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Host associated metagenome (Dental calculus) date/sample age information updates #1541

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Host associated metagenome (Dental calculus) date/sample age information updates#1541
@jfy133

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@jfy133
jfy133
opened on Jun 2, 2025

Originally compiled by @alwIV, and reported across separate issues. I'm condensing here into a single issue, and we will discuss how to go how to adjust.

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Perfect. Ps. These are the articles for which I didn't change any dates. Either because they were all correct or because the samples were not included in any > of my analyses:
Brealey2020 10.1093/molbev/msaa135
Brealey2021 10.1016/j.cub.2021.08.010
Eerkens2018 10.1016/j.ijpp.2018.05.001
Ferrari2018 10.3390/genes9090436
Fontani2023 10.1038/s41598-023-39250-y
Fotakis2020 10.1098/rstb.2019.0584
Jensen2019 10.1038/s41467-019-13549-9
Kimsis2023 10.1111/1758-2229.13157
Klapper2023 10.1126/science.adf5300
McDonough2018 10.1093/jmammal/gyy080
Moraitou2022 10.1093/molbev/msac263
Ozga2016 10.1002/ajpa.22960
Ozga2019 10.1038/s41598-019-53802-1
Sarhan2023 10.1186/s12915-022-01509-7
Sawafuji2020 10.1371/journal.pone.0226654
Scorrano2022 10.1038/s42003-022-04190-2
White2021 10.3390/biology10121324
Willmann2018 10.1371/journal.pone.0196482
Zhou2018 10.1016/j.cub.2018.05.058

#1505 (comment)

and here is the table I use for my analyses
public_data_table_14_05_2025.txt

and here is the table I use for my analyses

public_data_table_14_05_2025.txt

Re-generated table from all the issues (however should be x-ref'd with the public data table in link above)

