EMBO/SourceData huggingface dataset:
Figure legend: "G qPCR analysis of the expression levels of Pparg, Bglap and Acan in control or knockdown group (n=3 independent experiments). The statistical significance of differences was analyzed by one-way ANOVAs with Tukey's multiple comparison tests. Data represented Mean ± SD. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"Acan: 11595
Bglap: 12096
Pparg: 19016"
Figure legend: "F Immunostaining of Sca-1 on femur sections of 8-week-old Lepr-Cre; tdTomato mice. Arrows indicated Sca-1+ tdTomato+ cells inside cortical bones of the femur diaphysis. Arrowheads indicated Sca-1+ tdTomato+ cells in the femur periosteum. B: Bone. BM: Bone marrow. Peri: Periosteum. Scale bars were 100 µm."
NCBI gene IDs:
"tdTomato: 
Cre: 2777477
Lepr: 16847"
Figure legend: "G Representative flow cytometry plots of long bone periosteum in 8-week-old Lepr-Cre; tdTomato mice. The percentage of DAPI- CD45- Ter119- Tie2- tdTomato+ Sca-1+/- cells were shown."
NCBI gene IDs:
"tdTomato: 
Cre: 2777477
Lepr: 16847"
Figure legend: "A, B Representative oil red staining after 7 days of adipogenic differentiation in Lepr-Cre+ subsets (A) and qPCR analysis of Adipoq and Pparg expression (B) (n=3 independent experiments). Scale bars were 100 µm."
NCBI gene IDs:
"Adipoq: 11450
Cre: 2777477
Lepr: 16847
Pparg: 19016"
Figure legend: "C, D In vitro chondrogenic differentiation of sorted periosteal cells. Representative alcian blue staining after chondrogenic differentiation for 21 days and cryosection (C). Scale bars were 100 µm. Chondrogenic efficiencies were quantified by qPCR analysis of Acan and Col2a1 expression (D) (n=3 independent experiments)."
NCBI gene IDs:
"Acan: 11595
Col2a1: 12824"
Figure legend: "E, F In vitro osteogenic differentiation of sorted periosteal cells. Representative alizarin red staining after osteogenic differentiation for 14 days. Scale bars were 200 µm. Osteogenic efficiencies were quantified by qPCR analysis of Sp7 and Bglap expression (F) (n=3 independent experiments)."
NCBI gene IDs:
"Bglap: 12096
Sp7: 170574"
Figure legend: "C Upper panel: senescence curve  of a representative est2∆ clone. DNA samples were prepared at the indicated time points  to analyze telomere length (middle panel) and t-circles production (lower panel and graph) during  senescence and cell immortalization. Telomeres  were analyzed by  Southern blot  of the XhoI    cut DNA hybridized with a  TG1-3  probe. The presence of t-circles was monitored by RCA and analyzed by TG1-3 probed dot blot. The graph shows signal intensities of the dots measured with the Fiji software (arbitrary units). Similar results were obtained with at least 16 other est2∆ clones."
NCBI gene IDs:
"est2: 851028"
Figure legend: "A  Senescence curve of a representative  est2∆ clone and corresponding dot blot  of the  RCA  product hybridized with the indicated subtelomeric  or telomeric  probes.  t-circle  amounts were evaluated based on signal intensity of the dots and were expressed as fold increase over the signal in the absence of Φ29 (lower graph)."
NCBI gene IDs:
"est2: 851028"
Figure legend: "B Senescence  curve of a representative est2∆ clone (upper panel). DNA samples were prepared at the indicated  time points to analyze  telomere length by Southern blot (middle panel) and  t-circles production by  RCA assay performed in the absence of dCTP and dATP.(lower panel). The graph shows signal intensities of the dots measured with the Fiji software (arbitrary units)."
NCBI gene IDs:
"est2: 851028"
Figure legend: "D Quantification of the RCA   product after co-IP of the  C-circles with Nic96-RFP showing the effect of ADA2  deletion. Dot signal intensities were quantified using the Fiji software and were calculated as the percentage of INPUT that was  immunoprecipitated  normalized to est2∆ signals. Relative signals were calculated by setting the mean of est2∆ signals from each independent experiment to 1. Means and s.e.m. of the six independent  co-IPs experiments each with 2-6 clones per genotype are shown. Outliers were removed using ROUT robust outlier test. The p-values from one-way ANOVA were adjusted using the Bonferroni's correction for multiple comparisons. est2∆ versus est2∆ NIC96-RFP (p=0,000007),  est2∆ NIC96-RFP versus   est2∆ ada2∆ NIC96-RFP  (p=0,00012).***P&lt;0,0001."
