GSE124024   Details

GSE Accession GSE124024
Title Serum Reponse of CF1 primary MEFs , E13
Submission Date 12/18/18
Last Update Date 5/10/19
Pubmed ID
Experiment Type Expression profiling by high throughput sequencing
Contributor Gerald,,Pao; Eugene Ke; Junko Ogawa; Nina Tonnu; Inder,M,Verma; Maryam Masnadi-Shirazi; Mano,R,Maurya; Shankar Subramaniam
Contact Name
Contact E-mail
Organization Name
Organism Mus musculus
Organism ID 10090
Organism Synonym house mouse; mouse
Summary The goal of this study was to find the longitudinal transcriptional response of Mouse Embryonic Fibroblast (MEF) primary cells during the progression of a cell cycle. Using RNASeq method (single-end 50-bp chemistry on Illumina Hi-seq 2500 instrument in high-throughput mode), we measured the transcriptional response for around two cell-cycles. Using the fold-change (with respect to average response before serum addition at t = 0) time-series data, we first identified, without using a priori knowledge, the duration and timing of cell cycle phases using a change-point detection algorithm. Next, using Least Absolute Shrinkage and Selection Operator (LASSO) and Estimation Stability with Cross Validation (ES-CV), we were able to, without any prior biological knowledge, extract information on the phase-specific causal interaction of cell cycle genes, as well as temporal interdependencies of biological mechanisms through a complete cell cycle.
Overall Design MEF cells were serum starved for 36 hours (Serum Starved Conditions - 0.5% FCS, DMEM High Glucose, L-glutamine, Penicillin Streptomycin, fungizone, non-essential amino acids) prior to adding serum at t = 0 hr. At t = 0, FCS was added to 20% level by volume to stimulate cell growth. Cells were extracted using Trizol RNA isolation protocol with scraping. Total RNA was isolated using Zymo Research Direct-zol 96 RNA (R2054) kit. TruSeq Stranded mRNA HT Kit (RS-122-2101) was used for library preparation. mRNA was sequenced (single-end 50-bp) using Illumina HiSeq 2500 in high throughput mode, with 12 samples per lane. Data processing steps are: 1) Demultiplexing using Casava [ --mismatches 1], 2) Mapping/Alignment using RNA-STAR [STAR --genomeDir mm9 --sjdbGTFfile mouse_splice.sjdb --outSammode FULL --outFilterType BySJout], and 3) Normalization and Quantification using Homer [ rna mm9 -count exons -strand both].
Platform ID
Timepoint Count 63
Timepoints gsm: [0h, 1h, 1.5h, 2h, 2.5h, 3h, 3.5h, 4h, 4.5h, 5h, 5.5h, 6h, 6.5h, 7h, 7.5h, 8h, 8.5h, 9h, 9.5h, 10h, 10.5h, 11h, 11.5h, 12h, 12.5h, 13h, 13.5h, 14h, 14.5h, 15h, 15.5h, 16h, 16.5h, 17h, 17.5h, 18h, 18.5h, 19h, 19.5h, 20h, 20.5h, 21h, 21.5h, 22h, 22.5h, 23h, 23.5h, 24h, 24.5h, 25h, 26h, 27h, 28h, 29h, 30h, 31h, 32h, 33h, 34h, 35h, 36h, 37h, 38h]
Disease ID