摘要
Single-cell RNA-sequencing data of stomach tissues from 21 vertebrate species with diverse feeding habits and gastric architectures. The dataset provides cell-level transcriptomic profiles, cell clustering, cell-type annotations, marker genes, and gene-expression information across species and, where available, individual stomach chambers. Users can interactively explore gastric cell landscapes and examine the expression patterns of genes of interest across different cell populations.
实验设计
Stomach tissues from 21 vertebrate species were subjected to single-cell RNA sequencing. After quality control and preprocessing, cells were clustered according to their transcriptomic profiles and annotated using established marker genes. For species with multiple stomach chambers, data from individual chambers were analyzed separately where available. The processed expression matrices, cell-cluster information, cell-type annotations, marker genes, and gene-expression profiles were incorporated into the online visualization platform for interactive exploration by species and stomach chamber.
平台与技术
物种
测序策略
平台
组织
实验方案
| 提取 | RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. |
|---|---|
| 文库构建 | RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols. |
| 数据处理 | CLC Genomics Workbench v 11.0.1 |
样本
38
| 样本 ID | 文库名称 | 物种 | 组织 | 细胞类型 | 疾病 | 年龄 | 性别 | 测序策略 | 平台 | 测序仪器 |
|---|---|---|---|---|---|---|---|---|---|---|
| SAMN53400447 | Sheep2_Rumen_scRNA_seq | Ovis aries | rumen | 2 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400437 | Goat_scRNA_seq | Capra hircus | mixed of rumen, omasum, reticulum and abomasum | 1 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400436 | Cattle_scRNA_seq | Bos taurus | mixed of rumen, omasum, reticulum and abomasum | 4 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400435 | Yak_scRNA_seq | Bos grunniens | mixed of rumen, omasum, reticulum and abomasum | 4 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400434 | Camel_Abomasum_scRNA_seq | Camelus bactrianus | abomasum | 5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400446 | Sheep1_scRNA_seq | Ovis aries | mix of rumen, omasum, reticulum and abomasum | 1.5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400433 | Camel_Reticulum_scRNA_seq | Camelus bactrianus | reticulum | 5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400424 | Tree_shrew_scRNA_seq | Tupaia belangeri | stomach | 6 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400432 | Camel_Rumen_scRNA_seq | Camelus bactrianus | rumen | 5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400445 | Buffalo_Abomasum_scRNA_seq | Bubalus bubalis | abomasum | 4 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400431 | Turkey_glandular_stomach_scRNA_seq | Meleagris gallopavo | muscular stomach | 10 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400430 | Turkey_muscular_stomach_scRNA_seq | Meleagris gallopavo | glandular stomach | 10 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400423 | Donkey_scRNA_seq | Equus asinus | stomach | 4 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400429 | Quail_scRNA_seq | Coturnix japonica | mixed of glandular and muscular stomach | 3 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400428 | Duck_scRNA_seq | Anas platyrhynchos | mixed of glandular and muscular stomach | 7 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400444 | Buffalo_Omasum_scRNA_seq | Bubalus bubalis | abomasum | 4 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400427 | Pigeon_scRNA_seq | Columba livia | mixed of glandular and muscular stomach | 6 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400422 | Cat_scRNA_seq | Felis catus | stomach | 1.5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400426 | Chicken_scRNA_seq | Gallus gallus | mixed of glandular and muscular stomach | 8 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400443 | Buffalo_Reticulum_scRNA_seq | Bubalus bubalis | abomasum | 4 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400425 | Horse_scRNA_seq | Equus caballus | stomach | 6 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400421 | Dog_scRNA_seq | Canis lupus familiaris | stomach | 1 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400454 | Sheep3_Abomasum_scRNA_seq | Ovis aries | abomasum | 1.5 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400442 | Buffalo_Rumen_scRNA_seq | Bubalus bubalis | abomasum | 4 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400420 | Pig_scRNA_seq | Sus scrofa | stomach | 2 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400453 | Sheep3_Omasum_scRNA_seq | Ovis aries | omasum | 1.5 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400441 | Deer_Abomasum_scRNA_seq | Cervus nippon | abomasum | 2.5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400452 | Sheep3_Reticulum_scRNA_seq | Ovis aries | reticulum | 1.5 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400419 | Mouse_scRNA_seq | Mus musculus | stomach | 2 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400451 | Sheep3_Rumen_scRNA_seq | Ovis aries | rumen | 1.5 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400418 | Rat_scRNA_seq | Rattus norvegicus | stomach | 2 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400440 | Deer_Omasum_scRNA_seq | Cervus nippon | omasum | 2.5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400450 | Sheep2_Abomasum_scRNA_seq | Ovis aries | abomasum | 2 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400417 | Rabbit_scRNA_seq | Oryctolagus cuniculus | stomach | 8 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400449 | Sheep2_Omasum_scRNA_seq | Ovis aries | omasum | 2 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400439 | Deer_Reticulum_scRNA_seq | Cervus nippon | reticulum | 2.5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400448 | Sheep2_Reticulum_scRNA_seq | Ovis aries | reticulum | 2 | female | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 | ||
| SAMN53400438 | Deer_Rumen_scRNA_seq | Cervus nippon | rumen | 2.5 | male | scRNA-Seq 10x Chromium | ILLUMINA | Illumina NovaSeq 6000 |
数据文件
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