CROST——空间转录组学的综合数据库

docs/2024-11/CROST__空间转录组学的综合数据库.md

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+---
+title: "CROST——空间转录组学的综合数据库"
+date: 2024-11-22T01:12:58Z
+draft: ["false"]
+tags: [
+  "fetched",
+  "生信技能树"
+]
+categories: ["Acdemic"]
+---
+CROST——空间转录组学的综合数据库 by 生信技能树
+------
+<div><section data-tool="mdnice编辑器" data-website="https://www.mdnice.com"><p data-tool="mdnice编辑器">文章：Wang, G., Wu, S., Xiong, Z., Qu, H., Fang, X., &amp; Bao, Y. (2024). CROST: a comprehensive repository of spatial transcriptomics. Nucleic Acids Research, 52(D1), D882-D890. https://academic.oup.com/nar/article/52/D1/D882/7288834</p><p data-tool="mdnice编辑器">空间转录组数据库如雨后春笋般冒出来了，今天我们要介绍的是CROST，该网站链接：https://ngdc.cncb.ac.cn/crost/</p><p data-tool="mdnice编辑器">科研人员搜集了来自NCBI、European Bioinformatics Institute (EBI) 、 China National Center for Bioinformation (CNCB)、Broad Institute Single Cell Portal、10× Genomics 、DNA Data Bank of Japan (DDBJ)的数据，采用关键词 ‘spatial transcriptomics’, ‘spatial transcriptome’, ‘spatial genome’, ‘spatial RNA-seq’ and ‘spatial sequencing.’</p><p data-tool="mdnice编辑器">最后拿到了<strong>182 个空间转录组数据集</strong>，涵盖来自 <strong>8 个不同物种</strong>（ (Homo sapiens, Mus musculus, Danio rerio, Gallus gallus, Canis lupus familiaris, Phalaenopsis aphrodite and Rattus norvegicus)）、35 种组织和 56 种疾病的 <strong>1033 个样本</strong>。</p><p data-tool="mdnice编辑器"><img data-imgfileid="100045106" data-ratio="0.8037316110513096" data-src="https://mmbiz.qpic.cn/mmbiz_jpg/cZNhZQ6j4wwKEc44BzDviabMP7pauCeozlAval7rKtRGXDRt0IchImw1ZFiahicEMgibaEwoV2VnCnlPqQGJIfk7Cw/640?wx_fmt=jpeg&amp;from=appmsg" data-type="jpeg" data-w="2787" src="https://mmbiz.qpic.cn/mmbiz_jpg/cZNhZQ6j4wwKEc44BzDviabMP7pauCeozlAval7rKtRGXDRt0IchImw1ZFiahicEMgibaEwoV2VnCnlPqQGJIfk7Cw/640?wx_fmt=jpeg&amp;from=appmsg"></p><p data-tool="mdnice编辑器">CROST 包括四个主要模块：</p><ul data-tool="mdnice编辑器"><li><section><p>Browse module: basic information, sample characteristics, biological status, experimental protocols, and quality assessment<img data-imgfileid="100045108" data-ratio="1.4792663476874004" data-src="https://mmbiz.qpic.cn/mmbiz_jpg/cZNhZQ6j4wwKEc44BzDviabMP7pauCeozXlicrdam8T7ZXhTJfQcn4NmGvAJAc3ywpawmfXibPPrvtZkLa0QIMANA/640?wx_fmt=jpeg&amp;from=appmsg" data-type="jpeg" data-w="2508" src="https://mmbiz.qpic.cn/mmbiz_jpg/cZNhZQ6j4wwKEc44BzDviabMP7pauCeozXlicrdam8T7ZXhTJfQcn4NmGvAJAc3ywpawmfXibPPrvtZkLa0QIMANA/640?wx_fmt=jpeg&amp;from=appmsg"></p></section></li><li><section><p>Cancer SVG module: <strong>48043 SVGs</strong> significantly enriched primarily in the kidney cancer (8323 genes), liver cancer (6380 genes) and melanoma (5964 genes)<img data-imgfileid="100045107" data-ratio="1.385506163615988" data-src="https://mmbiz.qpic.cn/mmbiz_jpg/cZNhZQ6j4wwKEc44BzDviabMP7pauCeoz01QvMvqmv7c51LecjQ2grlHBCcNoSmU3khMuwRUSKsIbEIKqxEYuHQ/640?wx_fmt=jpeg&amp;from=appmsg" data-type="jpeg" data-w="2677" src="https://mmbiz.qpic.cn/mmbiz_jpg/cZNhZQ6j4wwKEc44BzDviabMP7pauCeoz01QvMvqmv7c51LecjQ2grlHBCcNoSmU3khMuwRUSKsIbEIKqxEYuHQ/640?wx_fmt=jpeg&amp;from=appmsg"></p></section></li><li><section><p>Online