GEO series

Insulin resistance is associated with mammary mitochondrial dysfunction at the onset of human lactation

GSE342640 Homo sapiens (human) RNA-seq (gene expression) 159 samples Submitted 2026/08/07 Platform GPL24247Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 159 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: Homo sapiens (human)
Samples: 159 samples: 23 conditions, mostly with about 5 replicates eachGroups 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)

Insulin resistance (IR) has emerged as a risk factor for lactation insufficiency and delays the onset of milk secretion after childbirth, termed secretory activation (SA). This may cause inadequate infant weight gain and early breastfeeding cessation. However, the mechanisms underlying delayed SA in insulin resistant women are unknown.

Read the full summary ↓

To investigate this, we characterized the mammary transcriptomes and IR-related hormones of 75 breastfeeding women with healthy term infants during postpartum days 1-5. Participants were divided into IR tertiles based on plasma leptin-to-adiponectin ratio measurements. Those in the highest tertile had later SA onset with greater neonatal weight loss during postpartum days 1-5. Transcriptomic analysis on postpartum day 2 (n=4 high IR vs. n=8 low IR participants) showed transient suppression of mammary insulin and prolactin signaling genes, increased pro-inflammatory gene expression and altered expression of >200 mammary mitochondrial genes. These alterations were absent on postpartum days 3-5. Cultured mammary epithelial cells (MECs) treated with insulin showed upregulation of prolactin signaling and oxidative phosphorylation (OXPHOS) genes, with imaging and bioenergetic studies demonstrating that insulin promotes mitochondrial biogenesis and OXPHOS. Thus, our findings delineate roles for insulin in mammary bioenergetics and highlight mitochondrial dysfunction as a mechanism for delayed SA in insulin resistant women.

This dataset

Open GSE342640 in finder → Find more 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 GSE342640_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 PRJNA1508691 and SRA study SRP724715. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

23 conditions, mostly with about 5 replicates each

Milk fat globule_day 4_high insulin resistanc… ×13 Milk fat globule_day 4_medium insulin resista… ×13 Milk fat globule_day 3_high insulin resistanc… ×12 Milk fat globule_day 3_medium insulin resista… ×12 Milk fat globule_day 4_low insulin resistance… ×11 Milk fat globule_day 5_high insulin resistanc… ×10 Milk fat globule_day 2_low insulin resistance… ×8 Milk fat globule_day 2_medium insulin resista… ×7 +15 more

Supports a case/control comparison: 10 samples read as cases, 10 as controls.

How we read this: 23 replicated groups read from 159 sample titles; they account for 159 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

GSM9935071 HC11 cells_8h control_biol rep 1 HC11 cells_8h control_b…
GSM9935072 HC11 cells_8h control_biol rep 2 HC11 cells_8h control_b…
GSM9935073 HC11 cells_8h control_biol rep 3 HC11 cells_8h control_b…
GSM9935074 HC11 cells_8h control_biol rep 4 HC11 cells_8h control_b…
GSM9935075 HC11 cells_8h control_biol rep 5 HC11 cells_8h control_b…
GSM9935076 HC11 cells_8h 100nM insulin_biol rep 1 HC11 cells_8h 100nM ins…
GSM9935077 HC11 cells_8h 100nM insulin_biol rep 2 HC11 cells_8h 100nM ins…
GSM9935078 HC11 cells_8h 100nM insulin_biol rep 3 HC11 cells_8h 100nM ins…
GSM9935079 HC11 cells_8h 100nM insulin_biol rep 4 HC11 cells_8h 100nM ins…
GSM9935080 HC11 cells_8h 100nM insulin_biol rep 5 HC11 cells_8h 100nM ins…
GSM9935081 WT 0nM insulin control, biol rep 1 WT 0nM insulin control,…
GSM9935082 WT 0nM insulin control, biol rep 2 WT 0nM insulin control,…
GSM9935083 WT 0nM insulin control, biol rep 3 WT 0nM insulin control,…
GSM9935084 WT 0nM insulin control, biol rep 4 WT 0nM insulin control,…
GSM9935085 WT 0nM insulin control, biol rep 5 WT 0nM insulin control,…
GSM9935086 Akt knockdown, 0nM insulin, biol rep 1 Akt knockdown, 0nM insu…
GSM9935087 Akt knockdown, 0nM insulin, biol rep 2 Akt knockdown, 0nM insu…
GSM9935088 Akt knockdown, 0nM insulin, biol rep 3 Akt knockdown, 0nM insu…
GSM9935089 Akt knockdown, 0nM insulin, biol rep 4 Akt knockdown, 0nM insu…
GSM9935090 Akt knockdown, 0nM insulin, biol rep 5 Akt knockdown, 0nM insu…
GSM9935091 10nM insulin, 1h, biol rep 1 10nM insulin, 1h, biol
GSM9935092 10nM insulin, 1h, biol rep 2 10nM insulin, 1h, biol
GSM9935093 10nM insulin, 1h, biol rep 3 10nM insulin, 1h, biol
GSM9935094 10nM insulin, 4h, biol rep 1 10nM insulin, 4h, biol
GSM9935095 10nM insulin, 4h, biol rep 2 10nM insulin, 4h, biol
GSM9935096 10nM insulin, 4h, biol rep 3 10nM insulin, 4h, biol
GSM9935097 10nM insulin, 4h, biol rep 4 10nM insulin, 4h, biol
GSM9935098 10nM insulin, 4h, biol rep 5 10nM insulin, 4h, biol
GSM9935099 10nM insulin, 8h, biol rep 1 10nM insulin, 8h, biol
GSM9935100 10nM insulin, 8h, biol rep 2 10nM insulin, 8h, biol
GSM9935101 10nM insulin, 8h, biol rep 3 10nM insulin, 8h, biol
GSM9935102 10nM insulin, 8h, biol rep 4 10nM insulin, 8h, biol
GSM9935103 10nM insulin, 8h, biol rep 5 10nM insulin, 8h, biol
GSM9935104 100nM insulin, 1h, biol rep 1 100nM insulin, 1h, biol
GSM9935105 100nM insulin, 1h, biol rep 2 100nM insulin, 1h, biol
GSM9935106 100nM insulin, 1h, biol rep 3 100nM insulin, 1h, biol
GSM9935107 100nM insulin, 1h, biol rep 4 100nM insulin, 1h, biol
GSM9935108 100nM insulin, 1h, biol rep 5 100nM insulin, 1h, biol
GSM9935109 100nM insulin, 4h, biol rep 1 100nM insulin, 4h, biol
GSM9935110 100nM insulin, 4h, biol rep 2 100nM insulin, 4h, biol

+ 119 more — browse all 159 samples with per-sample file links →

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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.