Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14415827_1.fastq.gz | Fastqsanger.gz | |||
| SRR14415827_2.fastq.gz | Fastqsanger.gz | |||
| SRR14415828_1.fastq.gz | Fastqsanger.gz | |||
| SRR14415828_2.fastq.gz | Fastqsanger.gz | |||
| SRR14415829_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with increased risk for colorectal cancer (CRC). A molecular understanding of the functional consequences of this genetic variation is complicated because most GWAS SNPs are located in non-coding regions. After identifying H3K27Ac peaks in HCT116 colon cancer cells that harbor SNPs associated with an increased risk for CRC, we used CRISPR/Cas9 nuclease to delete 2 CRC risk-associated H3K27Ac peaks (E7 and E24), a peak that is not associated with CRC risk (18qE) and a region that doesn?t have H3K27Ac peak (18qNE) from HCT116 cells and analyzed effects on the transcriptome and epigenome. We also deleted E7 region from HEK 293 cells and analyzed effects on the transcriptome of HEK 293. We also confirmed the physical interaction between enhancers of our interest and their putative target genes. Analysis of RNA-seq data and ChIP-seq between control clones and enhancer deleted clones in HCT116 cell. For Control, gRNA empty vectorplasmid was transfected with Cas9-GFP. For Deletion, gRNAs that have enhancer target sequences were transfected along with Cas9-GFP. Cells with high GFP expression were identified using fluorescence-activated cell sorting. Sorted cells were plated into individual wells of a 24 well plate and then re-plated as single cells in 10cm dishes and subsequently expanded for further analyses. Samples used in this study were clonal populations. Interaction profiling of enhancers of interest with putative target genes using 4C-seq
2016-01-12 | E-GEOD-72631 | biostudies-arrayexpress
Project description:Background: In vitro models are an essential tool towards understanding the molecular characteristics of colorectal cancer (CRC) and the testing of therapies for CRC. To this end we established 21 novel CRC cell lines of which six were derived from liver metastases. Extensive genetic, genomic, transcriptomic and methylomic profiling was performed in order to characterize these new cell lines and all data is made publically available. Additionally, sensitivity of oxaliplatin was tested as a measure for chemotherapy resistance. Results: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC. Conclusions: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC. SNP-array analysis of 21 novel CRC cell lines; 16 with Illumina HumanExome-12 v1.2 BeadChip and 5 with Illumina HumanExome-12 v1.0.
2016-02-29 | E-GEOD-67774 | biostudies-arrayexpress
Project description:Background: In vitro models are an essential tool towards understanding the molecular characteristics of colorectal cancer (CRC) and the testing of therapies for CRC. To this end we established 21 novel CRC cell lines of which six were derived from liver metastases. Extensive genetic, genomic, transcriptomic and methylomic profiling was performed in order to characterize these new cell lines and all data is made publically available. Additionally, sensitivity of oxaliplatin was tested as a measure for chemotherapy resistance. Results: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC. Conclusions: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC.
2016-02-29 | GSE67774 | GEO
Project description:Pseudomonas protegens Crc-2 transcriptome - Crc-2_6
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Project description:Pseudomonas protegens Crc-1 transcriptome - Crc-1_5
| PRJNA538139 | ENA
Project description:Pseudomonas protegens Crc-1 transcriptome - Crc-1_6
| PRJNA538140 | ENA
Project description:Pseudomonas protegens Crc-1 transcriptome - Crc-1_7
| PRJNA538141 | ENA
Project description:Pseudomonas protegens Crc-1 transcriptome - Crc-1_8
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Project description:Pseudomonas protegens Crc-2 transcriptome - Crc-2_7
| PRJNA538137 | ENA
Project description:Pseudomonas protegens Crc-2 transcriptome - Crc-2_8
| PRJNA538138 | ENA