From 6ef229e67f6a356705a433ff203535ffca7d3f73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Mon, 7 Oct 2024 17:51:28 +0200 Subject: [PATCH 1/3] Fix the archive_accession codes of some of the Liu2024 samples - add ERS numbers of second sequencing runs - correct the sample names in the library tables --- ...ientmetagenome-environmental_libraries.tsv | 29 ++++--- ...ncientmetagenome-environmental_samples.tsv | 80 +++++++++---------- 2 files changed, 54 insertions(+), 55 deletions(-) diff --git a/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv b/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv index d0e05e783..ce885ee66 100644 --- a/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv +++ b/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv @@ -794,23 +794,22 @@ Liu2024 2024 10.1126/sciadv.adn8490 ESL055 ENA PRJEB74036 ERS18499349 200327_A00 Liu2024 2024 10.1126/sciadv.adn8490 ESL057 ENA PRJEB74036 ERS18499350 191011_SND405_A_L006_APMG-5-4 single AccuPrime Pfx DNA none NA Illumina HiSeq 2500 PAIRED WGS 65841536 ERR12814456 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/056/ERR12814456/ERR12814456_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/056/ERR12814456/ERR12814456_2.fastq.gz bc09b495db7b32a47508755d9f847fc3;738b2435225befb6c42c1027c60d0ca3 2093460910;1883465567 Liu2024 2024 10.1126/sciadv.adn8490 ESL057 ENA PRJEB74036 ERS18499351 210602_A00902_B_L001_APMG-34-4 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 116825718 ERR12814457 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/057/ERR12814457/ERR12814457_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/057/ERR12814457/ERR12814457_2.fastq.gz 1be05deffd2c5befcc96e849efd38f22;ed700bf283072f9deddd47eba80b19e4 3504362865;3831029578 Liu2024 2024 10.1126/sciadv.adn8490 ESL058 ENA PRJEB74036 ERS18499352 210602_A00902_B_L001_APMG-34-7 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 133731816 ERR12814458 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/058/ERR12814458/ERR12814458_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/058/ERR12814458/ERR12814458_2.fastq.gz a308576219016f78f0e278019f97b77a;90b83994d8f8e97d902289f45d5a1a6f 4008794184;4371426082 -Liu2024 2024 10.1126/sciadv.adn8490 ESL061 ENA PRJEB74036 ERS18499353 210602_A00902_B_L002_APMG-35-2 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 1261074 ERR12814459 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/059/ERR12814459/ERR12814459_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/059/ERR12814459/ERR12814459_2.fastq.gz 2359058b9e31d1781c86ceca9bf85907;ee4983a0a21505e0ff66f2184365b24f 23973986;28551509 -Liu2024 2024 10.1126/sciadv.adn8490 ESL063 ENA PRJEB74036 ERS18499354 200327_A00902_B_L1-2_APMG-10-16 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 83057198 ERR12814460 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/060/ERR12814460/ERR12814460_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/060/ERR12814460/ERR12814460_2.fastq.gz d2312879e4ac7fe018b804b7632ebc2c;8637a4be98bcf236c3a1335bf71a1162 2066645692;2455413113 -Liu2024 2024 10.1126/sciadv.adn8490 ESL065 ENA PRJEB74036 ERS18499355 200327_A00902_B_L1-2_APMG-10-17 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 97756838 ERR12814461 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/061/ERR12814461/ERR12814461_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/061/ERR12814461/ERR12814461_2.fastq.gz ca194f4ba55a86525bb2cfac5abfb4ec;948a365a60602da568228a12f7ad8c9e 2497558200;2869677020 +Liu2024 2024 10.1126/sciadv.adn8490 ESL061 ENA PRJEB74036 ERS18499354 200327_A00902_B_L1-2_APMG-10-16 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 83057198 ERR12814460 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/060/ERR12814460/ERR12814460_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/060/ERR12814460/ERR12814460_2.fastq.gz d2312879e4ac7fe018b804b7632ebc2c;8637a4be98bcf236c3a1335bf71a1162 2066645692;2455413113 +Liu2024 2024 10.1126/sciadv.adn8490 ESL063 ENA PRJEB74036 ERS18499355 200327_A00902_B_L1-2_APMG-10-17 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 97756838 ERR12814461 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/061/ERR12814461/ERR12814461_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/061/ERR12814461/ERR12814461_2.fastq.gz