NCBI gene IDs:
"RFP: 
ADA2: 852059
ada2: 852059
est2: 851028
NIC96: 850552"
Figure legend: "E Quantification of the RCA  product after co-IP  of the C-circles  with  Nic96-RFP  showing the effect of SUS1  deletion. The graph shows means and s.e.m. of the three independent  co-IPs  with 2-5 clones per genotype. Outliers were removed using ROUT robust outlier test. The p-values from one-way ANOVA were were adjusted using the Bonferroni's correction for multiple comparisons. est2∆ versus est2∆ NIC96-RFP (p=0,002), est2∆ versus est2∆ sus1∆ NIC96-RFP (p= 0,0006). **P&lt;0,001, ***P&lt;0,0001."
NCBI gene IDs:
"RFP: 
est2: 851028
NIC96: 850552
SUS1: 1466445
sus1: 1466445"
Figure legend: "A Senescence  curves of two  est2∆ and two est2∆ ADA2-Myc  clones used to generate  type II survivors for Co-IP-RCA. This experiment is representative out of the 4 independent experiments performed during this study."
NCBI gene IDs:
"Myc: 
ADA2: 852059
est2: 851028"
Figure legend: "C Detection of the  C-circles co-immunoprecipitated with Ada2-Myc   in type II survivors. The DNA co-immunoprecipitated  with Ada2-Myc was amplified by RCA, loaded on a dot blot  and detected with a telomeric TG1-3 probe. The numbers above the blot  refer to clones in (A) and correspond to type II survivors   produced in independent cultures. The lower panel shows the efficiency of Ada2-Myc IP analyzed by western blot  with anti-Myc  antibody."
NCBI gene IDs:
"Myc: 
Ada2: 852059"
Figure legend: "A Mean  senescence profiles of the est2∆ (n=7) and  est2∆ sus1∆ (n=8) clones isolated from the same heterozygous diploid. The error bars are SDs. B Mean  senescence profiles of the  est2∆ (n=10) and est2∆ sac3∆ (n=10) clones isolated from one heterozygous diploid. The error bars are SDs."
NCBI gene IDs:
"est2: 851028
sac3: 851737
sus1: 1466445"
Figure legend: "A Mean senescence profiles  of the est2∆ (n=10) and est2∆ shs1∆ (n=16) clones. The error bars are SDs. B Mean senescence profiles of the est1∆ (n=6) and  est1∆ bud6∆ (n=7) clones. Est1, similarly to  Est2, is essential for telomere maintenance. est1∆ has been used in this experiment instead of est2∆ because EST2  and BUD6 genes are linked on  chromosome XII. The error bars are SDs."
NCBI gene IDs:
"bud6: 851029
BUD6: 851029
est1: 850934
Est1: 850934
EST2: 851028
est2: 851028
Est2: 851028
shs1: 851373"
Figure legend: "(d-e) Average levels of (d) mRNA quantified by RNAseq (red) or qRT-PCR (grey) or (e) protein quantified by  mass spectrometry (light green) or  western blot (grey) for select  p53 target genes under oscillatory p53. Data information: , n=2 biological replicates, error bars represent std dev."
NCBI gene IDs:
"p53: 7157"
Figure legend: "(f-g) Average levels of (f) mRNA quantified by  RNAseq (blue) or qRT-PCR  (grey) or (g) protein quantified by  mass spectrometry (dark green) or  western blot (grey) for select p53 target genes under  rising p53. Data information: n=2 biological replicates, error bars represent std dev."
NCBI gene IDs:
"p53: 7157"
Figure legend: "A In silico analysis of Sirt7 mRNA expression in different tissues of the BXD genetic reference population (www.genenetwork.org). Adr: Adrenal Gland mRNA, Bla: Bladder mRNA, Bone: Bone Tibia mRNA, CNS: CNS mRNA, Cec: Cecum mRNA, Epi: Epididymis mRNA, Eso: Esophagus mRNA, Eye: Eye mRNA, Fat: Peritoneal Fat mRNA, GI: GI Track mRNA, Hea: Heart mRNA, Kid: Kidney mRNA, Liv: Liver mRNA, Lung: Lung mRNA, Mus: Gastrocnemius Muscle mRNA, Ova: Ovary mRNA, Pro: Prostate mRNA, Sal: Salivary Gland mRNA, Skin: Skin Back mRNA, Sn: Sciatic Nerve mRNA, Spl: Spleen mRNA, Tes: Testis mRNA, Thy: Thymus mRNA, Ton: Tongue mRNA, Tra: Trachea mRNA, and Ute: Uterus mRNA."