sample_name updated_sample_age Old_sample_age
H10 3200 4400
H24 3200 4400
S108 250 300
S454 250 300
S40_S37 1350 1400
AYIM22BN 4800 4700
G218M5-3N 4950 4900
GMGM1 4050 4100
XHM100 3750 3800
XHM110 3700 3900
XHM75 3700 3900
L5209 3700 3900
L5213 3700 3900
L4964 3700 3900
L6101 3650 3600
L6103 3700 3600
L6105 3700 3900
L6106 3700 3900
AMNH98137_Q01 0 100
364459 50 100
Spy1 35810 35800
Spy2 36350 36000
EuroHG1 7550 7600
EuroHG2 7550 7600
EuroLBK1 7440 7400
EuroLBK2 7440 7400
EuroLBK3 7440 7400
AfrSF1 2320 2300
AfrSF2 3835 3800
AfrPP2 570 600
AfrPP1 740 600
IndRev1 100 200
IndRev2 100 200
B61 950 900
G12 950 900
EFE003 1000 990
EFE004 260 155
EFE005 310 155
FUT021 300 305
S1 2900 2875
S2 2850 2875
S5 2900 2875
S6 2900 2875
S9 3000 2875
S10 2900 2875
S14 2600 2610
S15 2600 2610
S17 2800 2875
S18 2500 2550
S20 2100 2250
S23 2800 2875
S27 2150 2200
S29 2700 2875
S31 2850 2875
NMU128 260 220
PAH001 2650 2550
TON004 2500 2550
TON005 2500 2550
TON006 2500 2550
TON007 2500 2550
CMB001 150 200
CMB002 150 200
CMB003 150 200
CMB004 150 200
CMB005 150 200
CMB006 150 200
CMB007 150 200
CMB008 150 200
ELR003 1000 500
ELR004 1000 500
ELR006 1000 500
ELR008 1000 500
ELR010 1000 500
IVE002 1000 900
IVE003 1000 900
IVE005 1000 900
IVE007 1000 900
MID022 150 200
MID023 150 200
MID024 150 200
MID025 150 200
MID026 150 200
MID027 150 200
MID028 150 200
MID029 150 200
MID030 150 200
MID031 150 200
MID032 150 200
MID033 150 200
MID034 150 200
MID035 150 200
MID036 150 200
MID037 150 200
MID038 150 200
MID039 150 200
MID040 150 200
MID041 150 200
MID042 150 200
MID043 150 200
MID044 150 200
MID045 150 200
MID046 150 200
MID047 150 200
MID048 150 200
MID049 150 200
MID050 150 200
MID051 150 200
MID052 150 200
MID053 150 200
MID054 150 200
MID055 150 200
MID056 150 200
MID057 150 200
MID058 150 200
MID059 150 200
MID060 150 200
MID061 150 200
MID062 150 200
MID063 150 200
MID064 150 200
MID065 150 200
MID066 150 200
MID067 150 200
MID068 150 200
MID070 150 200
MID071 150 200
MID072 150 200
MID073 150 200
MID074 150 200
MID075 150 200
MID076 150 200
MID077 150 200
MID078 150 200
MID079 150 200
MID080 150 200
MID081 150 200
MID082 150 200
MID083 150 200
MID084 150 200
MID085 150 200
MID086 150 200
MID087 150 200
MID088 150 200
MID089 150 200
MID090 150 200
MID091 150 200
MID092 150 200
MID093 150 200
MID094 150 200
MID097 150 200
MID101 150 200
MID102 150 200
CS01 150 200
CS02 150 200
CS03 150 200
CS04 150 200
CS05 150 200
CS06 150 200
CS07 150 200
CS08 150 200
CS09 150 200
CS10 150 200
CS11 150 200
CS12 150 200
CS13 150 200
CS14 150 200
CS15 150 200
CS16 150 200
CS17 150 200
CS18 150 200
CS19 150 200
CS20 150 200
CS21 150 200
CS22 150 200
CS23 150 200
CS24 150 200
CS26 150 200
CS27 150 200
CS28 150 200
CS29 150 200
CS30 150 200
CS31 150 200
CS32 150 200
CS33 150 200
CS34 150 200
CS35 150 200
CS36 150 200
CS37 150 200
CS38 150 200
CS39 150 200
CS40 150 200
CS42 150 200
CS43 150 200
CS44 150 200
CS45 150 200
CS46 150 200
CS47 150 200
CS48 150 200
2H10 5150 4500
BIC__T2 7630 6900
Fer__T64 4600 4300
Fer__T65 4600 4300
Fer__T67 4600 4300
Fer__T69 4600 4300
Fer__T75 4600 4300
GR__T12 4500 4100
GR__T15A 4500 4100
GR__T16 4500 4100
GR__T34a 4500 4100
GR__T34b 4500 4100
GR__T8 4500 4100
CND40_IDA 7500 6700
CND40_IDB 7500 7300
CND43 7500 7300
CND91 7400 6600
CND92 7500 7300
MELT1 4500 4800
MELT2 4500 4800
MELT3 4500 4800
PA__12 29000 24800
PA__140 15450 15500
PA__157 15450 15500
PA__38 15450 15500
PA__39 15450 15500
