Utility

The original intent of assembling a data set of publicly-available tumor-infiltrating T cells (TILs) with paired TCR sequencing was to expand and improve the scRepertoire R package. However, after some discussion, we decided to release the data set for everyone, a complete summary of the sequencing runs and the sample information can be found in the meta data of the Seurat object.

Folder Structure

├── code
│   ├── Processing_Utility.Rmd - general processing script
│   └── Summarize_Data.Rmd - script to get summary data
├── data
│   ├── SequencingRuns - 10x Outputs
│   └── processedData - Processed .rds and larger combined cohorts
├── NEWS.txt - changes made
├── outputs
│   └── qc - plots for quality control purposes
├── README.md
└── summaryInfo
    ├── TcellSummaryTable.csv
    ├── cohortSummaryTable.csv
    ├── meta.data.headers.txt - what the meta data headers mean
    ├── sample.directory.xlsx - all the available data for the cohort
    ├── sessionInfo.txt - what I am running in terms of the pipeline
    └── tumorSummaryTable.csv

Sample ID:

Cohort Information

Here is the current list of data sources, the number of cells that passed filtering by tissue type. Please cite the data if you are using uTILity.

	Tumor	Normal	Blood	Juxta	LN	Met	Cancer Type	Citations
CCR-20-4394	26760	0	0	0	0	0	Ovarian	cite
EGAS00001004809	181667	0	0	0	0	0	Breast	cite
GSE114724	27651	0	0	0	0	0	Breast	cite
GSE121636	11436	0	12319	0	0	0	Renal	cite
GSE123814	78034	0	0	0	0	0	Multiple	cite
GSE139555	93160	78625	25363	0	0	0	Multiple	cite
GSE145370	66592	40916	0	0	0	0	Esophageal	cite
GSE148190	2263	0	6201	0	15644	0	Melanoma	cite
GSE154826	14491	13414	0	0	0	0	Lung	cite
GSE159251	8356	0	47721	0	5705	0	Melanoma	cite
GSE162500	14644	0	23401	3761	0	0	Lung	cite
GSE164522	36990	86811	46027	0	46376	36648	Colorectal	cite
GSE168844	0	0	55302	0	0	0	Lung	cite
GSE176021	436609	128411	132673	0	71063	32011	Lung	cite
GSE179994	78574	0	0	0	0	62341	Lung	cite
GSE180268	23215	0	0	0	29699	0	HNSCC	cite
GSE181061	40429	27622	37426	0	0	0	Renal	cite
GSE185206	163294	17231	0	0	9820	0	Lung	cite
GSE195486	122512	0	0	0	0	0	Ovarian	cite
GSE200218	0	0	0	0	0	18495	Melanoma	cite
GSE200996	86235	0	152722	0	0	0	HNSCC	cite
GSE201425	22888	0	27781	0	11350	12253	Biliary	cite
GSE211504	0	0	33685	0	0	0	Melanoma	cite
GSE212217	0	0	229505	0	0	0	Endometrial	cite
GSE213243	2835	0	18363	0	0	2693	Ovarian	cite
GSE215219	26303	0	66000	0	0	0	Lung	cite
GSE227708	53087	0	0	0	0	0	Merkel Cell	cite
GSE242477	41595	0	21595	0	0	0	Melanoma	cite
PRJNA705464	98892	15113	30340	0	3505	0	Renal	cite