CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.
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DOI：
10.1093/nar/gku895
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发表时间：
2015-01
影响因子：
14.9
通讯作者：
Gottgens B
中科院分区：
文献类型：
--
作者：
Sánchez-Castillo M;Ruau D;Wilkinson AC;Ng FS;Hannah R;Diamanti E;Lombard P;Wilson NK;Gottgens B
CODEX（http：//codex.stemcells.cam.ac.uk/）是一个用户友好的数据库，用于直接访问和查询公开的下一代测序（NGS）数据，特别针对实验生物学家。在一个多中心基因组数据集生成的时代，CODEX提供了一个单一的数据库，这些样本被收集，统一处理和审查。CODEX的主要驱动力是为更广泛的科学界提供即时访问高质量的NGS数据，无论出版实验室如何，都是直接可比的。CODEX允许用户立即可视化或下载已处理的数据集，或将用户生成的数据与数据库的累积知识库进行比较。CODEX包含四种类型的NGS实验：转录因子染色质免疫沉淀结合高通量测序（ChIP-Seq）、组蛋白修饰ChIP-Seq、DNase-Seq和RNA-Seq。这些主要包含在两个专门的储存库中，HAEMCODE和ESCODE，分别侧重于造血和胚胎干细胞样本。迄今为止，CODEX包含超过1000个样本，包括221个独特的TF和93个独特的细胞类型。因此，CODEX提供了一个最完整的公开可用的NGS数据资源，用于直接询问在哺乳动物发育、稳态和疾病背景下调节细胞身份和命运的转录程序。
CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.
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影响因子：
14.9
作者：
Rustici G;Kolesnikov N;Brandizi M;Burdett T;Dylag M;Emam I;Farne A;Hastings E;Ison J;Keays M;Kurbatova N;Malone J;Mani R;Mupo A;Pedro Pereira R;Pilicheva E;Rung J;Sharma A;Tang YA;Ternent T;Tikhonov A;Welter D;Williams E;Brazma A;Parkinson H;Sarkans U
通讯作者：
Sarkans U
影响因子：
14.9
作者：
Chacon D;Beck D;Perera D;Wong JW;Pimanda JE
通讯作者：
Pimanda JE
影响因子：
16
作者：
Heinz S;Benner C;Spann N;Bertolino E;Lin YC;Laslo P;Cheng JX;Murre C;Singh H;Glass CK
通讯作者：
Glass CK
影响因子：
14.9
作者：
Karolchik D;Barber GP;Casper J;Clawson H;Cline MS;Diekhans M;Dreszer TR;Fujita PA;Guruvadoo L;Haeussler M;Harte RA;Heitner S;Hinrichs AS;Learned K;Lee BT;Li CH;Raney BJ;Rhead B;Rosenbloom KR;Sloan CA;Speir ML;Zweig AS;Haussler D;Kuhn RM;Kent WJ
通讯作者：
Kent WJ
影响因子：
14.9
作者：
Maglott D;Ostell J;Pruitt KD;Tatusova T
通讯作者：
Tatusova T