← All datasets

GSE157049

GSE GEO
View on GEO Export SRA CSV

RNA-seq of metformin treatment in liver in WT, Raptor Ser-Ala mutant, Tsc2-null, Raptor mutant;Tsc2-null, and Ampk-null

Organism: Mus musculus
Platform: GPL24247
Samples: 29
Experiment Types:
Expression profiling by high throughput sequencing
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

SubSeries of: GSE157051 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA659988 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP279198

Summary

Despite being the frontline therapy for Type 2 diabetes, the mechanisms of action of the biguanide drug metformin are still being discovered. In particular, the detailed molecular interplays between the AMPK and the mTORC1 pathway in the hepatic benefits of metformin are still ill-defined. Metformin-dependent activation of AMPK classically inhibits mTORC1 via TSC/RHEB. But several lines of evidence suggest additional mechanisms at play in metformin inhibition of mTORC1. Here we investigated the role of direct AMPK-mediated serine phosphorylation of RAPTOR in a new RaptorAA mouse model, in which AMPK phospho-serine sites Ser722 and Ser792 of RAPTOR were mutated to alanine. Metformin treatment of intact murine liver requires AMPK regulation of both RAPTOR and TSC2 to fully inhibit mTORC1, and this regulation is critical for the transcriptional response to metformin. Transcriptionally, AMPK and mTORC1 were both important for regulation of anabolic metabolism and inflammatory programs triggered by metformin treatment. The hepatic transcriptional response in mice on high fat diet treated with metformin was largely ablated by AMPK-deficiency under the conditions examined, indicating the essential role of this kinase and its targets in metformin action in vivo.

Overall Design

Mice maintained on 45% high fat diet for 12 weeks, fasted overnight, refed for 1h, and treated with 200 mpk metformin or saline for 4 hours

Analysis (14 steps)

View Data Processing
Processing steps for GSE157049
  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.

Supplementary Files (1)

GSE157049_normed_liver.txt.gz Download
GEO Samples (29)
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

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

SRA Experiments (29) and Runs (29)

