RNA-sequencing of tumor-infiltrated T cells in colorectal tumors
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA746001 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15110349_1.fastq.gz | Fastqsanger.gz | |||
| SRR15110349_2.fastq.gz | Fastqsanger.gz | |||
| SRR15110350_1.fastq.gz | Fastqsanger.gz | |||
| SRR15110350_2.fastq.gz | Fastqsanger.gz | |||
| SRR15110351_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 40 |
Similar Datasets
Project description:The goal of this study is to identify differentially expressed genes in colorectal tumor samples enriched for exhausted T cells. CD38 expression was used as a representative marker for T cell exhaustion. The comparison was made between CD38high (top 33rd percentile of all samples) and CD38low (bottom 33rd percentile of all samples) samples.
2021-09-10 | GSE179975 | GEO
Project description:We have performed bulk RNA sequencing on colorectal tumors in order to determine their transcriptome-based molecular subtypes. RNA was isolated from fresh frozen human colorectal tumor specimens with Trizol extraction. RNA library preparation was performed with KAPA stranded mRNA sequencing kit, during which mRNA selection was performed with polyT capture beads. Sequencing was performed on Illumina HiSeq4000 as single-end 51 bp reads. File names include dataset name (KUL3), patient code(SCXXX), sample region (core or border) and sample code (EXTXXX): DATASETNAME_PATIENTCODE_SAMPLEREGION_rSAMPLE_CODE_...fastq.gz
2020-04-05 | E-MTAB-8412 | biostudies-arrayexpress
Project description:Single cell RNA-sequencing has been applied to core and border regions of 9 colorectal tumors as well as to matched adjacent non-malignant colon tissue for the purpose of generating a cellular map of colorectal tumors and their tumor microenvironment.
2023-07-06 | E-MTAB-8410 | biostudies-arrayexpress
Project description:We performed gene expression profiling of 26 colorectal tumors and matched histologically normal adjacent colonic tissue samples using the Illumina Ref-8 whole-genome expression BeadChip. We performed an integrated analysis of promoter DNA methylation and gene expression data to investigate the effects of DNA hypermethylation on gene expression. Total RNA was isolated from 26 pairs of fresh frozen colorectal tumor and matched adjacent non-tumor tissue samples. Their gene expression profiles were obtained using the Illumina Ref-8 whole-genome expression BeadChip (HumanRef-8 v3.0, 24,526 transcripts).
2011-06-03 | E-GEOD-25070 | biostudies-arrayexpress
Project description:We report the changes in the transcription profiles of the 4T1 breast cancer cells (control, RNF2 knockout (KO), and RSF1 KO), isolated and enriched from the tumor implanted in the 4th mammary pads by Fluorescence activated cell sorting, and the changes in the infiltrated NK cells. The transcription profiles were measured by RNA sequencing. We found that upon RNF2 KO or RSF1 KO, 4T1 tumor cells express multiple immune related genes, including chemokines, MHCII, and CD74 etc, which are otherwise repressed in cancer cells. We also found that the infiltrated NK cells in RNF2 KO tumors and RSF1 KO tumors express significantly higher levels of granzymes, compared to the NK cells infiltrated into control tumors, suggesting the activated status of these infiltrated NK cells.
2021-06-01 | GSE143352 | GEO
Project description:A pair of stage III colorectal cancer (CRC) tumor and adjacent normal tissue were collected from a patient without Transcatheter Arterial Infusion chemotherapy (TAI) during surgical resection of CRC tumors. Another pair of stage III CRC tumor and adjancent normal tissue were collected from another patient who had been treated with TAI one week before surgical resection. Total RNA of the collected tissues were extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The integrity of the RNA was checked with an ultraviolet spectrophotometry and 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Construction of small RNA libraries from size fractionated RNA was carried out by following Solexa protocol and the obtained libraries were sequenced by Illumina HiSeq 2000 sequencer. We identified some de-regulated miRNAs in CRC tumor tissues. The expression levels of miR-142-5p were significantly reduced in tumor tissues of stage III CRC, then were increased significantly in tumor tissues receiving TAI and higher than tumor tissues without TAI. miR-142-5p is a potential tumor suppressor in CRC and is upregulated in tumor tissues after TAI, suggesting its potential clinical values for testing the functionality of TAI and predicting progress of CRC. Examination of small RNA transcriptomes in colorectal tumor and adjancent normal tissues without and with Transcatheter Arterial Infusion chemotherapy using Illumina HiSeq2000 sequencer.
2014-01-15 | E-GEOD-43550 | biostudies-arrayexpress
Project description:Solid tumors are complex organs comprising neoplastic cells and stroma, yet cancer cell lines remain widely used to study tumor biology, biomarkers and experimental therapy. Here, we performed a fully integrative analysis of global proteomic data comparing human colorectal cancer (CRC) cell lines to primary tumors and normal tissues. We found a significant, systematic difference between cell line and tumor proteomes, with a major contribution from tumor stroma proteomes. Nevertheless, cell lines overall mirrored the proteomic differences observed between tumors and normal tissues, in particular for genetic information processing and metabolic pathways, indicating that cell lines provide a system for the study of the intrinsic molecular programs in cancer cells. Intersection of cell line data with tumor data provided insights into tumor cell specific proteome alterations driven by genomic alterations. Our integration of cell line proteogenomic data with drug sensitivity data highlights the potential of proteomic data in predicting therapeutic response. We identified representative cell lines for the proteomic subtypes of primary tumors, and linked these to drug sensitivity data to identify subtype-specific drug candidates.
2016-12-01 | MSV000080374 | GNPS
Project description:Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry-based approach, which allows the direct sampling and sequencing of these peptides. While the few tumor-specific antigens identified to date derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer-derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30 000 unique MHC I-associated peptides. We identified 19 putative tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from non-coding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell-based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses.
2022-04-13 | PXD028309 | Pride
Project description:Bulk RNA sequencing of colorectal tumors for molecular subtyping
| PRJEB34752 | ENA
Project description:In order to find the differentially expressed RNAs and signaling pathways related to the dwarf phenotype induced by NlCSP11, 35S-NlCSP11, 35S-XopQ and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed RNAs in the infiltrated leaves (NlCSP11_Z/XopQ_Z) and the upper uninfiltrated leaves (NlCSP11_U/XopQ_U) of N. benthamiana. KEGG annotation revealed a large number of differentially expressed RNAs involved in plant-pathogen interactions, indicating that NlCSP11 resulted in a more strong systemic resistance in N. benthamiana.
2024-05-30 | GSE267686 | GEO