ca194f4ba55a86525bb2cfac5abfb4ec;948a365a60602da568228a12f7ad8c9e 2497558200;2869677020 Liu2024 2024 10.1126/sciadv.adn8490 ESL065 ENA PRJEB74036 ERS18499356 191011_SND405_A_L006_APMG-5-6 single AccuPrime Pfx DNA none NA Illumina HiSeq 2500 PAIRED WGS 60991982 ERR12814462 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/062/ERR12814462/ERR12814462_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/062/ERR12814462/ERR12814462_2.fastq.gz 867bc522c5fb2ac5101d287742da9c9c;f45b58e8fa752d4124581d82df343827 1916754127;1766885487 -Liu2024 2024 10.1126/sciadv.adn8490 ESL068 ENA PRJEB74036 ERS18499357 210602_A00902_B_L001_APMG-34-6 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 90083718 ERR12814463 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/063/ERR12814463/ERR12814463_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/063/ERR12814463/ERR12814463_2.fastq.gz 2ef2c0506f4c2c1b897c3cda14f941fc;358af31e59fbb2b1b51670820f370f20 2656478724;2875468938 -Liu2024 2024 10.1126/sciadv.adn8490 ESL069 ENA PRJEB74036 ERS18499358 200327_A00902_B_L1-2_APMG-10-18 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 98080872 ERR12814464 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/064/ERR12814464/ERR12814464_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/064/ERR12814464/ERR12814464_2.fastq.gz 6fbd16521cbd38c2f30ffa0227163d41;ff636ea9137358056827e644159e5793 2510912598;2860892098 -Liu2024 2024 10.1126/sciadv.adn8490 ESL071 ENA PRJEB74036 ERS18499359 210409_A00902_B_L1-2_APMG-28-11 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 209914566 ERR12814465 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/065/ERR12814465/ERR12814465_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/065/ERR12814465/ERR12814465_2.fastq.gz c09c141c0fb6d8d9283d62659195c155;9b11f3de2718b7f121ef633ee69b7dd7 6220875315;6002553550 -Liu2024 2024 10.1126/sciadv.adn8490 ESL072 ENA PRJEB74036 ERS18499361 200327_A00902_B_L1-2_APMG-10-19 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 3884428 ERR12814467 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/066/ERR12814466/ERR12814466_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/066/ERR12814466/ERR12814466_2.fastq.gz 129cc737515d53efe6d26a27e22d0757;678f5fd7634ad76ef001d64c6f705792 2399183461;2776570290 +Liu2024 2024 10.1126/sciadv.adn8490 ESL065 ENA PRJEB74036 ERS18499357 210602_A00902_B_L001_APMG-34-6 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 90083718 ERR12814463 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/063/ERR12814463/ERR12814463_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/063/ERR12814463/ERR12814463_2.fastq.gz 2ef2c0506f4c2c1b897c3cda14f941fc;358af31e59fbb2b1b51670820f370f20 2656478724;2875468938 +Liu2024 2024 10.1126/sciadv.adn8490 ESL068 ENA PRJEB74036 ERS18499358 200327_A00902_B_L1-2_APMG-10-18 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 98080872 ERR12814464 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/064/ERR12814464/ERR12814464_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/064/ERR12814464/ERR12814464_2.fastq.gz 6fbd16521cbd38c2f30ffa0227163d41;ff636ea9137358056827e644159e5793 2510912598;2860892098 +Liu2024 2024 10.1126/sciadv.adn8490 ESL069 ENA PRJEB74036 ERS18499359 210409_A00902_B_L1-2_APMG-28-11 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 209914566 ERR12814465 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/065/ERR12814465/ERR12814465_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/065/ERR12814465/ERR12814465_2.fastq.gz c09c141c0fb6d8d9283d62659195c155;9b11f3de2718b7f121ef633ee69b7dd7 6220875315;6002553550 +Liu2024 2024 10.1126/sciadv.adn8490 ESL071 ENA PRJEB74036 ERS18499361 200327_A00902_B_L1-2_APMG-10-19 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 3884428 ERR12814467 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/066/ERR12814466/ERR12814466_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/066/ERR12814466/ERR12814466_2.fastq.gz 129cc737515d53efe6d26a27e22d0757;678f5fd7634ad76ef001d64c6f705792 2399183461;2776570290 Liu2024 2024 10.1126/sciadv.adn8490 ESL072 ENA PRJEB74036 ERS18499362 191011_SND405_A_L006_APMG-5-5 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 