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Series GSE114012 Query DataSets for GSE114012
Status Public on May 21, 2018
Title Identifying dormant cells in colorectal cancer spheroids
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Cellular dormancy and heterogeneous cell cycle lengths provide important explanations for treatment failure following adjuvant therapy with S-phase cytotoxics in colorectal cancer (CRC) yet the molecular control of the dormant versus cycling state remains unknown. In CRCs dormant cells are found to be highly clonogenic and resistant to chemotherapies. We sought to understand the molecular features of dormant CRC cells to facilitate rationale identification of compounds to target both dormant and cycling tumour cells.
 
Overall design Six colorectal cancer cell lines (DLD1, HCT15, HT55, SW948, RKO and SW48) were labelled with the cell permeable dye CFSE and then grown in non-adherent spheroid culture for 6 days to enable identification of dormant cells that retain CFSE (LRC) and cycling cells (BULK). LRCs and BULK populations were then FACS sorted from each cell line in quadruplicate. As a control experiment, to identify off-target effects of the CFSE dye and culture artefacts, BULK populations from DLD1 cells at d1 and d6 after seeding both with and without CFSE labelling were included in the RNAseq analysis. RNA was extracted using the RNAeasy Micro Plus kit (Qiagen) and quantified using the Qubit RNA Assay Kit (Thermo Fisher Scientific). RNA quality was assessed using the Agilent Bioanalyser system as per manufacturer’s instructions. Following normalisation and sample randomisation, Truseq library (Illumina) preparation was carried out at the CRUK CI genomics facility and subsequent single end, 50bp sequencing using the HiSeq system (Illumina). Following human genome alignment (hg19), read counts were normalised and differential expression tested using the DEseq protocol.
 
Contributor(s) Buczacki SJ
Citation(s) 29853607
Submission date May 03, 2018
Last update date May 21, 2019
Contact name Chandra Chilamakuri
E-mail(s) datasubmissions@cruk.cam.ac.uk
Organization name Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (64)
GSM3130612 CON_CFSED1_1_57
GSM3130613 CON_CFSED1_2_58
GSM3130614 CON_CFSED1_3_59
This SubSeries is part of SuperSeries:
GSE114014 Itraconazole targets cell cycle heterogeneity in colorectal cancer
Relations
BioProject PRJNA454879
SRA SRP144495

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE114012_RAW.tar 11.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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