GEO series

Leptin Receptor Signaling Regulates Protein Synthesis Pathways and Neuronal Differentiation in Pluripotent Stem Cells

GSE155704 Mus musculus (mouse) RNA-seq (gene expression) 19 samples Submitted 2024/08/04 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 19 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 19 samples: 7 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

The role of leptin receptor (OB-R) in linking pluripotency with growth, development, and the consequences on the progression of metabolic disease is poorly understood. Using a global unbiased proteomics approach we report that embryonic fibroblasts (MEFs) carrying db/db mutation exhibited metabolic abnormalities, while their reprogrammed induced pluripotent stem cells (iPSCs) demonstrated alterations in the expression of proteins involved in embryonic development.

Read the full summary ↓

An upregulation in the expression of eukaryotic translation initiation factor4e (eIF4e) and Stat3 binding to the eIF4e promoter was supported by enhanced protein synthesis in mutant iPSCs. Directed differentiation of db/db iPSCs towards the neuronal lineage showed defects compared to controls. Gene editing to correct point mutation in db/db iPSCs using CRISPR/Cas9, restored the metabolic defects, expression of neuronal markers, and protein synthesis as corroborated by RNAseq analyses. These data imply a direct role for OB-R in regulating metabolic properties in embryonic fibroblasts and key developmental pathways in iPSCs.

This dataset

Open GSE155704 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE155704_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA655248 and SRA study SRP275846. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

7 conditions, mostly in duplicate

aB6_B1 ×2 bB6_A5 ×2 bB6_B1 ×2 adb_db5 ×2 adb_db7 ×2 bdb_db5 ×2 bdb_db7 ×2 aB6_A5 ×1 +4 more

Supports a between-group comparison across 14 samples.

How we read this: 7 replicated groups read from 19 sample titles; they account for 14 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM4710929 aB6_A5_1
GSM4710930 aB6_B1_1 aB6_B1
GSM4710931 aB6_B1_2 aB6_B1
GSM4710932 bB6_A5_1 bB6_A5
GSM4710933 bB6_A5_2 bB6_A5
GSM4710934 bB6_B1_1 bB6_B1
GSM4710935 bB6_B1_2 bB6_B1
GSM4710936 adb_db5_1 adb_db5
GSM4710937 adb_db5_2 adb_db5
GSM4710938 adb_db7_1 adb_db7
GSM4710939 adb_db7_2 adb_db7
GSM4710940 bdb_db5_1 bdb_db5
GSM4710941 bdb_db5_2 bdb_db5
GSM4710942 bdb_db7_1 bdb_db7
GSM4710943 bdb_db7_2 bdb_db7
GSM4710944 db_c_1a
GSM4710945 db_c_1b
GSM4710946 db_c_2a
GSM4710947 db_c_2b

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.