analysis module：ssGSEA + SpatialAP</p></section></li><li><section><p>Explore module: visualization, communication, cell-type colocalization, and cell-type correlation<img data-imgfileid="100045105" data-ratio="0.7745856353591161" data-src="https://mmbiz.qpic.cn/mmbiz_png/cZNhZQ6j4wwKEc44BzDviabMP7pauCeozH5ZibzdIWTsntUp0abkz9bZbHNWiak2kBD0Nt9ia9AvcRVwFcAiaMglw1w/640?wx_fmt=png&amp;from=appmsg" data-type="png" data-w="1810" src="https://mmbiz.qpic.cn/mmbiz_png/cZNhZQ6j4wwKEc44BzDviabMP7pauCeozH5ZibzdIWTsntUp0abkz9bZbHNWiak2kBD0Nt9ia9AvcRVwFcAiaMglw1w/640?wx_fmt=png&amp;from=appmsg"></p></section></li></ul><p data-tool="mdnice编辑器">另外分享其它实用的空间转录组数据库</p><ul data-tool="mdnice编辑器"><li><section>STOmicsDB（Spatial Transcript Omics DataBase）， 数据库链接：https://db.cngb.org/stomics/，（17个物种的218个人工处理的数据集），2022，<strong>深圳国家基因库</strong>和<strong>深圳华大生命科学研究院</strong>，</section></li><li><section>SpatialDB，http://spatialomics.org/SpatialDB/index.php，2019，中国科学院生物物理研究所，发表在《<strong>Nucleic acids research</strong>》，5个物种（人类、小鼠、果蝇、秀丽隐杆线虫和斑马鱼）的24个空间转录组数据集</section></li><li><section>SPASCER， https://ccsm.uth.edu/SPASCER</section></li><li><section>Spatial Omics DataBase (SODB) ，2023 在《<span><em>Nature Methods</em></span>》发表，附带Python开发的软件工具，https://pysodb.readthedocs.io/en/latest/</section><section><br></section></li></ul><h4 data-tool="mdnice编辑器">文末友情宣传</h4><p data-tool="mdnice编辑器">强烈建议你推荐给身边的<strong>博士后以及年轻生物学PI</strong>，多一点数据认知，让他们的科研上一个台阶：</p><section><a target="_blank" href="http://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&amp;mid=2247529099&amp;idx=1&amp;sn=fe3be2d43a6284a36c15625c23dc9a3e&amp;chksm=9b4b3230ac3cbb26b875bd0a294f24dfbd41a2b59996fbfe79087330d267c4ec70882683c3bd&amp;scene=21#wechat_redirect" textvalue="生物信息学马拉松‍授课（买一得五）" linktype="text" imgurl="" imgdata="null" data-itemshowtype="0" tab="innerlink" data-linktype="2">生物信息学马拉松授课（买一得五）</a> ，你的生物信息学入门课</section><ul data-tool="mdnice编辑器"><li><section> <a target="_blank" href="http://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&amp;mid=2247528363&amp;idx=1&amp;sn=5e02f3e9b2e148191e23ebc2c0d780e7&amp;chksm=9b4b2f10ac3ca606c1c4bac8cf112bb9b0f18e3c4262f5f2b8c0dba3bfedf2ba201507247005&amp;scene=21#wechat_redirect" textvalue="2024的共享服务器交个朋友福利价仍然是800" linktype="text" imgurl="" imgdata="null" data-itemshowtype="0" tab="innerlink" data-linktype="2" hasload="1">2024的共享服务器交个朋友福利价仍然是800</a></section></li><li><section><a target="_blank" href="http://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&amp;mid=2247519765&amp;idx=1&amp;sn=ce5a8c8182f854c88043059f8c2cb9ff&amp;chksm=9b4bceaeac3c47b88c19941d43dbb1401f3a92206481a0afc41159927868199643f795d62a7e&amp;scene=21#wechat_redirect" textvalue="千呼万唤始出来的独享生物信息学云服务器" linktype="text" imgurl="" imgdata="null" data-itemshowtype="0" tab="innerlink" data-linktype="2" hasload="1">千呼万唤始出来的独享生物信息学云服务器</a></section></li></ul><p><span> </span></p></section><p><mp-style-type data-value="3"></mp-style-type></p></div>  
+<hr>
+<a href="https://mp.weixin.qq.com/s/j6yrLYqaV4Cz7sFCTrevUA",target="_blank" rel="noopener noreferrer">原文链接</a>