P__T7c 6375 5700
US1034 7350 6500
US1054 7000 6100
US1056_I 7000 6100
US1056_II 7000 6100
Rip__USD304 6200 6300
Rip__USD346 6200 6300
Rip__USD35 6200 6300
Rip__USD359 6200 6300
Rip__USD360 6200 6300
Rip__USD41 6200 6300
Rip__USD527 6200 6300
Rip__USD613 6200 6300
Rip__USD618 6200 6300
Rip__USD625 6200 6300
Rip__USD628 6200 6300
Rip__USD687 6200 6300
Rip__USD688 6200 6300
RipUSD68817 6200 6300
RipUSD68824 6200 6300
RipUSD691A 6200 6300
RipUSD691B 6200 6300
Rip__USD697 6200 6300
TR175 4800 5300
TR177 4800 5300
PCA0088 1650 1700
PCA0090 1650 1700
AJ9 7900 7100
CL2 14150 12600
CT10_GC_2 10300 8300
CT11_GC_66 15700 13800
CT13_GC_74 10300 8300
CT17_GC_67 15700 13800
CT2_GC_36_A 12550 11600
CT4_GC_61_L 13450 1150
CT5_GC_59 13000 10600
CT7_GC_65 15700 14800
CT8_GC_10_H 15700 14800
H53 7900 7000
H64 8460 8100
HV29 8500 8200
LG10b_AC_IX_BB 6650 5800
LG20b_AQ_1_ZAM 6600 5800
LG21a_AQ_1_RICH 7150 6300
LG3b_AC_T1_Tin 6500 5700
LG7b_AC_V_BB 6600 5800
LG8b_AC_VII_BB 6400 5800
LV20 11400 10300
LV29 300 400
LV32a 7850 7300
LV50 10320 9500
LV8 7650 7100
PAD12 9000 7500
PAD16 10000 9300
PAD18B 10800 9700
PAD20 10000 7500
PAD25 9000 7500
PAD26 9000 7500
PAD30 5200 8800
PAD9 10840 9900
VK1 9400 9500
VL44 10000 7600
VL45 8500 8100
CT3_-_GC_82_F 4200 3300
ANSP11833 150 100
ANSP3271 150 100
PI-420A-C 730 700
Abusir1519 4100 4000
Abusir1594 2250 2200
PsP_6417 5400 3400
PsP_6416 5400 3400
PsP_6410 5400 3400
PsP_6408 5400 3400
PsP_6407 5400 3400
PsP_6405 5400 3400
P__O_898-11 950 1000
H10 3200 4400
H24 3200 4400
S108 250 300
S454 250 300
H10 3200 4400
H24 3200 4400
S108 250 300
S454 250 300
T2 350 400
T3 350 400
T9 350 400
ZA_11C 350 400
ZA_12C 350 400
ZA_1C 400 500
ZA_8C 350 400
ZA_C22 350 400
T2 350 400
T3 350 400
T9 350 400
MAWB_15 1050 1300
MAWB_12 1050 1300
MAWB_11 1050 1300
MAWB_10 1050 1300
MAWB_6 1150 1300
MAWB_5 1350 2000
MAWB_3 2010 1400
SA_011 3550 3600
SA_010 3550 3600
SA_009 3550 3600
SA_008 3110 3400
SA_007 3110 3400
SA_006 3110 3400
SA_005 3110 3400
SA_004 2950 3000
SA_003 2950 3000
SA_002 2950 3000
SA_001 2950 3000
KGH2-F 4000 3800
KGH2-B 4000 3800
KGH1-E 4000 3800
KGH1-A 4000 3800
WAMP02 600 700
WAMP03 600 700
WAMP04 600 700
WAMP05 600 700
WAMP06 600 700
WAMP07 600 700
WAMP09 600 700
WAMP10 600 700
WAMP11 600 700
WAMP33 600 700
WAMP27 600 700
WAMP25 600 700
WAMP24 600 700
WAMP29 600 700
WAMP26 600 700
WAMP23 600 700
WAMP22 600 700
WAMP19 600 700
WAMP12 600 700
WAMP21 600 700
WAMP20 600 700
WAMP15 600 700
WAMP14 600 700
WAMP13 600 700
WAMP18 600 700
WAMP34 600 700
2081 6700 6800
2092 1260 1300
2097 1414 1300
Jewbury8815 700 800
Jewbury8822 700 800
Jewbury8830 700 800
Jewbury8835 700 800
Jewbury8838 700 800
Jewbury8839 700 800
18501_Pictish3 U U
16961_PostMedieval_StBrides_SB79 U U
16950_Medieval_StMaryGraces_MIN86 575 600
16949_Medieval_StMaryGraces_MIN86 475 500
16944_Medieval_StMaryGraces_MIN86 575 600
16942_Medieval_StMaryGraces_MIN86 475 500
16941_Medieval_StMaryGraces_MIN86 475 500
16940_Medieval_StMaryGraces_MIN86 575 600
16939_Medieval_StMaryGraces_MIN86 475 500
16938_Medieval_StMaryGraces_MIN86 475 500
16937_Medieval_StMaryGraces_MIN86 475 500
16933_Medieval_StMaryGraces_MIN86 475 500
16931_Medieval_StMaryGraces_MIN86 575 600
16930_Medieval_StMaryGraces_MIN86 475 500
16926_PostMedieval_ChelseaOldChurch_OCU00 175 200
16923_PostMedieval_ChelseaOldChurch_OCU00 175 200
16921_PostMedieval_ChelseaOldChurch_OCU00 175 200
16919_PostMedieval_ChelseaOldChurch_OCU00 175 200
