- neurofascin, anti- LAMP1 and anti-Cath D antibodies. Accumulation of LAMP1 and CathD positive vacuoles at the distal end of AIS was observed in Tmem106b-/- motor neurons. Representative images from three independent mice were shown. Scale bar = 10 µm. n=3. Data presented as mean ± SEM. Unpaired Student's t test. ****, p&lt;0.0001."
NCBI gene IDs:
"Tmem106b: 71900"
Figure legend: "(C-F) Western blot analysis of p62, ubiquitin (Ub), TDP-43 and p-TDP-43 in RIPA- and urea-soluble fractions from brain (C and E) and spinal cord (D and F) of 16-month-old WT and Tmem106b-/- mice. n=5. Data presented as mean ± SEM. Unpaired Student's t test. *, p&lt;0.05, ***, p&lt;0.001, ****, p&lt;0.0001."
NCBI gene IDs:
"Tmem106b: 71900"
Figure legend: "(A) Tmem106b-/-Grn-/- mice do not show any changes in body weight. Body weight of 5-month-old mice of indicated genotypes were measured and analyzed. n=6-10."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(B Tmem106b-/-Grn-/- mice show reduced activities in the open field test. 4.5-month-old mice were used in the study."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "C) Tmem106b-/-Grn-/- mice show reduced activities in the open field test. 4.5-month-old mice were used in the study. Total movement was quantified. n=8-10. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ****, p&lt;0.0001."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(D Tmem106b-/-Grn-/- mice show abnormal hindlimb clasping behavior. 5-month-old mice were used in the study."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "E) Tmem106b-/-Grn-/- mice show abnormal hindlimb clasping behavior. 5-month-old mice were used in the study. Severity score was quantified. n= 8-10. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p&lt;0.001, ****, p&lt;0.0001."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(A-D) Western blot analysis of NeuN, PSD95, SYN, GFAP, TMEM106B, PGRN and GAPDH in spinal cord (C5-C8) (A, B) and brain (C, D) lysates from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(C Increase in apoptosis in Grn-/- and Tmem106b-/-Grn-/- retina as indicated by TUNEL assay. TUNEL positive signals per section were quantified. Data information: ONL: outer nuclear layer; INL: Inner nuclear layer; OPL: outer plexiform layer; IPL: inner plexiform layer; GCL: ganglion cell layer."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "D) Increase in apoptosis in Grn-/- and Tmem106b-/-Grn-/- retina as indicated by TUNEL assay. TUNEL positive signals per section were quantified."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(E Increase in Müller glial activation in Tmem106b-/-Grn-/- retina as indicated by GFAP staining. GFAP intensity per section was quantified and normalized to WT control. Data information: ONL: outer nuclear layer; INL: Inner nuclear layer; OPL: outer plexiform layer; IPL: inner plexiform layer; GCL: ganglion cell layer."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "F) Increase in Müller glial activation in Tmem106b-/-Grn-/- retina as indicated by GFAP staining. GFAP intensity per section was quantified and normalized to WT control."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(G, H) Increase in microglia activation in Grn-/- and Tmem106b-/-Grn-/- retina as indicated by IBA1 staining. The number of IBA1 positive cells per section was quantified. Data information: ONL: outer nuclear layer; INL: Inner nuclear layer; OPL: outer plexiform layer; IPL: inner plexiform layer; GCL: ganglion cell layer."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(A Heatmap illustrating gene expression changes in WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- cortex samples isolated from 2.7-month-old mice. n=3. Genes with FDR p≤0.05, LogFC≥0.5 or ≤0.5 between WT and Tmem106b-/-Grn-/- groups are plotted based on hierarchical clustering analysis. Data information: Inflammation genes are highlighted in magenta and lysosomal genes are highlighted in blue."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "B) Heatmap illustrating gene expression changes in WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- spinal cord samples isolated from 2.7-month-old mice. n=3. Genes with FDR p≤0.05, LogFC≥0.5 or ≤0.5 between WT and Tmem106b-/-Grn-/- groups are plotted based on hierarchical clustering analysis. Data information: Inflammation genes are highlighted in magenta and lysosomal genes are highlighted in blue."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "(C) Heatmap illustrating gene expression changes in the inflammation and lysosome pathways in WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- spinal cord samples. Data information: Inflammation genes are highlighted in magenta and lysosomal genes are highlighted in blue."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "Western blot analysis of Galectin-3 and GPNMB in the spinal cord lysates from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p&lt;0.001, ****, p&lt;0.0001."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"
Figure legend: "Western blot analysis of Galectin-3 and GPNMB in the brain lysates from 5-month-old WT, Tmem106b-/-, Grn-/-, and Tmem106b-/-Grn-/- mice. n=3. Data presented as mean ± SEM. One-way ANOVA tests with Bonferroni's multiple comparisons: ***, p&lt;0.001, ****, p&lt;0.0001."
NCBI gene IDs:
"Grn: 14824
Tmem106b: 71900"