If there are studies with data that hasnt been converted to G25 provide them here

[Capsian20]

Yes please this study its older but isn't there any G25
here link
https://www.nature.com/articles/s41467-019-12154-0

This doesn't seem to have any Human samples. It's only bacterial DNA

Looks like some of these have a lot of human DNA. For example NAB004 has 1181048 out of 1240K snps.

Yes because I think there people know this study and they has file BAM this samples

[Capsian20]

There have been many papers without G25 coordinates (recently and perhaps older ones too).
If you know of any studies which dont have G25 coordinates please send me their raw data or at least the study they come from. Teepean has been helping me so I can help the community gong forward

Yes please this study its older but isn't there any G25
here link
https://www.nature.com/articles/s41467-019-12154-0

This doesn't seem to have any Human samples. It's only bacterial DNA

https://academic.oup.com/mbe/article/38/10/4059/6277411

[miquirumba]

I see ancient celtic-basque samples in Theytree https://www.theytree.com/portal/index/sa...ient%20DNA
but I cannot find their G25 in updated ancient G25 sheet
Do you know if they were processed?
https://www.nature.com/articles/s41467-024-45438-1
https://www.ebi.ac.uk/ena/browser/view/PRJEB71003

[AimSmall]

Yes please this study its older but isn't there any G25
here link
https://www.nature.com/articles/s41467-019-12154-0

This doesn't seem to have any Human samples. It's only bacterial DNA

https://academic.oup.com/mbe/article/38/10/4059/6277411

There are human samples in that study... unless I'm misreading these.

Below is an example entry. Note, these plague samples are from individuals that lived in the 16th century. Not exactly old, but could be useful to somebody's research.

Code:

PRJEB44124
SAMEA8512267
ERX5375573
ERR5660082
9606
Homo sapiens
ena-STUDY-Institute of Clinical Molecular Biology-02-04-2021-18:37:38:435-757
webin-reads-ELW017_plague
webin-reads-ELW017_plague
N/A
ERR5660082.fastq.gz
ELW017.bam
ELW017.bam.bai
ELW017_plague
ELW017_plague

[ilabv]

This doesn't seem to have any Human samples. It's only bacterial DNA

https://academic.oup.com/mbe/article/38/10/4059/6277411

There are human samples in that study... unless I'm misreading these.

Below is an example entry.  Note, these plague samples are from individuals that lived in the 16th century.  Not exactly old, but could be useful to somebody's research.

Code:

PRJEB44124
SAMEA8512267
ERX5375573
ERR5660082
9606
Homo sapiens
ena-STUDY-Institute of Clinical Molecular Biology-02-04-2021-18:37:38:435-757
webin-reads-ELW017_plague
webin-reads-ELW017_plague
N/A
ERR5660082.fastq.gz
ELW017.bam
ELW017.bam.bai
ELW017_plague
ELW017_plague

In the original Nature link he sent it didn't have PRJEB44124 - it was only the bacterial ones. Thanks I'll look into these

[ilabv]

I see ancient celtic-basque samples in Theytree https://www.theytree.com/portal/index/sa...ient%20DNA
but I cannot find their G25 in updated ancient G25 sheet
Do you know if they were processed?
https://www.nature.com/articles/s41467-024-45438-1
https://www.ebi.ac.uk/ena/browser/view/PRJEB71003

I am confused. It says "No new DNA data were generated for this study". I still downloaded, converted, and sent to Davidski. But IDK what those samples even represent. As the study claims, they aren't new (?)

[ilabv]

Yes please this study its older but isn't there any G25
here link
https://www.nature.com/articles/s41467-019-12154-0

This doesn't seem to have any Human samples. It's only bacterial DNA

https://academic.oup.com/mbe/article/38/10/4059/6277411

This is a different study from the previous one is it not?

[ilabv]

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA006152

Population dynamics in Iron Age Xinjiang inferred from ancient genomes of the Zhagunluke site

---------
https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA023312

Ancient genomes reveal the temporal change of Yellow River millet farmers-related ancestry in Xinjiang

No idea how to even download these. Download button doesn't even work on the first link, on the 2nd study I can't even find it.

[miquirumba]

I see ancient celtic-basque samples in Theytree https://www.theytree.com/portal/index/sa...ient%20DNA
but I cannot find their G25 in updated ancient G25 sheet
Do you know if they were processed?
https://www.nature.com/articles/s41467-024-45438-1
https://www.ebi.ac.uk/ena/browser/view/PRJEB71003

I am confused. It says "No new DNA data were generated for this study". I still downloaded, converted, and sent to Davidski. But IDK what those samples even represent. As the study claims, they aren't new (?)