NCBI gene IDs:
"Sirt7: 209011"
Figure legend: "B Correlation plot for kidney mRNA expression of Sirt7 and Slc12a7 that codifies KCC4 in the mouse BxD genetic reference population (www.genenetwork.org)."
NCBI gene IDs:
"Sirt7: 209011
Slc12a7: 20499"
Figure legend: "C Oocytes injected with cRNA encoding KCC4 were incubated with NAD+ 200 μM and NAM 10 mM for 4 h. Lysates were immunoprecipitated with an anti-KCC4 antibody and then analyzed by SDS-PAGE/immunoblotting using an anti-acetylated-lysine (AcK) or anti-KCC4 antibody. Non-injected oocytes (UI) were used as a control."
NCBI gene IDs:
"KCC4: 10723"
Figure legend: "E Oocytes injected with H20 or KCC4 were incubated for the indicated times, and KCC4 protein levels were analyzed by SDS-PAGE/immunoblotting."
NCBI gene IDs:
"KCC4: 10723"
Figure legend: "F Oocytes were injected with either WT, K114R or K114Q KCC4 and incubated with vehicle (V), NAD+ or NAM for 48 h, and KCC4 protein levels (upper pannel), and activity (lower pannel) were analyzed as in D."
NCBI gene IDs:
"KCC4: 10723"
Figure legend: "C KCC4 activity was evaluated in Xenopus oocytes injected with cRNA encoding KCC4 and coinjected with either wild-type (SIRT7 WT) or the catalytically inactive SIRT7 (SIRT7 H188Y) for 48 h."
NCBI gene IDs:
"KCC4: 10723"
Figure legend: "D Oocytes were injected with either KCC4 WT, K114R or K114Q for 48 h and then incubated with vehicle (V), NAD+ or NAM for 24 h, and KCC4 and SIRT7 protein levels were analyzed by SDS-PAGE/immunoblotting."
NCBI gene IDs:
"KCC4: 10723"
Figure legend: "E Oocytes were injected with either KCC4 WT, K114R or K114Q with and without SIRT7 for 48 h and then incubated with vehicle (V) or NAM for 4 h. After lysis, KCC4 was immunoprecipitated using an anti-KCC4 antibody, and the acetylation status of KCC4 was determined by SDS-PAGE/Western blotting using and anti-acetyl lysine antibody."
NCBI gene IDs:
"SIRT7: 209011
KCC4: 10723"
Figure legend: "F, G FLAG-KCC4 and SIRT7 were transfected into HEK293 cells and treated for the indicated times with NAD+ (F) or NAM (G) and then analyzed by SDS-PAGE/immunoblotting using an anti-KCC4 or anti-SIRT7 antibody. Non-transfected cells (UT) were used as a control."
NCBI gene IDs:
"FLAG: 
SIRT7: 209011
KCC4: 20499"
Figure legend: "H FLAG-KCC4 and SIRT7 were transfected into HEK293 cells and treated for the indicated times with NAD+ and NAM. After lysis, KCC4 immunoprecipitation using an anti-FLAG antibody was performed, and the interaction with SIRT7 was determined by SDS-PAGE/Western blotting."
NCBI gene IDs:
"FLAG: 
SIRT7: 209011
KCC4: 20499"
Figure legend: "I HEK293 cells expressing KCC4 were incubated with NAD+ 200 μM and cycloheximide (CHX) for 0, 3, 6 and 9 h. KCC4 protein levels are shown at the indicated times in cells transfected with a scramble shRNA (+SIRT7) or a shRNA against SIRT7 (-SIRT7)."
NCBI gene IDs:
"SIRT7: 51547"
Figure legend: "A KCC4 acetylation at the indicated pH in HEK293 transfected with KCC4. After lysis, KCC4 was immunoprecipitated using an anti-FLAG antibody, and then analyzed by SDS-PAGE/Western blotting using an anti-acetylated-lysine (AcK) or anti-KCC4 antibody. Non-transfected cells (UT) were used as a control."
NCBI gene IDs:
"KCC4: 20499"
Figure legend: "B HEK293 cells were transfected with KCC4 together with SIRT7 with a scramble shRNA (-) or a shRNA against SIRT7 (+), and KCC4 activity and protein level were determined at the indicated pH. SIRT7 expression in these conditions is presented in C."
