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做过ChIP-seq或ATAC-seq的物种速查
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作者：小丫 来源：嘉因
上周分享了各物种ATAC-seq数据统计，有小伙伴儿问ChIP-seq都做过哪些物种，其实我也好奇。
粗略检索了一下，居然有285个物种有ChIP-seq数据。下次再有人问某某物种做没做过ChIP的时候，我就淡定的打开此文，搜索该物种的拉丁名。
把策略放在这里，便于重复：
在SRA搜索ChIP-seq，send to File；
Library Strategy一列标为ChIP-seq和MNase-seq的认定是ChIP-seq。有些人对核小体定位感兴趣，用MNase酶切做组蛋白修饰的ChIP-seq，这样能看到核小体分辨率的组蛋白修饰，就标成了MNase-seq。所以，很多MNase-seq其实是ChIP-seq；
Experiment Title中有ChIP-seq字样的认定是ChIP-seq；
统计2、3步认定为ChIP-seq的Organism Name的个数，即该物种ChIP-seq数据个数。
强调一下，是粗略检索！用户提交的信息不是很规范，难免有Organism Name、Experiment Title或Library Strategy的出入。对某个物种感兴趣的小伙伴，如果要把数量写进毕业论文前言里，需要自己仔细核对。
各物种ChIP-seq数量如下：
Organism Name | 数量 |
| Homo sapiens | 33845 |
| Mus musculus | 30045 |
| Saccharomyces cerevisiae | 5125 |
| Drosophila melanogaster | 4037 |
| Caenorhabditis elegans | 2284 |
| Arabidopsis thaliana | 1731 |
| Schizosaccharomyces pombe | 1209 |
| Rattus norvegicus | 729 |
| metagenome | 373 |
| Zea mays | 293 |
| Macaca mulatta | 276 |
| Gallus gallus | 267 |
| Danio rerio | 224 |
| Mycobacterium tuberculosis H37Rv | 221 |
| Pan troglodytes | 221 |
| Xenopus tropicalis | 165 |
| Callithrix jacchus | 163 |
| Xenopus laevis | 145 |
| Neurospora crassa | 142 |
| Escherichia coli str. K-12 substr. MG1655 | 133 |
| Escherichia coli | 129 |
| Plasmodium falciparum 3D7 | 124 |
| Candida albicans | 115 |
| Plasmodium falciparum | 108 |
| Saccharomyces cerevisiae S288C | 106 |
| Otolemur garnettii | 102 |
| Schistosoma mansoni | 97 |
| Pseudomonas aeruginosa | 80 |
| Drosophila virilis | 78 |
| Chlamydomonas reinhardtii | 76 |
| Physcomitrella patens | 69 |
| Oryza sativa | 66 |
| Microcebus murinus | 66 |
| Camponotus floridanus | 66 |
| Canis lupus familiaris | 65 |
| Monodelphis domestica | 64 |
| Bos taurus | 62 |
| Ascaris suum | 62 |
| Schmidtea mediterranea | 60 |
| Salmonella enterica subsp. enterica serovar Typhimurium | 59 |
| Cryptococcus neoformans | 56 |
| Malus fusca | 56 |
| Drosophila simulans | 53 |
| Tetrahymena thermophila | 50 |
| Plasmodium vivax | 49 |
| Oryza sativa Japonica Group | 47 |
| Bacillus subtilis PY79 | 45 |
| [Candida] glabrata | 44 |
| Solanum lycopersicum | 41 |
| synthetic construct | 41 |
| Glycine max | 40 |
| Human gammaherpesvirus 8 | 38 |
| Drosophila pseudoobscura | 37 |
| Gasterosteus aculeatus | 36 |
| Schizosaccharomyces pombe 972h- | 36 |
| Phaseolus vulgaris | 36 |
| Drosophila yakuba | 35 |
| Zea mays subsp. mays | 33 |
| Aspergillus nidulans | 33 |
| Francisella tularensis subsp. holarctica LVS | 32 |
| Sus scrofa | 31 |
| Trypanosoma brucei brucei | 30 |
| Streptomyces venezuelae | 29 |