They said that because EIA celtic-basque samples from South Navarre (Spain) werw published in last year Luka Papac paper https://rua.ua.es/dspace/handle/10045/138845 no link for download all those samples have been added yet. new paper I mentioned is the first Open Sharing submission in ENA

[ilabv]

I see ancient celtic-basque samples in Theytree https://www.theytree.com/portal/index/sa...ient%20DNA
but I cannot find their G25 in updated ancient G25 sheet
Do you know if they were processed?
https://www.nature.com/articles/s41467-024-45438-1
https://www.ebi.ac.uk/ena/browser/view/PRJEB71003

I am confused. It says "No new DNA data were generated for this study". I still downloaded, converted, and sent to Davidski. But IDK what those samples even represent. As the study claims, they aren't new (?)

They said that because EIA celtic-basque samples from South Navarre (Spain) werw published in last year Luka Papac paper https://rua.ua.es/dspace/handle/10045/138845 no link for download all those samples have been added yet. new paper I mentioned is the first Open Sharing submission in ENA

Good summary thank you

[ilabv]

Sarmatian from this study: https://www.cell.com/current-biology/ful...23)01634-2

Scaled:

Sarmatian:C10271,0.094473,0.129988,-0.046386,-0.023579,-0.029852,-0.008367,0.006345,-0.006692,-0.051131,-0.022962,-0.00065,0.009292,-0.013825,0.000413,0.009636,-0.005967,0.001565,0.002027,0.001257,0.013256,0.004118,-0.004451,0.002835,-0.006386,-0.003233

Unscaled:

Sarmatian:C10271,0.0083,0.0128,-0.0123,-0.0073,-0.0097,-0.003,0.0027,-0.0029,-0.025,-0.0126,-0.0004,0.0062,-0.0093,0.0003,0.0071,-0.0045,0.0012,0.0016,0.001,0.0106,0.0033,-0.0036,0.0023,-0.0053,-0.0027

[ilabv]

Yes please this study its older but isn't there any G25
here link
https://www.nature.com/articles/s41467-019-12154-0

This doesn't seem to have any Human samples. It's only bacterial DNA

https://academic.oup.com/mbe/article/38/10/4059/6277411

Germany plague victims from this study: https://academic.oup.com/mbe/article/38/...ogin=false

Code:

Scaled:
Germany_Plague:ELW005,0.113823,0.136081,0.045254,0.028747,0.037545,0.015897,0.008225,0.010846,0.003886,0.003098,-0.004222,-0.003297,0.002081,-0.006744,0.00475,-0.001458,-0.008214,0.015836,-0.004525,-0.009379,0.009858,-0.00136,0.006409,0.02181,0.014969
Germany_Plague:ELW008,0.121791,0.146236,0.040729,0.024548,0.019388,0.010319,0.00188,0.004846,-0.005113,-0.005285,-0.000812,-0.001199,-0.013825,-0.015964,0.005157,0.00358,0.006519,-0.012162,-0.004022,-0.008754,0.002246,-0.009027,-0.005423,0.00012,0.003473
Germany_Plague:ELW010,0.135449,0.135065,0.051288,0.018734,0.0437,-0.00251,0.00611,-0.001154,0.011249,0.01385,-0.015102,-0.008992,-0.004162,-0.009909,-0.004072,-0.000663,-0.002347,0.001647,-0.005531,0.000875,0.006613,0.005935,-0.009244,0.010242,-0.001796

Unscaled:
Germany_Plague:ELW005,0.01,0.0134,0.012,0.0089,0.0122,0.0057,0.0035,0.0047,0.0019,0.0017,-0.0026,-0.0022,0.0014,-0.0049,0.0035,-0.0011,-0.0063,0.0125,-0.0036,-0.0075,0.0079,-0.0011,0.0052,0.0181,0.0125
Germany_Plague:ELW008,0.0107,0.0144,0.0108,0.0076,0.0063,0.0037,0.0008,0.0021,-0.0025,-0.0029,-0.0005,-0.0008,-0.0093,-0.0116,0.0038,0.0027,0.005,-0.0096,-0.0032,-0.007,0.0018,-0.0073,-0.0044,0.0001,0.0029
Germany_Plague:ELW010,0.0119,0.0133,0.0136,0.0058,0.0142,-0.0009,0.0026,-0.0005,0.0055,0.0076,-0.0093,-0.006,-0.0028,-0.0072,-0.003,-0.0005,-0.0018,0.0013,-0.0044,0.0007,0.0053,0.0048,-0.0075,0.0085,-0.0015

[ilabv]

Double Feature: First genetic evidence of a mother-daughter double burial in Roman Period Austria - a recent example of the great advantage of applying scientific methods in Roman archaeology

https://www.ebi.ac.uk/ena/browser/view/PRJEB72858

Roman Austrians from this study: https://www.sciencedirect.com/science/ar...via%3Dihub

