Gene expression and splicing counts from the Yepez, Gusic et al study - strand-specific

File description:

geneCounts: gene-level counts 

k_j: split counts spanning from one exon to another.

k_theta: non-split counts covering a splice site

n_psi3: total split counts from a given acceptor site

n_psi5: total split counts from a given donor site

n_theta: total split and non-split counts for a given splice site

Sample annotation describing each sample from the dataset

Description file with global information from the dataset

The gene counts were originated using the GTF file from release 34 of GENCODE https://www.gencodegenes.org/human/release_34, and the split and non-split counts contain only the annotated junctions from the same release.

Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, DROP can be used to compute expression and splicing outliers (https://github.com/gagneurlab/drop).

Number of samples: 269
Tissue: Fibroblast
Organism: Homo sapiens
Genome assembly: hg19
Gene annotation: gencode34
Disease (ICD-10: N): E72: 4, E75: 2, E77: 1, E88: 199, F82: 1, F89: 7, G31: 14, G40: 2, G71: 3, G82: 1, G93: 2, I42: 1, K72: 4, NONE: 18, P94: 2, Q02: 1, Q78: 1, R16: 2, R27: 3, R29: 1
Strand specific: TRUE
Paired end: TRUE
Protocol: poly(A) enrichment
Dataset contact: Vicente Yepez, [e-mail]; Julien Gagneur, [e-mail]; Holger Prokisch, [e-mail]

Citation: Cite both the resource using Zenodo's citation and the publication under References

### 文件说明
- `geneCounts`：基因水平计数（gene-level counts）
- `k_j`：跨外显子的剪接断裂计数（split counts），即跨越一个外显子至另一个外显子的测序计数
- `k_theta`：覆盖剪接位点的非剪接断裂计数（non-split counts）
- `n_psi3`：给定受体剪接位点的总剪接断裂计数
- `n_psi5`：给定供体剪接位点的总剪接断裂计数
- `n_theta`：给定剪接位点的总剪接断裂与非剪接断裂计数
- 样本注释：用于描述数据集中每个样本的详细信息
- 数据集全局信息说明文件

本数据集的基因计数源自GENCODE第34版的GTF文件（https://www.gencodegenes.org/human/release_34），其剪接断裂与非剪接断裂计数仅包含该版本注释的剪接连接位点。

### 使用说明
本计数矩阵旨在为关注利用RNA测序数据开展诊断研究的科研人员提供支持。研究者可将自有数据集与本下载数据集进行合并，但需保证二者在组织类型、基因组组装版本、链特异性及双端测序规格上保持一致。完成合并后，可使用DROP工具计算表达与剪接异常值（https://github.com/gagneurlab/drop）。

### 数据集基本信息
- 样本量：269
- 组织类型：成纤维细胞（Fibroblast）
- 物种：智人（Homo sapiens）
- 基因组组装版本：hg19
- 基因注释版本：gencode34
- 疾病分类（ICD-10: N）：E72: 4例，E75: 2例，E77: 1例，E88: 199例，F82: 1例，F89: 7例，G31:14例，G40:2例，G71:3例，G82:1例，G93:2例，I42:1例，K72:4例，NONE:18例，P94:2例，Q02:1例，Q78:1例，R16:2例，R27:3例，R29:1例
- 链特异性：是
- 双端测序：是
- 实验方案：poly(A)富集（poly(A) enrichment）
- 数据集联系人：Vicente Yepez，邮箱：[e-mail]；Julien Gagneur，邮箱：[e-mail]；Holger Prokisch，邮箱：[e-mail]

### 引用说明
引用本资源时，请同时标注Zenodo平台的引用信息及参考文献中的相关论文。