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Series GSE66216 Query DataSets for GSE66216
Status Public on Dec 20, 2016
Title Nucleosome dynamics in human colorectal cancer specimens reveal activation of a CNOT3-regulated pathway of embryonic stem cell self-renewal
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Temporal chromatin dynamics can reveal transcriptional determinants of cell differentiation, and we reasoned that dynamic changes in nucleosome configuration might similarly disclose transcriptional regulators in cancer. To this end, we identified thousands of cis-regulatory sites where chromatin marks and configuration in human CRCs differed from those in their respective precursor adenomas. (based on H3K4me2 mark).
At such sites in selected cases, we observed an abundance of sequence motifs and binding of CNOT3, which is overexpressed in scattered tumor cells in cases associated with unfavorable prognosis. In primary CRCs and cell lines, CNOT3 binding is highly enriched at genes that correspond to both the active and silenced limbs of the ESC gene signature expressed in aggressive carcinomas and these arms respond in coordinated, opposite fashion to CNOT3 loss.
Overall design H3K4me2 ChIPseq analysis of human primary adenomas and matched colorectal carcinomas. CNOT3 ChIPseq analysis of the human colorectal cancer cell line (HCT116) and of two primary colorectal carcinomas. RNAseq analysis of HCT116 control and CNOT3 depleted cells.
Contributor(s) Cejas P, Cavazza A, Yandava C, Moreno V, Horst D, Moreno-Rubio J, Burgos E, Mendiola M, Taing L, Goel A, Feliu J, Shivdasani RA
Citation(s) 27899379
Submission date Feb 23, 2015
Last update date May 15, 2019
Contact name Paloma Cejas
Phone 6178406690
Organization name Dana Farber Cancer Institute
Department Medical Oncology
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (45)
GSM1617353 Adenoma_1 - H3K4me2_ChIPseq
GSM1617354 Adenoma_2 - H3K4me2_ChIPseq
GSM1617355 Adenoma_3 - H3K4me2_ChIPseq
BioProject PRJNA276129
SRA SRP055442

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Supplementary file Size Download File type/resource
GSE66216_HCT116.differential_expression_table.txt.gz 895.2 Kb (ftp)(http) TXT
GSE66216_HCT116.fpkm_table.txt.gz 460.3 Kb (ftp)(http) TXT
GSE66216_RAW.tar 1.3 Gb (http)(custom) TAR (of BED, FPKM_TRACKING, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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