16915_Medieval_StBenetSherehog_ONE94 575 650
16914_Medieval_StBenetSherehog_ONE94 575 650
16907_PostMedieval_StBenetSherehog_ONE94 125 100
16903_PostMedieval_StBenetSherehog_ONE94 275 300
16901_PostMedieval_CrossBones_REW92 220 300
16900_PostMedieval_CrossBones_REW92 220 300
16899_PostMedieval_CrossBones_REW92 220 300
16898_PostMedieval_CrossBones_REW92 220 300
16897_PostMedieval_CrossBones_REW92 220 300
16896_PostMedieval_CrossBones_REW92 220 300
16895_PostMedieval_CrossBones_REW92 220 300
16894_PostMedieval_CrossBones_REW92 220 300
16893_PostMedieval_CrossBones_REW92 220 300
16892_PostMedieval_CrossBones_REW92 220 300
16889_Medieval_MertonPriory_MPY86 620 650
16887_Medieval_MertonPriory_MPY86 620 650
16881_Medieval_MertonPriory_MPY86 620 650
16880_Medieval_MertonPriory_MPY86 650 600
16864_Medieval_MertonPriory_MPY86 620 650
16863_Medieval_MertonPriory_MPY86 620 650
Oakington16540 1420 1400
Oakington16500 1420 1480
Oakington16496 1420 1480
Oakington15811 1420 1480
Oakington15810 1420 1480
Oakington15809 1420 1480
Oakington15807 1420 1480
Oakington15806 1420 1480
BreedonOnTheHill12864 2600 -676
BreedonOnTheHill12861 2600 -676
BreedonOnTheHill12859 2600 -676
BreedonOnTheHill12858 2600 -676
BreedonOnTheHill12857 2600 -676
NewarkBay8888 770 800
StHelensOnWalls8875 625 650
StHelensOnWallsy8874 625 650
StHelensOnWalls8873 625 650
P18 850 900
P68 850 900
P45 850 900
P112 850 900
OME002**A 0 200
OME003**A 0 200
OME005**A 0 200
OME007**A 0 200
OME009**A 0 200
MTK001**A 50 200
MTM001**A 50 200
MTM002**A 50 200
MTM003**A 50 200
MTM004**A 50 200
MTM005**A 50 200
MTM006**A 50 200
MTM008**A 50 200
MTM009**A 50 200
MTM011**A 50 200
MTM012**A 50 200
MTM013**A 50 200
MTS001**A 50 200
MTS002**A 50 200
MTS003**A 50 200
MTM010**A 50 200
ABM006**A 0 200
DJA002**A 0 200
EBO001**A 0 200
EBO003**A 0 200
GDC002**A 0 200
GDC004**A 0 200
GDC005**A 0 200
LOB001**A 0 200
BIT001**A 0 200
FDM001**A 0 200
IBA001**A 0 200
IBA002**A 0 200
WAL001**A 0 200
CDC005**A 15 200
CDC006**A 15 200
CDC007**A 15 200
CDC008**A 15 200
CDC009**A 15 200
CDC010**A 15 200
CDC011**A 15 200
KNP001**A 0 200
KNP003**A 0 200
KNP004**A 0 200
KNP005**A 0 200
KNP006**A 0 200
KNP007**A 0 200
KNP009**A 0 200
ABM007**A 0 200
ABM008**A 0 200
DJA006**A 0 200
DJA007**A 0 200
EBO008**A 0 200
EBO009**A 0 200
OAK004**A 6800 6400
OAK005**A 6600 7500
EMN001**A 18700 9000
PYK001**A 100 200
PYK002**A 100 200
PYK003**A 100 200
PYK004**A 100 200
PYK005**A 100 200
Jewbury8809 700 800
Jewbury8810 700 800
Jewbury8811 700 800
Jewbury8813 700 800
Jewbury8815 700 800
Jewbury8816 700 800
Jewbury8818 700 800
Jewbury8819 700 800
Jewbury8820 700 800
Jewbury8822 700 800
Jewbury8825 700 800
Jewbury8826 700 800
Jewbury8827 700 800
Jewbury8829 700 800
Jewbury8830 700 800
Jewbury8831 700 800
Jewbury8833 700 800
Jewbury8834 700 800
Jewbury8835 700 800
Jewbury8838 700 800
Jewbury8839 700 800
Jewbury8840 700 800
Jewbury8843 700 800
Jewbury8844 700 800
Jewbury8855 700 800
Jewbury8856 700 800
Jewbury8857 700 800
CM55 4750 4700
CM59 4750 4700
CM82 4750 4700
CM165 4750 4700
3DT21 1700 1500
WG1561 750 700
SMD_2711-1-2710 1100 1000
A18023_Japan_Edo_4 275 230
A18022_Japan_Edo_3 275 230
A18021_Japan_Edo_2 275 230
A18020_Japan_Edo_1 275 230
A18033_Japan_Edo_10 275 230
A18032_Japan_Edo_9 275 230
A18027_Japan_Edo_8 275 230
A18026_Japan_Edo_7 275 230
A18025_Japan_Edo_6 275 230
A18024_Japan_Edo_5 275 230
CS32 150 200

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