88696490 ERR12814468 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/067/ERR12814467/ERR12814467_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/067/ERR12814467/ERR12814467_2.fastq.gz e9c600a94be6620f7a2d8a8f39f05a2c;aff9223a6226043e5a1363f97fbf49ea 465069249;485292439 -Liu2024 2024 10.1126/sciadv.adn8490 ESL073 ENA PRJEB74036 ERS18499363 210602_A00902_B_L001_APMG-34-5 single AccuPrime Pfx DNA none NA Illumina HiSeq 2500 PAIRED WGS 15399092 ERR12814469 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/068/ERR12814468/ERR12814468_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/068/ERR12814468/ERR12814468_2.fastq.gz e2f87c815174fc2bd18551edf24604ca;ef7ab54bdfe1cc5cec2f1dc7872706e7 3507789532;3222876847 -Liu2024 2024 10.1126/sciadv.adn8490 ESL074 ENA PRJEB74036 ERS18499364 210409_A00902_B_L1-2_APMG-28-10 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 106828472 ERR12814470 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/069/ERR12814469/ERR12814469_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/069/ERR12814469/ERR12814469_2.fastq.gz da7778fb9cfed62273af777b6e9f3001;d3fb3c412e8be82070cad4eda19c40c1 2308509705;2437998354 -Liu2024 2024 10.1126/sciadv.adn8490 ESL075 ENA PRJEB74036 ERS18499365 200327_A00902_B_L1-2_APMG-10-20 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 91018898 ERR12814471 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/071/ERR12814471/ERR12814471_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/071/ERR12814471/ERR12814471_2.fastq.gz bc407500c04c274a28ea3d9b4891a3da;a46dc11d060df909087cdf0d4af588b6 2765036775;2327542522 -Liu2024 2024 10.1126/sciadv.adn8490 ESL076 ENA PRJEB74036 ERS18499366 210409_A00902_B_L1-2_APMG-28-9 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 113819524 ERR12814472 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/072/ERR12814472/ERR12814472_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/072/ERR12814472/ERR12814472_2.fastq.gz eae8f7dc05f61ce1ce72e3378296490d;1e8d905d356c1a5329fbe3fa91078c72 3436948124;3459344043 -Liu2024 2024 10.1126/sciadv.adn8490 ESL077 ENA PRJEB74036 ERS18499367 200327_A00902_B_L1-2_APMG-10-21 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 109660044 ERR12814473 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/073/ERR12814473/ERR12814473_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/073/ERR12814473/ERR12814473_2.fastq.gz 12f90800ae8795d646f1aafa6ad83ace;77ce76b3c6eeeba08bd317e1b3ccf1cb 2793224289;3258698776 -Liu2024 2024 10.1126/sciadv.adn8490 ESL078 ENA PRJEB74036 ERS18499368 210409_A00902_B_L1-2_APMG-28-8 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 82609702 ERR12814474 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/074/ERR12814474/ERR12814474_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/074/ERR12814474/ERR12814474_2.fastq.gz 5dab614f4198cbedb3542d0b88330ef6;c2628f6e6a055a191bdac3f29f5e05be 2390002791;2534714308 -Liu2024 2024 10.1126/sciadv.adn8490 ESL079 ENA PRJEB74036 ERS18499369 210409_A00902_B_L1-2_APMG-28-7 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 134931132 ERR12814475 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/075/ERR12814475/ERR12814475_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/075/ERR12814475/ERR12814475_2.fastq.gz 7e120573673c7a1783005f7ad911a5ff;1ea4590ef271b2e74017f1e92404d770 4090579685;3924358144 -Liu2024 2024 10.1126/sciadv.adn8490 ESL001 ENA PRJEB74036 ERS18499370 200327_A00902_B_L1-2_APMG-10-22 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 85518486 ERR12814476 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/076/ERR12814476/ERR12814476_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/076/ERR12814476/ERR12814476_2.fastq.gz 2a5e7c3250bcdfcf9e815571c6efca1c;c5a94cd6c3b2236dbf477960b3bc8dde 2277648738;2617729740 +Liu2024 2024 10.1126/sciadv.adn8490 ESL072 ENA PRJEB74036 ERS18499363 210602_A00902_B_L001_APMG-34-5 single AccuPrime Pfx DNA none NA Illumina HiSeq 2500 PAIRED WGS 15399092 ERR12814469 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/068/ERR12814468/ERR12814468_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/068/ERR12814468/ERR12814468_2.fastq.gz e2f87c815174fc2bd18551edf24604ca;ef7ab54bdfe1cc5cec2f1dc7872706e7 