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GSE157051

GSE GEO
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AMPK regulation of Raptor and TSC2 mediate Metformin effects on transcriptional control of anabolism and inflammation

Organism: Mus musculus
Platform: GPL17021
Samples: 160
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Aug 28 2020
Last Updated: Aug 10 2023
Status: Public on Aug 10 2023
Contact: April,Elizabeth,Williams (Salk Institute for Biological Studies)

Relations

SuperSeries of: GSE157048 SuperSeries of: GSE157049 SuperSeries of: GSE157050 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA659984

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (14 steps)

View Data Processing
Processing steps for GSE157051
  1. Raw RNA sequencing reads in FASTQ files were quality-tested using FASTQC (v0.11.8) (Andrews 2010) and mapped to the mouse reference genome (mm10) with STAR (v2.5.3a) aligner with default parameters (Dobin et al.
  2. 2012).
  3. Raw or normalized gene expression levels were quantified across all the exons of RefSeq genes with analyzeRepeats.pl in HOMER (v4.11.1) (Heinz et al.
  4. 2010).
  5. Differential expression analysis was performed with raw gene counts using R package, edgeR (v3.26.7) (Robinson et al.
  6. 2010), using replicates to compute within-group dispersion and correcting for batch effects.
  7. Genes with false discovery rate (FDR) < 0.05 and an absolute fold-change (FC) >= 1.5 were identified as significantly different when comparing two conditions.
  8. Normalized counts were log transformed, filtered, scaled, and centered prior to clustering and heatmap generation with Cluster3 (de Hoon et al.
Showing first 8 steps.
GEO Samples (160)
GSM4751546 GSM4751547 GSM4751548 GSM4751549 GSM4751550 GSM4751551 GSM4751552 GSM4751553 GSM4751554 GSM4751555 GSM4751556 GSM4751557 GSM4751558 GSM4751559 GSM4751560 GSM4751561 GSM4751562 GSM4751563 GSM4751564 GSM4751565 GSM4751566 GSM4751567 GSM4751568 GSM4751569 GSM4751570 GSM4751571 GSM4751572 GSM4751573 GSM4751574 GSM4751575 GSM4751576 GSM4751577 GSM4751578 GSM4751579 GSM4751580 GSM4751581 GSM4751582 GSM4751583 GSM4751584 GSM4751585 GSM4751586 GSM4751587 GSM4751588 GSM4751589 GSM4751590 GSM4751591 GSM4751592 GSM4751593 GSM4751594 GSM4751595 GSM4751596 GSM4751597 GSM4751598 GSM4751599 GSM4751600 GSM4751601 GSM4751602 GSM4751603 GSM4751604 GSM4751605 GSM4751606 GSM4751607 GSM4751608 GSM4751609 GSM4751610 GSM4751611 GSM4751612 GSM4751613 GSM4751614 GSM4751615 GSM4751616 GSM4751617 GSM4751618 GSM4751619 GSM4751620 GSM4751621 GSM4751622 GSM4751623 GSM4751624 GSM4751625 GSM4751626 GSM4751627 GSM4751628 GSM4751629 GSM4751630 GSM4751631 GSM4751632 GSM4751633 GSM4751634 GSM4751635 GSM4751636 GSM4751637 GSM4751638 GSM4751639 GSM4751640 GSM4751641 GSM4751642 GSM4751643 GSM4751644 GSM4751645 GSM4751646 GSM4751647 GSM4751648 GSM4751649 GSM4751650 GSM4751651 GSM4751652 GSM4751653 GSM4751654 GSM4751655 GSM4751656 GSM4751657 GSM4751658 GSM4751659 GSM4751660 GSM4751661 GSM4751662 GSM4751663 GSM4751664 GSM4751665 GSM4751666 GSM4751667 GSM4751668 GSM4751669 GSM4751670 GSM4751671 GSM4751672 GSM4751673 GSM4751674 GSM4751675 GSM4751676 GSM4751677 GSM4751678 GSM4751679 GSM4751680 GSM4751681 GSM4751682 GSM4751683 GSM4751684 GSM4751685 GSM4751686 GSM4751687 GSM4751688 GSM4751689 GSM4751690 GSM4751691 GSM4751692 GSM4751693 GSM4751694 GSM4751695 GSM4751696 GSM4751697 GSM4751698 GSM4751699 GSM4751700 GSM4751701 GSM4751702 GSM4751703 GSM4751704 GSM4751705

Dataset Citations (1)

AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation.
PMID 32912901 · 2020 · Genes & development
Jeanine L Van Nostrand, Kristina Hellberg, En-Ching Luo, Eric L Van Nostrand, Alina Dayn, Jingting Yu, Maxim N Shokhirev, Yelena Dayn, Gene W Yeo, Reuben J Shaw

Linked Publications (1)

AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation.
Genes & development · 2020