NCBI gene IDs:
"SIRT7: 209011
SIRT7: 51547
KCC4: 20499"
Figure legend: "A, B Sirt7 mRNA (A) and protein (B) abundance in microdissected renal tubules normalized to Rpl26 or Ponceau, respectively. Enrichment for each segment was previously validated by immunoblotting against segment-specific markers as indicated in material and methods (Spirli et al, 2019)."
NCBI gene IDs:
"Rpl26: 19941
Sirt7: 209011"
Figure legend: "C Immunolocalization of SIRT7 and ATPase in the kidneys of C57BL6 mice with metabolic acidosis (SIRT7, red; ATPase, green; DAPI, Blue). Scale bar: 20 μm. Controls of the specificity of antibodies using kidney of SIRT7-deficient mice are provided in Appendix Fig S4."
NCBI gene IDs:
"SIRT7: 209011"
Figure legend: "A KCC4 protein levels were determined in the kidneys of wild-type (SIRT7+/+) and SIRT7-deficient mice (SIRT7-/-). SIRT7 protein expression are absent in the kidneys of SIRT7-deficient mice."
NCBI gene IDs:
"SIRT7: 209011"
Figure legend: "B KCC4 protein levels, acetylation status of KCC4, and interaction with SIRT7 in kidneys of SIRT7+/+ and SIRT7-/-mice under normal conditions (Control) or with metabolic acidosis."
NCBI gene IDs:
"SIRT7: 209011"
Figure legend: "C Immunolocalization of KCC4 and H-ATPase in the kidneys of SIRT7+/+ and SIRT7-/- mice under normal conditions (Control) or with metabolic acidosis (NH4Cl). (KCC4, red; H-ATPase, green). Scale bar: 20 μm. Cell count was performed automatically using the Gen5 software to report the percentage of KCC4+ cells among H-ATPase+ cells (lower panel)."
NCBI gene IDs:
"SIRT7: 209011"
Figure legend: "D NCC and NKCC2 protein levels in the kidney of SIRT7+/+ and SIRT7-/- mice under basal conditions."
NCBI gene IDs:
"SIRT7: 209011"
Figure legend: "a, Expression levels of ISX, TWIST1, Snail1, Fibronectin (FN1), VEGF, and E-cadherin (CDH1) mRNA were examined in a ISX-GFP inducible Tet-ON transformants at 8 h after addition of DOX. Data are presented as mean ± SD in graph (p&lt; 0.001 compared to time point 0h; Student's t‐test) of 3 independent experiments, each performed in triplicate."
NCBI gene IDs:
"GFP: 
CDH1: 999
E-cadherin: 999
FN1: 2335
Fibronectin: 2335
ISX: 91464
Snail1: 6615
TWIST1: 7291
VEGF: 7422"
Figure legend: "b, Western blotting analysis of the protein levels of ISX, HIF1α, TWIST1, Snail1, Slug, ZEB1, Bmi1, E-cadherin (E-Cad.), Fibronectin, N-cadherin (N-Cad.), Vimentin, and VEGF in A549 and H1299 cells with DOX-inducible ISX expression system 8hs after DOX induction."
NCBI gene IDs:
"ISX: 91464"
Figure legend: "ISX transcriptionally activates luciferase activity driven by TWIST1 (c) promoter regions in A549 cells. Data are presented as mean ± SD in bar graph (p &lt; 0.001 , Student's t‐test) of 3 independent experiments, each performed in triplicate."
NCBI gene IDs:
"ISX: 91464
TWIST1: 7291"
Figure legend: "d, ISX transcriptionally activates luciferase activity driven by Snail1 (d) promoter regions in A549 cells. Data are presented as mean ± SD in bar graph (p &lt; 0.001 , Student's t‐test) of 3 independent experiments, each performed in triplicate."
NCBI gene IDs:
"ISX: 91464
Snail1: 6615"
Figure legend: "e, ChIP analysis of ISX binding to the TWIST1 promoter region in A549 and H1299 cells (10% input of each groups were pull down and applied to qPCR). Data are presented as mean ± SD in bar graph (p &lt; 0.001 , Student's t‐test) of 3 independent experiments, each performed in triplicate."