| Equus asinus x caballus | 29 |
| Bombyx mori | 29 |
| Caulobacter crescentus NA1000 | 28 |
| Cricetulus griseus | 28 |
| Fusarium graminearum | 28 |
| Cucumis melo var. cantalupo | 27 |
| Caulobacter crescentus CB15 | 27 |
| Saccharomyces cerevisiae W303 | 27 |
| Cucumis melo | 25 |
| Synechococcus elongatus PCC 7942 | 25 |
| Mus musculus domesticus | 24 |
| Tupaia belangeri | 24 |
| Capsaspora owczarzaki | 24 |
| Caulobacter vibrioides | 23 |
| Nematostella vectensis | 23 |
| Alcaligenes sp. | 23 |
| Saccharomyces cerevisiae BY4741 | 22 |
| Methanocaldococcus jannaschii DSM 2661 | 21 |
| Heterocephalus glaber | 21 |
| Malus domestica | 20 |
| Amphimedon queenslandica | 20 |
| Rhodobacter capsulatus | 20 |
| Apis mellifera | 20 |
| Oryzias latipes | 20 |
| Plasmodium falciparum NF54 | 19 |
| Bacillus subtilis subsp. subtilis | 19 |
| Anolis carolinensis | 18 |
| Bacillus subtilis subsp. subtilis str. 168 | 18 |
| Miniopterus natalensis | 18 |
| Mus spretus | 17 |
| Drosophila miranda | 17 |
| Mycobacterium tuberculosis | 17 |
| Columba livia | 16 |
| Rhodobacter sphaeroides | 16 |
| Sordaria macrospora | 15 |
| Cavia porcellus | 15 |
| Oryctolagus cuniculus | 15 |
| Mustela putorius furo | 15 |
| Mus musculus musculus | 14 |
| Arabidopsis lyrata | 14 |
| Avena sativa | 14 |
| Eucalyptus grandis | 14 |
| Sarcophilus harrisii | 14 |
| Heliconius erato lativitta | 14 |
| Vibrio cholerae O1 str. C6706 | 14 |
| Saccharomyces cerevisiae SK1 | 14 |
| Neurospora crassa OR74A | 14 |
| Populus | 14 |
| Trichomonas vaginalis | 13 |
| Felis catus | 13 |
| Arabidopsis | 13 |
| Drosophila ananassae | 12 |
| Staphylococcus aureus subsp. aureus NCTC 8325 | 12 |
| Chlorocebus sabaeus | 12 |
| Ustilago maydis | 12 |
| Zymoseptoria tritici | 12 |
| Mycobacterium bovis BCG str. Pasteur 1173P2 | 11 |
| Phaeodactylum tricornutum | 11 |
| Streptomyces venezuelae ATCC 10712 | 11 |
| Drosophila busckii | 11 |
| Torulaspora delbrueckii CBS 1146 | 11 |
| Mycobacterium smegmatis | 11 |
| Eucommia ulmoides | 11 |
| marine metagenome | 10 |
| Pyrus x bretschneideri | 10 |
| Helicobacter pylori G27 | 10 |
| Sulfolobus acidocaldarius DSM 639 | 10 |
| Escherichia coli ETEC H10407 | 10 |
| Waddlia chondrophila | 10 |
| Escherichia coli K-12 | 10 |
| Pseudomonas syringae | 10 |
| Dictyostelium discoideum | 10 |
| Mus musculus castaneus | 10 |
| Avena sativa/Zea mays addition line | 10 |
| Pseudomonas fluorescens | 9 |
| Equus caballus | 9 |
| Fusarium fujikuroi | 9 |
| Pyrococcus furiosus DSM 3638 | 9 |
| Candida glabrata CBS 138 | 9 |
| Escherichia coli str. K-12 substr. MG1655star | 9 |
| Equus asinus | 8 |