Total: 26467 MB
SRX9029512 SRP279198 RNA-Seq PAIRED
GSM4751611: liver_WT Sal rep1; Mus musculus; RNA-Seq
Sample: SRS7280794
BioProject: PRJNA659988
BioSample: SAMN15931628
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: wild type
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539831 29721943 3031638186 835.91 1362_WTSal_JVN3_S3_R1_001.fastq.gz, 1362_WTSal_JVN3_S3_R2_001.fastq.g… SRA
SRX9029513 SRP279198 RNA-Seq PAIRED
GSM4751612: liver_WT Sal rep2; Mus musculus; RNA-Seq
Sample: SRS7280795
BioProject: PRJNA659988
BioSample: SAMN15931627
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: wild type
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539832 24666921 2516025942 697.52 4354_WTSal_JVN1_S1_R1_001.fastq.gz, 4354_WTSal_JVN1_S1_R2_001.fastq.g… SRA
SRX9029514 SRP279198 RNA-Seq PAIRED
GSM4751613: liver_WT Sal rep3; Mus musculus; RNA-Seq
Sample: SRS7280796
BioProject: PRJNA659988
BioSample: SAMN15931626
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: wild type
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539833 31127183 3174972666 877.55 4357_WTSal_JVN2_S2_R1_001.fastq.gz, 4357_WTSal_JVN2_S2_R2_001.fastq.g… SRA
SRX9029515 SRP279198 RNA-Seq PAIRED
GSM4751614: liver_WT Met rep1; Mus musculus; RNA-Seq
Sample: SRS7280797
BioProject: PRJNA659988
BioSample: SAMN15931625
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: wild type
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539834 39000252 3978025704 1088.39 1087_WTMet_JVN6_S6_R1_001.fastq.gz, 1087_WTMet_JVN6_S6_R2_001.fastq.g… SRA
SRX9029516 SRP279198 RNA-Seq PAIRED
GSM4751615: liver_WT Met rep2; Mus musculus; RNA-Seq
Sample: SRS7280798
BioProject: PRJNA659988
BioSample: SAMN15931624
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: wild type
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539835 35231934 3593657268 987.2 4359_WTMet_JVN4_S4_R1_001.fastq.gz, 4359_WTMet_JVN4_S4_R2_001.fastq.g… SRA
SRX9029517 SRP279198 RNA-Seq PAIRED
GSM4751616: liver_WT Met rep3; Mus musculus; RNA-Seq
Sample: SRS7280799
BioProject: PRJNA659988
BioSample: SAMN15931623
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: wild type
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539836 34874431 3557191962 976.47 4360_WTMet_JVN5_S5_R1_001.fastq.gz, 4360_WTMet_JVN5_S5_R2_001.fastq.g… SRA
SRX9029518 SRP279198 RNA-Seq PAIRED
GSM4751617: liver_AA Sal rep1; Mus musculus; RNA-Seq
Sample: SRS7280800
BioProject: PRJNA659988
BioSample: SAMN15931622
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539837 33378187 3404575074 931.78 1268_AASal_JVN8_S8_R1_001.fastq.gz, 1268_AASal_JVN8_S8_R2_001.fastq.g… SRA
SRX9029519 SRP279198 RNA-Seq PAIRED
GSM4751618: liver_AA Sal rep2; Mus musculus; RNA-Seq
Sample: SRS7280801
BioProject: PRJNA659988
BioSample: SAMN15931621
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539838 35586259 3629798418 1004.64 1269_AASal_JVN9_S9_R1_001.fastq.gz, 1269_AASal_JVN9_S9_R2_001.fastq.g… SRA
SRX9029520 SRP279198 RNA-Seq PAIRED
GSM4751619: liver_AA Sal rep3; Mus musculus; RNA-Seq
Sample: SRS7280802
BioProject: PRJNA659988
BioSample: SAMN15931620
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539839 31988719 3262849338 894.77 1289_AASal_JVN7_S7_R1_001.fastq.gz, 1289_AASal_JVN7_S7_R2_001.fastq.g… SRA
SRX9029521 SRP279198 RNA-Seq PAIRED
GSM4751620: liver_AA Met rep1; Mus musculus; RNA-Seq
Sample: SRS7280803
BioProject: PRJNA659988
BioSample: SAMN15931619
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539840 34386731 3507446562 967.41 1202_AAMet_JVN12_S12_R1_001.fastq.gz, 1202_AAMet_JVN12_S12_R2_001.fas… SRA
SRX9029522 SRP279198 RNA-Seq PAIRED
GSM4751621: liver_AA Met rep2; Mus musculus; RNA-Seq
Sample: SRS7280804
BioProject: PRJNA659988
BioSample: SAMN15931618
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539841 36684477 3741816654 1036.6 1277_AAMet_JVN10_S10_R1_001.fastq.gz, 1277_AAMet_JVN10_S10_R2_001.fas… SRA
SRX9029523 SRP279198 RNA-Seq PAIRED
GSM4751622: liver_AA Met rep3; Mus musculus; RNA-Seq
Sample: SRS7280805
BioProject: PRJNA659988
BioSample: SAMN15931617
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539842 32801104 3345712608 926.2 1367_AAMet_JVN11_S11_R1_001.fastq.gz, 1367_AAMet_JVN11_S11_R2_001.fas… SRA
SRX9029524 SRP279198 RNA-Seq PAIRED
GSM4751623: liver_Tsc Sal rep1; Mus musculus; RNA-Seq
Sample: SRS7280806
BioProject: PRJNA659988
BioSample: SAMN15931616
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539843 27474886 2802438372 790.15 1038_TSCSal_JVN13_S13_R1_001.fastq.gz, 1038_TSCSal_JVN13_S13_R2_001.f… SRA
SRX9029525 SRP279198 RNA-Seq PAIRED
GSM4751624: liver_Tsc Sal rep2; Mus musculus; RNA-Seq
Sample: SRS7280807
BioProject: PRJNA659988
BioSample: SAMN15931615
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539844 30508247 3111841194 859.08 1364_TSCSal_JVN14_S14_R1_001.fastq.gz, 1364_TSCSal_JVN14_S14_R2_001.f… SRA
SRX9029526 SRP279198 RNA-Seq PAIRED
GSM4751625: liver_Tsc Met rep1; Mus musculus; RNA-Seq
Sample: SRS7280808
BioProject: PRJNA659988
BioSample: SAMN15931614
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539845 30425446 3103395492 857.89 1291_TSCMet_JVN17_S17_R1_001.fastq.gz, 1291_TSCMet_JVN17_S17_R2_001.f… SRA