Code:

Scaled:
Roman_Austria:196735_S3_L002.q30,0.125205,0.148267,0.036581,-0.01938,0.054472,-0.004741,-0.003055,0.00923,0.047859,0.029522,0.011367,0.004496,-0.01115,-0.026286,-0.009772,-0.016441,-0.001434,0.009248,-0.01433,0.019134,-0.003993,0.013354,0.009244,-0.006386,-0.005389
Roman_Austria:196736_S4_L002.q30,0.118376,0.156392,0.0445,0.015181,0.044931,0.000279,0.0047,0.013615,0.020248,0.019681,-0.001949,0.007493,-0.000297,0.001514,0.006243,0.005436,-0.002999,-0.004307,0.006411,0.015257,-0.006738,0.01558,-0.01405,0.004699,-0.007424

Unscaled:
Roman_Austria:196735_S3_L002.q30,0.011,0.0146,0.0097,-0.006,0.0177,-0.0017,-0.0013,0.004,0.0234,0.0162,0.007,0.003,-0.0075,-0.0191,-0.0072,-0.0124,-0.0011,0.0073,-0.0114,0.0153,-0.0032,0.0108,0.0075,-0.0053,-0.0045
Roman_Austria:196736_S4_L002.q30,0.0104,0.0154,0.0118,0.0047,0.0146,0.0001,0.002,0.0059,0.0099,0.0108,-0.0012,0.005,-0.0002,0.0011,0.0046,0.0041,-0.0023,-0.0034,0.0051,0.0122,-0.0054,0.0126,-0.0114,0.0039,-0.0062

[ilabv]

I see ancient celtic-basque samples in Theytree https://www.theytree.com/portal/index/sa...ient%20DNA
but I cannot find their G25 in updated ancient G25 sheet
Do you know if they were processed?
https://www.nature.com/articles/s41467-024-45438-1
https://www.ebi.ac.uk/ena/browser/view/PRJEB71003

Down Syndrome etc samples from this study: https://www.nature.com/articles/s41467-024-45438-1

Code:

Scaled:
Trisomy_Study:CRU013_ss.A0101,0.114961,0.148267,0.05242,0.008075,0.065858,0.001952,-0.010575,0.005077,0.029656,0.042461,-0.009581,0.01139,-0.021258,-0.020368,0.014115,-0.006629,-0.005867,0.003801,0.002388,-0.003377,0.009358,-0.000989,-0.007888,-0.009158,0.004191
Trisomy_Study:CRU024_ss.A0101,0.124067,0.147252,0.052797,0.005168,0.060934,-0.000279,-0.009165,0.002308,0.02352,0.03991,-0.00406,0.011989,-0.020961,-0.026699,0.005565,-0.006895,0.004433,-0.003167,0.007919,-0.007253,0.01672,0.002473,-0.010106,-0.010724,-0.000718
Trisomy_Study:ERE004_ss.A0101,0.106994,0.14319,0.04714,0.007106,0.061858,-0.003626,-0.005875,-0.003923,0.03211,0.042279,-0.001949,0.003747,-0.008028,-0.003441,0.004343,-0.001326,0.001956,0.002407,0.011061,-0.005253,0.009858,0.001607,-0.015283,-0.017352,0.000838

Unscaled:
Trisomy_Study:CRU013_ss.A0101,0.0101,0.0146,0.0139,0.0025,0.0214,0.0007,-0.0045,0.0022,0.0145,0.0233,-0.0059,0.0076,-0.0143,-0.0148,0.0104,-0.005,-0.0045,0.003,0.0019,-0.0027,0.0075,-0.0008,-0.0064,-0.0076,0.0035
Trisomy_Study:CRU024_ss.A0101,0.0109,0.0145,0.014,0.0016,0.0198,-0.0001,-0.0039,0.001,0.0115,0.0219,-0.0025,0.008,-0.0141,-0.0194,0.0041,-0.0052,0.0034,-0.0025,0.0063,-0.0058,0.0134,0.002,-0.0082,-0.0089,-0.0006
Trisomy_Study:ERE004_ss.A0101,0.0094,0.0141,0.0125,0.0022,0.0201,-0.0013,-0.0025,-0.0017,0.0157,0.0232,-0.0012,0.0025,-0.0054,-0.0025,0.0032,-0.001,0.0015,0.0019,0.0088,-0.0042,0.0079,0.0013,-0.0124,-0.0144,0.0007

[ilabv]

Once again, if you notice any samples missing from G25 please let me know. There are Swiss, Calabria N, and 2019 study on Euro plague victims on the way.

Two studies from IA Xinjiang and Yellow River Farmers don't seem to have download links that work so idk what to do about those:

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA006152

https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA023312