| Ciona intestinalis | 8 |
| Prunus persica | 8 |
| Brucella abortus | 8 |
| Kluyveromyces lactis | 8 |
| Acyrthosiphon pisum | 8 |
| Magnaporthe oryzae | 8 |
| Rhodobacter capsulatus SB 1003 | 8 |
| Mesoplodon bidens | 8 |
| Tetrahymena thermophila CU428 | 8 |
| Listeria monocytogenes | 8 |
| Penicillium chrysogenum | 8 |
| Bacillus subtilis subsp. subtilis str. JH642 | 8 |
| Naumovozyma castellii | 8 |
| Blastomyces dermatitidis ATCC 26199 | 8 |
| Taeniopygia guttata | 8 |
| Human betaherpesvirus 5 | 8 |
| Mus caroli | 8 |
| Aplysia californica | 8 |
| Leishmania major | 7 |
| Litopenaeus vannamei | 7 |
| Toxoplasma gondii | 7 |
| Musa acuminata AAA Group | 7 |
| Cucumis sativus | 7 |
| Cyanidioschyzon merolae strain 10D | 7 |
| Pantherophis guttatus | 7 |
| Human gammaherpesvirus 4 | 7 |
| Arabis alpina | 7 |
| Lethenteron camtschaticum | 6 |
| soil metagenome | 6 |
| Zea mays subsp. mexicana | 6 |
| Merkel cell polyomavirus | 6 |
| Xenopus tropicalis x Xenopus laevis | 6 |
| Triticum aestivum | 6 |
| Scheffersomyces stipitis | 6 |
| Papio anubis | 6 |
| Eutrema salsugineum | 6 |
| Pseudomonas aeruginosa UCBPP-PA14 | 6 |
| Aspergillus fumigatus | 6 |
| Mus musculus x Mus spretus | 6 |
| Candida parapsilosis | 6 |
| Leishmania tarentolae | 6 |
| Bacillus subtilis | 5 |
| Streptomyces albus | 5 |
| Gossypium hirsutum | 5 |
| Pseudomonas syringae pv. tomato str. DC3000 | 5 |
| Delphinus delphis | 5 |
| Populus x canadensis | 5 |
| Drosophila willistoni | 5 |
| Pongo pygmaeus pygmaeus | 5 |
| Saccharomyces bayanus | 5 |
| Thermobifida fusca YX | 4 |
| Sorghum bicolor | 4 |
| Zea mays subsp. huehuetenangensis | 4 |
| Zea mays subsp. parviglumis | 4 |
| Vitis vinifera | 4 |
| Synechocystis sp. PCC 6803 | 4 |
| Arabidopsis thaliana x Arabidopsis lyrata | 4 |
| Triticum urartu | 4 |
| Aegilops tauschii | 4 |
| Komagataella pastoris | 4 |
| Gossypium barbadense | 4 |
| Lagenorhynchus albirostris | 4 |
| Balaenoptera borealis | 4 |
| Sinorhizobium fredii CCBAU 45436 | 4 |
| Leptospira interrogans serovar Copenhageni | 4 |
| Clavispora lusitaniae | 4 |
| Solanum tuberosum | 4 |
| Escherichia coli CFT073 | 4 |
| Plasmodium berghei ANKA | 4 |
| Gorilla gorilla gorilla | 4 |
| Papio hamadryas | 4 |
| Drosophila erecta | 4 |
| Nostoc sp. PCC 7120 | 4 |
| Rhodobacter sphaeroides 2.4.1 | 4 |
| Plasmodium berghei | 4 |
| Pseudomonas savastanoi pv. phaseolicola | 4 |
| Sinorhizobium fredii | 4 |
| Mus musculus domesticus x M. m. molossinus | 4 |
| Streptomyces griseus | 4 |
| Setaria italica | 3 |
| Thermoplasma acidophilum DSM 1728 | 3 |
| Carica papaya | 3 |
| Fragaria vesca | 3 |
| Citrullus lanatus | 3 |
