Tsetse parasites sequenced → passed QC
ERP132258 · PRJEB47937 · ZENODO 6047732
追溯388个采采蝇阶段Smart-seq2细胞
本页把论文中的测序与质控数字、ENA当前公开运行、作者Zenodo处理对象和未来本站可视化边界分开记录。468条ENA运行、515个进入测序的采采蝇来源寄生虫和388个最终图谱细胞不是同一个统计口径。
936 paired FASTQ files
Cells × raw-count features
Deposited coordinates available
COUNTING BOUNDARY
388是通过质控的采采蝇来源细胞，不含46个体外验证单细胞
论文报告515个采采蝇来源寄生虫进入测序，388个通过质控：中肠78个、前胃34个、唾液腺276个。另有48个体外前循环型转录组用于方法验证，其中46个是单细胞，另外两个分别是无细胞与10细胞对照。
ENA · CURRENT REPOSITORY LAYER
468个运行均提供双端FASTQ，但不能直接等同于论文总数
ENA把论文所报ERP132258解析为项目PRJEB47937。当前文件报告含468个样本、468个实验和468个运行，共936个FASTQ.gz文件；另有468个CRAM和85个CRAI。SRA FTP字段为空。
RUN ALIAS GROUP
28745_8
Illumina HiSeq 4000
ENA RUNS450 exact processed-atlas matches
This run group does not occur in the 388-cell fly-stage metadata. Its size is close to the 46 validation single cells, but the ENA sample titles do not support assigning individual runs to the validation set with certainty.
RUN ALIAS GROUP
28959_8
Illumina HiSeq 2500
ENA RUNS201165 exact processed-atlas matches
165 author-processed fly-stage cells resolve exactly to this ENA run alias; 36 ENA runs are outside the final 388-cell matrix.
RUN ALIAS GROUP
29784_4
Illumina HiSeq 2500
ENA RUNS222222 exact processed-atlas matches
All 222 ENA aliases resolve to author-processed fly-stage cells. One additional processed cell, 29784_4#45, is absent from the current ENA report.
The current ENA report is not numerically identical to either the 515 tsetse parasites sequenced or the 388-cell author matrix. TrypCell preserves all three counts and does not infer missing run-to-cell relationships.
ZENODO · AUTHOR PROCESSED LAYER
原始计数、细胞元数据、基因元数据和SC3对象均已存档
FILE / ROLEROWSCOLUMNSSIZE
counts_howick_tryps_sce.csvRaw count matrix9,2253887.64 MB
coldata_howick_tryps_sce.csvCell metadata38848152.40 kB
rowdata_howick_tryps_sce.csvGene metadata9,225211.36 MB
howick_tryps_sce.rdsAuthor SC3 object3889,2258.59 MB
ARCHIVEvhowick/tryps_single_cell-v1.0.zip
SIZE35.79 MB
MD5
61deb6e0af0189b5b29130e700f1ad8aThe archive contains R Markdown, rendered analysis outputs and supporting CSV/RDS files for the main figures and supplementary analyses. The extracted release contains 43 files in 10 directories.
Processed-object SHA-256 checksums
counts_howick_tryps_sce.csv: b7a30be73b2c8bad31814fcfb5fe926ba59c9a81a7da3e76213eaa67a2634f86coldata_howick_tryps_sce.csv: 0330c662d10617933ea0ce0fc0b83c5017020b00a8cca4553fccbf433d2cff8frowdata_howick_tryps_sce.csv: bb63d9709815e454a5b209768ddcb113bf73d506f6a2e51480102caafbb88862howick_tryps_sce.rds: 4d37bb2ddeb134e6fa15b039f136f090f5142971da822c6a8b267ac3320fdcf2AUTHOR EMBEDDING · TRYPCELL INTERACTIVE VIEW
真实UMAP坐标已在作者元数据中，不需要从论文图片重画
The deposited cell metadata contains author fig1_UMAP_1 and fig1_UMAP_2 coordinates for every one of the 388 cells.
The deposited CSV is the author raw-count matrix. Smart-seq2 counts are not UMI counts and should not be merged directly with 10x UMI matrices.
The TrypCell view uses the deposited coordinates, cluster names and counts directly. TrypCell does not reconstruct coordinates by tracing points from the paper figure.