Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Barcode Sequencing Data of Capecitabine Resistant Caco-2 and Irinotecan Resistant HT-29 Cell Lines

ABSTRACT: Caco-2 and HT-29 cells were barcoded using the CloneTracker lentiviral barcode library and then irinotecan and capecitabine resistant derivatives of these cell lines were established. Four million barcoded Caco-2 and HT-29 cell were seeded into 15 cm cell culture dishes. When the cells reached confluency, two million cells per dish were seeded into four different 15 cm dishes with 25 mL medium (DMSO Control, Replica A, B, C) and two million cell pellets were stocked as initial cell population.For Caco-2 cell line, mediums in the dishes were changed twice a week with fresh mediums containing IC50 dose (4 months) and subsequently 2x IC50 dose (2 months) of capecitabine, for HT-29 cell line IC50 dose (6 months) of irinotecan. Caco-2 and HT-29 cell lines treated with DMSO were given the same amount of DMSO used in dissolving compounds as fresh medium. Following the end points of six months for each cell line, DNA isolation from harvested cell lines and collected medium of resistant B cell lines were carried out and barcodes were sequenced.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Kübra Yılmaz

PROVIDER: E-MTAB-12818 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Barcode and Whole Exome Sequencing Data of Dabrafenib Resistant 3D-HT-29 and Irinotecan Resistant 3D-HCT-116 Spheroids

Project description:HT-29 and HCT-116 cells were barcoded using the CloneTracker lentiviral barcode library and then dabrafenib and irinotecan resistant derivatives of these cell lines were established, respectively.10 million barcoded HT-29 and HCT-116 cells were seeded equally onto poly-HEMA coated 4xT75 flask (DMSO Control, Replica A, B, C for each drug). After seeding, cells were allowed to form spheroids and barcoded 3D-HT-29 spheroids were treated with dabrafenib at increasing doses starting from IC50/10 dose until IC50/2 dose with monthly doubling of the dosing (16 weeks), and barcoded 3D-HCT-116 cells were treated with irinotecan at increasing doses starting from IC50/4 dose until IC50 dose with weekly doubling of the dosing (4 weeks). Following the end points of treatment for each cell line, DNA was isolated from harvested cell lines and barcode sequencing and whole exome sequencing were carried out.

2023-09-01 | E-MTAB-13216 | biostudies-arrayexpress

Barcode Sequencing Data of Dabrafenib Resistant HT-29 Cell Line

Project description:HT-29 cells were barcoded using the CloneTracker lentiviral barcode library and then dabrafenib resistant derivative of these cells were established. Five million barcoded HT-29 cells were seeded into 15 cm cell culture dishes. When the cells reached confluency, two million cells per dish were seeded into four different 15 cm dishes (DMSO Control, Replica A, B, C) and two million cell pellets were stocked as initial cell population. Harvesting used medium through the experiment was performed at monthly intervals. Barcoded HT-29 cell line replicates A, B, and C were treated with 2XIC50 (199.6 nM) of dabrafenib concentration for the duration of 3 months. Following the end points of 3 months for each cell line, DNA isolation from harvested cell lines and collected medium of resistant A cell lines were carried out and barcodes were sequenced.

2023-09-06 | E-MTAB-13018 | biostudies-arrayexpress

Human colon cancer cell lines: NT(untreated) vs EGF, Cetuximab and Gefitinib treatments

Project description:Gene Expression Profiling of HT-29 and Caco-2 colon cancer cell lines untreated compared with EGF, Cetuximab, Gefitinib,EGF plus Cetuximab and EGF plus gefitinib treatments. Keywords: Gene Expression Profiling

2007-09-12 | GSE8967 | GEO

Expression profiles of piRNAs in Colorectal Cancer (CRC) cell lines

Project description:To investigate the presence and abundance of piRNAs in Colorectal Cancer (CRC), we performed deep-sequencing of the small RNA transcriptome of eight human CRC cell lines (HT-115, Caco-2, SW-1417, SW 403, COLO 205, HT-29, HCT 116 and RKO).

2020-08-06 | E-MTAB-8117 | biostudies-arrayexpress

Integrated mRNA/miRNA-seq of Caco-2 and HT-29 cells under chemical hypoxia (cobalt chloride, oxyquinoline)

Project description:To uncover hypoxia-induced miRNA-mRNA interactions landscape in colorectal cancer cell lines we performed integrated miRNA/mRNA sequencing of Caco-2 and HT-29 cells. Hypoxia was chemically induced via 24 h cobalt(II) chloride and oxyquinoline treatments.