| Mycoplasma pneumoniae M129 | 3 |
| Brassica napus | 3 |
| Streptomyces coelicolor A3(2) | 3 |
| Vibrio cholerae | 3 |
| Sulfolobus solfataricus | 3 |
| Gorilla gorilla | 3 |
| Anopheles gambiae | 3 |
| Caenorhabditis briggsae | 3 |
| Vibrio alginolyticus | 2 |
| Equus caballus x asinus | 2 |
| Zea mays subsp. mays x Zea luxurians | 2 |
| Tripsacum dactyloides | 2 |
| Zea luxurians | 2 |
| Zea diploperennis | 2 |
| Actinoplanes missouriensis 431 | 2 |
| Patiria miniata | 2 |
| Strongylocentrotus purpuratus | 2 |
| Cryptococcus neoformans var. grubii | 2 |
| Pseudomonas aeruginosa PAO1 | 2 |
| Leishmania donovani | 2 |
| Beta vulgaris subsp. vulgaris | 2 |
| Microtus ochrogaster | 2 |
| Nothobranchius furzeri | 2 |
| Escherichia coli O157:H7 | 2 |
| Burkholderia cenocepacia | 2 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu | 2 |
| Tribolium castaneum | 2 |
| Saguinus oedipus | 2 |
| Ovis aries | 2 |
| Hordeum vulgare | 2 |
| Oxytricha trifallax | 2 |
| Anabaena | 2 |
| Notamacropus eugenii | 2 |
| Gossypium raimondii | 1 |
| Vibrio vulnificus | 1 |
| wastewater metagenome | 1 |
| Helianthus annuus | 1 |
| oil field metagenome | 1 |
| Nelumbo nucifera | 1 |
| Rhodospirillum centenum | 1 |
| Vibrio mexicanus | 1 |
| Oreochromis niloticus | 1 |
| Vibrio fluvialis | 1 |
| Providencia rettgeri | 1 |
| Vibrio cholerae O139 | 1 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S | 1 |
| Streptomyces coelicolor | 1 |
| mixed culture metagenome | 1 |
| Candida tropicalis | 1 |
| Fusarium fujikuroi IMI 58289 | 1 |
| Tetraodon nigroviridis | 1 |
| Escherichia coli BL21(DE3) | 1 |
| Rhodobacter sphaeroides ATCC 17025 | 1 |
| Ambystoma mexicanum | 1 |
| Neurospora tetrasperma | 1 |
| Neurospora discreta | 1 |
| Thermococcus kodakarensis KOD1 | 1 |
Organism Name | 中文名 | 数量 |
| Homo sapiens | 人 | 6019 |
| Mus musculus | 小鼠 | 2223 |
| Drosophila melanogaster | 果蝇 | 122 |
| Danio rerio | 斑马鱼 | 25 |
| Saccharomyces cerevisiae | 酿酒酵母 | 23 |
| Arabidopsis thaliana | 拟南芥 | 23 |
| Strongylocentrotus purpuratus | 海胆 | 21 |
| Oryza sativa | 水稻 | 20 |
| Caenorhabditis elegans | 线虫 | 10 |
| Capsaspora owczarzaki | 变形虫 | 5 |
| Schizosaccharomyces pombe | 粟酒裂殖酵母 | 5 |
| Streptococcus agalactiae | 无乳链球菌 | 4 |
| Sorghum bicolor | 高粱 | 3 |
| Solanum lycopersicum | 番茄 | 2 |
| Medicago truncatula | 苜蓿 | 2 |
| Oryza sativa Japonica Group | 水稻 | 2 |
| Setaria italica | 小米 | 2 |
| Zea mays | 玉米 | 2 |
| Zea mays subsp. mays | 玉米 | 1 |
| Branchiostoma lanceolatum | 文昌鱼 | 1 |
| Oryzias latipes | 青鱂鱼 | 1 |
延伸查询
https://blog.sciencenet.cn/blog-3372875-1090484.html
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