SRX9029527 SRP279198 RNA-Seq PAIRED
GSM4751626: liver_Tsc Met rep2; Mus musculus; RNA-Seq
Sample: SRS7280809
BioProject: PRJNA659988
BioSample: SAMN15931613
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539846 31648110 3228107220 891.07 1369_TSCMet_JVN15_S15_R1_001.fastq.gz, 1369_TSCMet_JVN15_S15_R2_001.f… SRA
SRX9029528 SRP279198 RNA-Seq PAIRED
GSM4751627: liver_Tsc Met rep3; Mus musculus; RNA-Seq
Sample: SRS7280810
BioProject: PRJNA659988
BioSample: SAMN15931612
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539847 28453626 2902269852 800.46 1373_TSCMet_JVN16_S16_R1_001.fastq.gz, 1373_TSCMet_JVN16_S16_R2_001.f… SRA
SRX9029529 SRP279198 RNA-Seq PAIRED
GSM4751628: liver_AATsc Sal rep1; Mus musculus; RNA-Seq
Sample: SRS7280811
BioProject: PRJNA659988
BioSample: SAMN15931611
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539848 29677881 3027143862 838.91 1039_ATSal_JVN18_S18_R1_001.fastq.gz, 1039_ATSal_JVN18_S18_R2_001.fas… SRA
SRX9029530 SRP279198 RNA-Seq PAIRED
GSM4751629: liver_AATsc Sal rep2; Mus musculus; RNA-Seq
Sample: SRS7280812
BioProject: PRJNA659988
BioSample: SAMN15931610
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539849 30283556 3088922712 850.47 1406_ATSal_JVN20_S20_R1_001.fastq.gz, 1406_ATSal_JVN20_S20_R2_001.fas… SRA
SRX9029531 SRP279198 RNA-Seq PAIRED
GSM4751630: liver_AATsc Sal rep3; Mus musculus; RNA-Seq
Sample: SRS7280813
BioProject: PRJNA659988
BioSample: SAMN15931609
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539850 25912553 2643080406 728.54 1069_ATSal_JVN19_S19_R1_001.fastq.gz, 1069_ATSal_JVN19_S19_R2_001.fas… SRA
SRX9029532 SRP279198 RNA-Seq PAIRED
GSM4751631: liver_AATsc Met rep1; Mus musculus; RNA-Seq
Sample: SRS7280814
BioProject: PRJNA659988
BioSample: SAMN15931608
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539851 37574621 3832611342 1065.05 1408_ATMet_JVN22_S22_R1_001.fastq.gz, 1408_ATMet_JVN22_S22_R2_001.fas… SRA
SRX9029533 SRP279198 RNA-Seq PAIRED
GSM4751632: liver_AATsc Met rep2; Mus musculus; RNA-Seq
Sample: SRS7280815
BioProject: PRJNA659988
BioSample: SAMN15931607
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539852 34696654 3539058708 979.66 1071_ATMet_JVN23_S23_R1_001.fastq.gz, 1071_ATMet_JVN23_S23_R2_001.fas… SRA
SRX9029534 SRP279198 RNA-Seq PAIRED
GSM4751633: liver_AATsc Met rep3; Mus musculus; RNA-Seq
Sample: SRS7280817
BioProject: PRJNA659988
BioSample: SAMN15931606
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539853 36040637 3676144974 1029.37 1407_ATMet_JVN21_S21_R1_001.fastq.gz, 1407_ATMet_JVN21_S21_R2_001.fas… SRA
SRX9029535 SRP279198 RNA-Seq PAIRED
GSM4751634: liver_Adel Sal rep1; Mus musculus; RNA-Seq
Sample: SRS7280816
BioProject: PRJNA659988
BioSample: SAMN15931605
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539854 34033338 3471400476 958.49 4355_AdelSal_JVN24_S24_R1_001.fastq.gz, 4355_AdelSal_JVN24_S24_R2_001… SRA
SRX9029536 SRP279198 RNA-Seq PAIRED
GSM4751635: liver_Adel Sal rep2; Mus musculus; RNA-Seq
Sample: SRS7280818
BioProject: PRJNA659988
BioSample: SAMN15931604
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539855 37566733 3831806766 1058.61 4356_AdelSal_JVN25_S25_R1_001.fastq.gz, 4356_AdelSal_JVN25_S25_R2_001… SRA
SRX9029537 SRP279198 RNA-Seq PAIRED
GSM4751636: liver_Adel Sal rep3; Mus musculus; RNA-Seq
Sample: SRS7280819
BioProject: PRJNA659988
BioSample: SAMN15931603
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: Saline for 4h
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539856 35481959 3619159818 997.86 4363_AdelSal_JVN26_S26_R1_001.fastq.gz, 4363_AdelSal_JVN26_S26_R2_001… SRA
SRX9029538 SRP279198 RNA-Seq PAIRED
GSM4751637: liver_Adel Met rep1; Mus musculus; RNA-Seq
Sample: SRS7280820
BioProject: PRJNA659988
BioSample: SAMN15931631
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539857 32292134 3293797668 908.13 4364_AdelMet_JVN27_S27_R1_001.fastq.gz, 4364_AdelMet_JVN27_S27_R2_001… SRA
SRX9029539 SRP279198 RNA-Seq PAIRED
GSM4751638: liver_Adel Met rep2; Mus musculus; RNA-Seq
Sample: SRS7280821
BioProject: PRJNA659988
BioSample: SAMN15931630
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539858 29072018 2965345836 819.01 4365_AdelMet_JVN28_S28_R1_001.fastq.gz, 4365_AdelMet_JVN28_S28_R2_001… SRA
SRX9029540 SRP279198 RNA-Seq PAIRED
GSM4751639: liver_Adel Met rep3; Mus musculus; RNA-Seq
Sample: SRS7280822
BioProject: PRJNA659988
BioSample: SAMN15931629
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Liver
strain: C57BL/6 (F3 generation)
tissue: liver
age: 8 month old
Sex: male
genotype: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER
diet: 45% High Fat Diet for 12 weeks
tamoxifen treatment: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk
fasting treatment: Overnight Fast, 1h Refed with high fat diet
metformin treatment: 200 mpk Metformin for 4 hours
avertin treatment: subLethal dose of avertin 10' prior to collection
Original files (1)
Liver
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12539859 28853220 2943028440 809.51 4330_AdelMet_JVN29_S29_R1_001.fastq.gz, 4330_AdelMet_JVN29_S29_R2_001… SRA