2020-09-29 | GSE158632 | GEO

Whole Exome Sequencing Data of Dabrafenib Resistant HT-29 Cell Line

Project description:HT-29 cells were barcoded using the CloneTracker lentiviral barcode library and then dabrafenib resistant derivatives of these cell lines were established, respectively. Five million barcoded HT-29 cells were seeded into 15 cm cell culture dishes. When the cells reached confluency, two million cells per dish were seeded into four different 15 cm dishes (DMSO Control, Replica A, B, C) and two million cell pellets were stocked as initial cell population. Harvesting used medium through the experiment was performed at monthly intervals. Barcoded HT-29 cell line replicates A, B, and C were treated with 2XIC50 (199.6 nM) of dabrafenib concentration for the duration of 3 months.Barcoded data can be accessed via accession code E-MTAB-13018. Whole exome sequencing of dabrafenib-resistant A replicate and DMSO control cell lines were carried out.

2023-09-06 | E-MTAB-13338 | biostudies-arrayexpress

Human Transcriptome Array 2.0 (HTA) in matched colorectal cancer and normal colonic mucosa and in widely used cancer cell lines

Project description:We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines (Caco-2, HT-29,HCT-116), one human breast adenocarcinoma cell line (MCF-7) and one human prostate adenocarcinoma cell line (PC3) were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.

2016-12-31 | GSE73360 | GEO

Genomic landscape of metastatic colorectal cancer

Project description:Response to drug therapy in individual colorectal cancer (CRC) patients is associated with tumor biology. Here we describe the genomic landscape of tumor samples of a homogeneous well-annotated series of patients with metastatic CRC of two phase III clinical trials, CAIRO and CAIRO2. DNA copy number aberrations of 349 patients are determined. Within three treatment arms, 194 chromosomal sub-regions are associated with progression free survival PFS (uncorrected single-test p-values < 0.005). These sub-regions are filtered for effect on mRNA expression, using an independent data set from The Cancer Genome Atlas (TCGA) which returned 171 genes. Three chromosomal regions are associated with a significant difference in PFS between treatment arms with or without irinotecan. One of these regions, 6q16.1-q21, correlates in vitro with sensitivity to SN-38, the active metabolite of irinotecan. This genomic landscape of metastatic CRC reveals a number of DNA copy number aberrations associated with response to drug therapy. aCGH data of colorectal cancers of patients from 2 clinical trials (CAIRO, CAIRO2). 105 patients were treated with capecitabine first line (CAIRO arm A), 111 patients were treated with capecitabine and irinotecan first line (CAIRO arm B), and 133 patients were treated with capecitabine, oxaliplatin and bevacizumab (CAIRO2 arm A).

2014-11-14 | E-GEOD-36864 | biostudies-arrayexpress

Recurrent breakpoint genes in colorectal cancer

Project description:In this study our aim was to document recurrent DNA copy number aberration associated breakpoints in primary tumors of colorectal cancer patients that ultimately received systemic treatment in the context of metastatic disease. Such data can be used to catalogue copy number aberration associated breakpoints and thereby affected genes. To this end, high quality arrayCGH data set of clinically well annotated colorectal cancer specimens was generated using FFPE tumor samples from patients from two phase III clinical trials, namely CAIRO and CAIRO2. arrayCGH data of colorectal cancers of patients from 2 clinical trials. 108 patients were treated with capecitabine first line, 110 patients were treated with capecitabine and irinotecan first line and 134 patients were treated with capecitabine, oxaliplatin and bevacizumab.

2014-11-14 | E-GEOD-63216 | biostudies-arrayexpress

Characterization of novel a-Mangostin and Paeonol derivatives with cancer-selective cytotoxicity

Project description:a-Mangostin and Paeonol have shown anti-cancer and anti-inflammatory properties, however these two natural compounds have no clinical value because of their low solubility and low membrane permeability. In this study, we screened chemically synthesized derivatives from these two natural compounds as potential novel chemicals that increase cancer cell cytotoxicity over non-transformed human cells. We found the two derivative compounds, named a-Mangostin-1 (aMan1) and Paeonol-1 (Pae1) more efficiently and specifically induced cytotoxicity in HCT116, HT-29, and SW48 colorectal cancer cell lines than the parental compounds. Both, aMan1 and Pae1 arrested HCT116 cells in G1 and HT-29 and SW48 cells in G2/M phase of the cell cycle. Both aMan1 and Pae1 induced apoptosis in human cancer cells, through a Caspase-dependent mechanism. aMan1 and Pae1 induced selective transcriptional responses in CRC cells involving genes related to metabolic stress and DNA damage response signaling pathways. Finally, experiments on primary colon organoids showed that both the novel derivatives kill organoids derived from cancer without affecting the viability of organoids derived from healthy tissue, where the parental compounds and the currently-used chemotherapeutic drug Irinotecan failed in. In conclusion, our findings increase the knowledge about natural compound derivatives as anticancer compounds and open new research options on the derivation of lead compounds aimed to the development of novel CRC chemotherapeutic drugs that selectively target cancer, but not healthy cells.

2023-03-11 | PXD024999 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data