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Series GSE52339 Query DataSets for GSE52339
Status Public on Aug 31, 2014
Title A high-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Under continuous, glucose-limited conditions, budding yeast exhibit robust metabolic cycles associated with major oscillations of gene expression and metabolic state. However, how such fluctuations might be coordinately linked to changes in chromatin status is less well understood. Here, we examine the correlated genome-wide transcription and chromatin states across the yeast metabolic cycle (YMC) at unprecedented temporal resolution, revealing a "just in time supply chain" by which specific cellular processes such as ribosome biogenesis are coordinated in time with remarkable precision. We identify distinct chromatin and splicing patterns associated with different gene categories and determine the relative timing of chromatin modifications to maximal transcription. Additionally, we interrogate chromatin modifier occupancy and observe subtly distinct spatial and temporal patterns compared to the modifications themselves. Furthermore, we identify multiple lysine mutants in H3 or H4 tails that disrupt metabolic cycling, supporting a potentially cooperative role of histone modifications in the YMC.
Overall design 16 time points RNA-seq and ChIP-seq of 8 histone marks over one metabolic cycle, 14 time points ChIP-seq of 3 chromatin modifiers over one metabolic cycle
Contributor(s) Kuang Z, Cai L, Zhang X, Ji H, Tu BP, Boeke JD
Citation(s) 25173176
Submission date Nov 13, 2013
Last update date May 15, 2019
Contact name Zheng Kuang
Organization name UT Southwestern medical center
Department Immunology
Lab Lora Hooper
Street address 6000 Harry Hines Blvd. NA7.500
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
Platforms (3)
GPL9134 Illumina Genome Analyzer (Saccharomyces cerevisiae)
GPL10577 AB SOLiD System (Saccharomyces cerevisiae)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (202)
GSM1263339 RNA-seq_t1
GSM1263340 RNA-seq_t2
GSM1263341 RNA-seq_t3
BioProject PRJNA227448
SRA SRP032970

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52339_RAW.tar 167.6 Mb (http)(custom) TAR (of TXT)
GSE52339_RNAseq_genes.fpkm_tracking.gz 1.3 Mb (ftp)(http) FPKM_TRACKING
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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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