NCBI gene IDs:
"ISX: 91464
TWIST1: 7291"
Figure legend: "f, ISX transactivation activity analyzed by luciferase activity driven by the TWIST1 promoter. Data are presented as mean ± SD in graph (p &lt; 0.001 , Student's t‐test) of 3 independent experiments, each performed in triplicate."
NCBI gene IDs:
"ISX: 91464
TWIST1: 7291"
Figure legend: "g, ChIP analysis of ISX binding to the endogenous promoters of TWIST1 (-180/+35) and Snail1(-160/+40) in A549 and cells (10% input of each groups were pull down and applied to qPCR). Data are presented as mean ± SD in bar graph (p &lt; 0.001 , Student's t‐test) of 3 independent experiments, each performed in triplicate."
NCBI gene IDs:
"ISX: 91464
Snail1: 6615
TWIST1: 7291"
Figure legend: "h, Effect of forced expression and knockdown of ISX on cell migration (wound healing) measured in A549 cells. ISXi, ISX-specific shRNAi Data are presented as mean ± SD in graph (**, p &lt; 0.01, ***, p &lt; 0.001 , Student's t‐test) of 3 independent experiments, each performed in triplicate. Scale bar, 100μm."
NCBI gene IDs:
"ISX: 91464"
Figure legend: "i, Effect of forced expression and knockdown of ISX on cell invasion (transwell) activity measured in A549 cells. Data are presented as mean ± SD in bar graph (***, p &lt; 0.001 , Student's t‐test) of 3 independent experiments, each performed in triplicate. Scale bar, 100μm."
NCBI gene IDs:
"ISX: 91464"
Figure legend: "e, Western blotting analysis of the protein levels of ISX, PCAF, and EMT markers in DOX-inducible ISX expression system A549 cells treated with TH1834, Garcinol, C646, MB-3 for 8 h after DOX induction. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"ISX: 91464"
Figure legend: "g, Western blotting analysis of the protein levels of ISX, PCAF, and EMT markers in A549 cells with PCAF knockdown and DOX-inducible ISX expression system at 8 h time point after DOX induction. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"ISX: 91464
PCAF: 8850"
Figure legend: "The cell migration (wound healing, g) activity were determined in A549 cells with GFP-tagged wild or ISX mutants. Data are presented as mean ± SD in graph (***, p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Scale bar, 100μm. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"GFP: 
ISX: 91464"
Figure legend: "h, The cell invasion (transwell, h) activity were determined in A549 cells with GFP-tagged wild or ISX mutants. Data are presented as mean ± SD in graph (***, p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Scale bar, 100μm. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"GFP: 
ISX: 91464"
Figure legend: "j. Tumor xenografts metastasis activity of constitutively expressing RFP A549 cells transfected with wild type or ISX AC3 mutant cDNA were imaged by IVIS imaging system at fifth weeks Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"ISX: 91464"
Figure legend: "k, Kaplan-Meier survival curve analysis of nude mice xenograft injected with A549 cells carrying GFP, ISX-GFP and ISX Ac-GFP (AC3) (n = 10). p = 0.0003. p‐values were calculated by log‐rank (Mantel-Cox) test comparing the two Kaplan-Meier curves. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"GFP: 
ISX: 91464"
Figure legend: "d, The mCherry-tagged WT and BRD4 mutants were detected in anti-GFP immunoprecipitates by Western blotting in A549 cells. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"mCherry: 
BRD4: 23476"
Figure legend: "e and f, The mRNA levels of TWIST1(e) and Snail1(f) were verified in A549 cells co-expressing mCherry-tagged WT or mutant BRD4 and GFP-tagged ISX by RT-PCR. Data are presented as mean ± SD in bar graph (p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"GFP: 
mCherry: 
BRD4: 23476
ISX: 91464
Snail1: 6615
TWIST1: 7291"
Figure legend: "g and h, The DNA binding activity of TWIST1 and Snail1 were evaluated in anti-GFP-mCherry ChIP-ChIP immunoprecipitates by RT-PCR in A549 cells. Red, Hprt1 promoter (-190/+40 bp, negative control) (10% input of each groups were pulled down and used for qPCR analysis). Data are presented as mean ± SD in bar graph (p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"Hprt1: 3251
Snail1: 6615
TWIST1: 7291"