3507789532;3222876847 +Liu2024 2024 10.1126/sciadv.adn8490 ESL073 ENA PRJEB74036 ERS18499364 210409_A00902_B_L1-2_APMG-28-10 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 106828472 ERR12814470 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/069/ERR12814469/ERR12814469_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/069/ERR12814469/ERR12814469_2.fastq.gz da7778fb9cfed62273af777b6e9f3001;d3fb3c412e8be82070cad4eda19c40c1 2308509705;2437998354 +Liu2024 2024 10.1126/sciadv.adn8490 ESL074 ENA PRJEB74036 ERS18499365 200327_A00902_B_L1-2_APMG-10-20 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 91018898 ERR12814471 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/071/ERR12814471/ERR12814471_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/071/ERR12814471/ERR12814471_2.fastq.gz bc407500c04c274a28ea3d9b4891a3da;a46dc11d060df909087cdf0d4af588b6 2765036775;2327542522 +Liu2024 2024 10.1126/sciadv.adn8490 ESL075 ENA PRJEB74036 ERS18499366 210409_A00902_B_L1-2_APMG-28-9 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 113819524 ERR12814472 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/072/ERR12814472/ERR12814472_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/072/ERR12814472/ERR12814472_2.fastq.gz eae8f7dc05f61ce1ce72e3378296490d;1e8d905d356c1a5329fbe3fa91078c72 3436948124;3459344043 +Liu2024 2024 10.1126/sciadv.adn8490 ESL076 ENA PRJEB74036 ERS18499367 200327_A00902_B_L1-2_APMG-10-21 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 109660044 ERR12814473 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/073/ERR12814473/ERR12814473_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/073/ERR12814473/ERR12814473_2.fastq.gz 12f90800ae8795d646f1aafa6ad83ace;77ce76b3c6eeeba08bd317e1b3ccf1cb 2793224289;3258698776 +Liu2024 2024 10.1126/sciadv.adn8490 ESL077 ENA PRJEB74036 ERS18499368 210409_A00902_B_L1-2_APMG-28-8 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 82609702 ERR12814474 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/074/ERR12814474/ERR12814474_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/074/ERR12814474/ERR12814474_2.fastq.gz 5dab614f4198cbedb3542d0b88330ef6;c2628f6e6a055a191bdac3f29f5e05be 2390002791;2534714308 +Liu2024 2024 10.1126/sciadv.adn8490 ESL078 ENA PRJEB74036 ERS18499369 210409_A00902_B_L1-2_APMG-28-7 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 134931132 ERR12814475 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/075/ERR12814475/ERR12814475_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/075/ERR12814475/ERR12814475_2.fastq.gz 7e120573673c7a1783005f7ad911a5ff;1ea4590ef271b2e74017f1e92404d770 4090579685;3924358144 +Liu2024 2024 10.1126/sciadv.adn8490 ESL079 ENA PRJEB74036 ERS18499370 200327_A00902_B_L1-2_APMG-10-22 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 85518486 ERR12814476 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/076/ERR12814476/ERR12814476_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/076/ERR12814476/ERR12814476_2.fastq.gz 2a5e7c3250bcdfcf9e815571c6efca1c;c5a94cd6c3b2236dbf477960b3bc8dde 2277648738;2617729740 Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM2 ENA PRJEB59830 ERS14617135 VM2/SedaVM2 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 26089750 ERR10878152 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/052/ERR10878152/ERR10878152.fastq.gz c1e838afd1314ef5a80ef60344662943 796070627 Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM3 ENA PRJEB59830 ERS14617136 VM3/SedaVM3 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 55013661 ERR10878153 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/053/ERR10878153/ERR10878153.fastq.gz 9617733c3a010982961a11e71e77c7bb 1828721344 Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM11 ENA PRJEB59830 ERS14617137 VM11/SedaVM11 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 26094794 ERR10878154 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/054/ERR10878154/ERR10878154.fastq.gz 3af8a33732bc72684e7b94931b9c0285 846315529 diff --git a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv index b9ac50682..4ec9a3ec6 100644 --- a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv +++ b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv @@ -661,46 +661,46 @@ Murchie2023 2023 10.1002/edn3.493 Upper Goldbottom 63.90 -138.99 Canada faunal,f Murchie2023 2023 10.1002/edn3.493 Lucky Lady II 63.76 -138.89 Canada faunal,floral,microbial SET-272 270 LLII-12-84-3 13300 10.1038/s41467-021-27439-6 archeological site permafrost NA ENA PRJNA1004851 SRS18592488 Murchie2023 2023 10.1002/edn3.493 Lucky Lady II 63.76 -138.89 Canada faunal,floral,microbial SET-274 137 LLII 12-217-8 15500 10.1038/s41467-021-27439-6 archeological site 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ERS18499350,ERS18499351 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 406 ESL058 5500 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499352 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 382 ESL061 5000 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499354 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 366 ESL063 4700 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499355 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 348 ESL065 4300 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499357,ERS18499356 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 306 ESL068 3500 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499358 +Liu2024 2024 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99.75 China faunal,floral,microbial 04_NC 84 ESL075 1100 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499366 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 68 ESL076 900 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499367 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 58 ESL077 700 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499368 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 38 ESL078 500 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499369 +Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.1 99.75 China faunal,floral,microbial 04_NC 14 ESL079 100 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499370 Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 18 VM2 800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617135 Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 26 VM3 800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617136 Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 64 VM11 3000 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617137 From 6ff95c25a4c610b5ce22601b89b8371740ca5a3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Mon, 7 Oct 2024 17:54:19 +0200 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 57c3d31e6..9c931b19e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,10 +19,12 @@ and this project follows to [Calendar Versioning](https://calver.org/). - White 2021 10.3390/biology10121324 (added by @DianaSpurite, @jfy133, and @alexhbnr) #### Ancient Metagenome: Environmental -- Added: Zampirolo 2024 10.1016/j.cub.2024.08.047 (added by @GiuliaZ538) +- Zampirolo 2024 10.1016/j.cub.2024.08.047 (added by @GiuliaZ538) ### Changed +- Liu 2024 10.1126/sciadv.adn8490 + ### Removed ## v24.06: Su Nuraxi di Barumini @@ -41,7 +43,7 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Metagenome: Environmental -- Liu 2024 10.1126/sciadv.adn8490 (added by @rozwalak) +- Fix archive sample accession codes for Liu 2024 10.1126/sciadv.adn8490 (@alexhbnr) ### Changed From a647eb388e6010f3e90e86c1e42f95664fcaa3c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Mon, 7 Oct 2024 18:09:29 +0200 Subject: [PATCH 3/3] Point Lebrasseur 2024 DOI for the data to the publication --- .../ancientsinglegenome-hostassociated_libraries.tsv | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index 91cb58bc3..e2e5967e2 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -3100,11 +3100,11 @@ Sun2024 2024 10.1038/s41467-024-47358-6 XBQM20 GSA PRJCA020853 SAMC3135942 XBQM2 Sun2024 2024 10.1038/s41467-024-47358-6 XBQM46 GSA PRJCA020853 SAMC3135943 XBQM46 double PfuTurbo Cx Hotstart DNA full-udg HiSeq X Ten SINGLE Targeted-Capture 16540 CRR927092 fastq_mapped ftp://download.big.ac.cn/gsa2/CRA013222/CRR927092/CRR927092.fastq.gz 8abe20d7ad71529e7606cf357155ccbc 3868947 Sun2024 2024 10.1038/s41467-024-47358-6 XBQM125 GSA PRJCA020853 SAMC3135944 XBQM125 double PfuTurbo Cx Hotstart DNA none HiSeq X 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