Linked Publications (1)

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

Data Files (29)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 1038_TSCSal_JVN13_S13_R1_001.fastq.gz RNA-Seq 790.1 MB link
— 1039_ATSal_JVN18_S18_R1_001.fastq.gz RNA-Seq 838.9 MB link
— 1069_ATSal_JVN19_S19_R1_001.fastq.gz RNA-Seq 728.5 MB link
— 1071_ATMet_JVN23_S23_R1_001.fastq.gz RNA-Seq 979.7 MB link
— 1087_WTMet_JVN6_S6_R1_001.fastq.gz RNA-Seq 1.1 GB link
— 1202_AAMet_JVN12_S12_R1_001.fastq.gz RNA-Seq 967.4 MB link
— 1268_AASal_JVN8_S8_R1_001.fastq.gz RNA-Seq 931.8 MB link
— 1269_AASal_JVN9_S9_R1_001.fastq.gz RNA-Seq 1004.6 MB link
— 1277_AAMet_JVN10_S10_R1_001.fastq.gz RNA-Seq 1.0 GB link
— 1289_AASal_JVN7_S7_R1_001.fastq.gz RNA-Seq 894.8 MB link
— 1291_TSCMet_JVN17_S17_R1_001.fastq.gz RNA-Seq 857.9 MB link
— 1362_WTSal_JVN3_S3_R1_001.fastq.gz RNA-Seq 835.9 MB link
— 1364_TSCSal_JVN14_S14_R1_001.fastq.gz RNA-Seq 859.1 MB link
— 1367_AAMet_JVN11_S11_R1_001.fastq.gz RNA-Seq 926.2 MB link
— 1369_TSCMet_JVN15_S15_R1_001.fastq.gz RNA-Seq 891.1 MB link
— 1373_TSCMet_JVN16_S16_R1_001.fastq.gz RNA-Seq 800.5 MB link
— 1406_ATSal_JVN20_S20_R1_001.fastq.gz RNA-Seq 850.5 MB link
— 1407_ATMet_JVN21_S21_R1_001.fastq.gz RNA-Seq 1.0 GB link
— 1408_ATMet_JVN22_S22_R1_001.fastq.gz RNA-Seq 1.0 GB link
— 4330_AdelMet_JVN29_S29_R1_001.fastq.gz RNA-Seq 809.5 MB link
— 4354_WTSal_JVN1_S1_R1_001.fastq.gz RNA-Seq 697.5 MB link
— 4355_AdelSal_JVN24_S24_R1_001.fastq.gz RNA-Seq 958.5 MB link
— 4356_AdelSal_JVN25_S25_R1_001.fastq.gz RNA-Seq 1.0 GB link
— 4357_WTSal_JVN2_S2_R1_001.fastq.gz RNA-Seq 877.5 MB link
— 4359_WTMet_JVN4_S4_R1_001.fastq.gz RNA-Seq 987.2 MB link
— 4360_WTMet_JVN5_S5_R1_001.fastq.gz RNA-Seq 976.5 MB link
— 4363_AdelSal_JVN26_S26_R1_001.fastq.gz RNA-Seq 997.9 MB link
— 4364_AdelMet_JVN27_S27_R1_001.fastq.gz RNA-Seq 908.1 MB link
— 4365_AdelMet_JVN28_S28_R1_001.fastq.gz RNA-Seq 819.0 MB link