Figure legend: "i, The cell invasion (transwell) activity were determined in A549 cells co-transfected with cDNA coding for GFP-tagged ISX and mCherry-tagged BRD4 mutants. Data are presented as mean ± SD in bar graph (p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"GFP: 
mCherry: 
BRD4: 23476
ISX: 91464"
Figure legend: "The DNA binding activity of Snail (b) were evaluated in anti-GFP-mCherry ChIP-ChIP immunoprecipitates by RT-PCR in A549 cells. Red, Hprt1 promoter (-190-+40 bp, negative control). (10% input of each groups were pull down and applied to qPCR) Data are presented as mean ± SD in bar graph (p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"Hprt1: 3251
Snail: 6615"
Figure legend: "c, The DNA binding activity of TWIST1 (c) were evaluated in anti-GFP-mCherry ChIP-ChIP immunoprecipitates by RT-PCR in A549 cells. Red, Hprt1 promoter (-190-+40 bp, negative control). (10% input of each groups were pull down and applied to qPCR) Data are presented as mean ± SD in bar graph (p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"Hprt1: 3251
TWIST1: 7291"
Figure legend: "The cell migration (wound healing, d) activity were determined in A549 cells co-transfected with cDNAs for GFP-tagged ISX and mCherry-tagged BRD4 mutants. Data are presented as mean ± SD in bar graph (p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"GFP: 
mCherry: 
BRD4: 23476
ISX: 91464"
Figure legend: "e, The cell invasion (transwell, e) activity were determined in A549 cells co-transfected with cDNAs for GFP-tagged ISX and mCherry-tagged BRD4 mutants. Data are presented as mean ± SD in bar graph (p &lt; 0.001, Student's t‐test) of 3 independent experiments, each performed in triplicate. Data information: Each experiment was repeated at least three times."
NCBI gene IDs:
"GFP: 
mCherry: 
BRD4: 23476
ISX: 91464"
Figure legend: "Correlation analysis of mRNA expression for, (d) ISX and BRD4, in 157 lung cancer samples."
NCBI gene IDs:
"BRD4: 23476
ISX: 91464"
Figure legend: "e, Correlation analysis of mRNA expression for, (e) ISX and PCAF in 157 lung cancer samples."
NCBI gene IDs:
"ISX: 91464
PCAF: 8850"
Figure legend: "(B) VVA lectin immunoblot of secretomes from HepG2 SC, SCΔT1, SCΔT2 and SCΔT3."
NCBI gene IDs:
"T1: 2589
T2: 2590
T3: 2591"
Figure legend: "Histograms showing the distribution of M/L quantitation ratios of monoglycosylated peptides identified in (A) HepG2SCΔT1, (B) ΔT2 and (C) +T3. Glycopeptides with M/L ratio &lt; -1 are colored red and glycopeptides with a M/L ratio &gt; +1 are colored green. (D) Venn diagram showing the distribution of candidates for isoform-specific sites among HepG2SCΔT1, T2 and +T3 applying a log10 (+/-1) cut-off (excluding sites identified in both TCL and SEC for each isoform), and (E) TCL alone and (F) SEC alone."
NCBI gene IDs:
"T1: 2589
T2: 2590
T3: 2591"
Figure legend: "(H and I) Representative GUS staining images of cotyledons (H) and quantification of the relative HR efficiency (I). The reporter line and trigger line in either ddrm4-1 or Col-0 background were crossed and the F1 seedlings were used for GUS staining analysis. Scale bar = 1 mm. The number of blue sectors was scored. The data are presented as means ± SD (n &gt; 132 cotyledons) relative to the values of Col-0. The statistical significance was determined using two-tailed Students' t-test. ****, P &lt; 0.0001."
NCBI gene IDs:
"ddrm4: 844312"
Figure legend: "(K) eChIP-qPCR assays. The immunoprecipitated DNA and the input DNA were subjected to qPCR analysis. The ratios of eChIP and input are shown. UBQ5 serves as a negative control. The positions of the PCR fragment of 0.5 kb-4.5 kb were shown in (I). The data are represented as means ± SD (n = 3 technical replicates) relative to the values of Mock. The statistical significance was determined using two-tailed Students' t-test. ns, not significant; **, P &lt; 0.01; ***, P &lt; 0.001. The experiments were repeated three times with similar results."
NCBI gene IDs:
"UBQ5: 825398"
Figure legend: "(A and B) Yeast two-hybrid assays. PAF1 was fused with the activation domain (AD). SMC5 and SMC6B were fused with the DNA binding domain (BD). DDO, double dropout (SD/-Trp/-Leu) medium. QDO, quadruple dropout (SD/-Trp/-Leu/-His/-Ade) medium."
NCBI gene IDs:
"PAF1: 844312
SMC6B: 836267
SMC5: 831449"