Data Repository - Spatial Reconstruction Of Single Enterocytes Uncovers Broad Zonation Along The Intestinal Villus Axis

Data associated with the manuscript entitled "Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis". Files: table_A_LCM_TPM_values.tsv: Gene expression levels of microdissected villus quintiles. First column is the ensemble gene id. Next 15 columns are the raw Kallisto TPM values for villus segments 1 (bottom) to 5 (top) for three different mice (a to c). Additional columns include the external gene name, description, and gene biotype. table_B_scRNAseq_UMI_counts.tsv: Raw UMI counts of cells that were utilized in this study. Analysis is based on raw data from the NCBI GEO datasets GSM2644349 and GSM2644350. Each of the columns represents a single cell, column headers are the corresponding cell barcodes and enable retrieval of tSNE coordinates from table_C_scRNAseq_tsne_coordinates_zones.tsv. Values represent raw UMI counts. table_C_scRNAseq_tsne_coordinates_zones.tsv: tSNE coordinates and reconstructed zones of cells that were utilized in this study. Tab separated text file. Analysis is based on raw data from the NCBI GEO datasets GSM2644349 and GSM2644350. Columns: cell_id: cell barcode, corresponds to column header of Table S2. Seurat tSNE coordinate 1 and tSNE coordinate 2. Last column is the inferred zone (Crypt, V1..V6). table_D_zonation_reconstruction.tsv: Zonation table of reconstructed scRNAseq data. Tab separated text file. Columns: Gene names: gene id, mean expression in each of the crypt zone and 6 villus zones, standard error of the means in the Crypt zone and 6 villus zones, p-value and q-value for the zonation profiles. raw_data.zip: The raw and intermediary data for runnning the scripts in https://github.com/aemoor/Code_spatial_reconstruction_enterocytes本数据集关联于题为《单个肠上皮细胞的空间重构揭示沿肠绒毛轴的广泛分区特征》的研究手稿。 数据集文件： table_A_LCM_TPM_values.tsv：包含显微切割获取的绒毛五等分区段的基因表达水平数据。第一列为Ensembl基因ID（Ensembl gene ID），后续15列分别对应3只编号为a至c的小鼠的绒毛区段1（底端）至5（顶端）的原始Kallisto TPM值。其余列包含基因外部名称、功能注释及基因生物型。 table_B_scRNAseq_UMI_counts.tsv：包含本研究所用单细胞的原始唯一分子标识符（UMI）计数数据。分析基于NCBI基因表达综合数据库（NCBI GEO）数据集GSM2644349与GSM2644350的原始测序数据。每一列代表一个单细胞，列标题为对应的细胞条形码，可通过该条形码从table_C_scRNAseq_tsne_coordinates_zones.tsv中检索t分布邻域嵌入（tSNE）坐标。表格数值为原始UMI计数。 table_C_scRNAseq_tsne_coordinates_zones.tsv：包含本研究所用单细胞的tSNE坐标与重构得到的细胞分区信息，为制表符分隔的文本文件。分析基于NCBI GEO数据集GSM2644349与GSM2644350的原始数据。各列信息如下：cell_id：细胞条形码，与表B的列标题一一对应；Seurat单细胞分析工具（Seurat）生成的tSNE坐标1与tSNE坐标2；最后一列为推断得到的细胞分区（隐窝区、V1至V6）。 table_D_zonation_reconstruction.tsv：包含重构后单细胞RNA测序（scRNA-seq）数据的分区分析表，为制表符分隔的文本文件。各列信息如下：Gene names：基因ID；隐窝区与6个绒毛区段中的平均表达量；隐窝区与6个绒毛区段的均值标准误；分区特征分析对应的p值与校正q值。 raw_data.zip：该压缩包包含运行https://github.com/aemoor/Code_spatial_reconstruction_enterocytes 中脚本所需的原始数据与中间处理数据。