Mining transcriptomic data for gestational diabetes mellitus: What public datasets reveal

Table 1 Overview of transcriptomic datasets included in this mini-review on gestational diabetes mellitus

Series	Organisms	Tissues	Sample source (M/O/B)	Sequencing type	Research theme	Sample count
GSE267340	Homo sapiens	Placenta	M	scRNA-seq	Placenta-related	4
GSE173193	Homo sapiens	Placenta	M	scRNA-seq	Placenta-related	8
GSE249311	Homo sapiens	Placenta	M	RNA-seq	Placenta-related	54
GSE154414	Homo sapiens	Placenta	M	RNA-seq	Placenta-related	8
GSE144276	Rattus norvegicus	Placenta	M	RNA-seq	Placenta-related	6
E-MTAB-11439	Mus musculus	Liver	M	RNA-seq	Placenta-related	8
E-MTAB-9203	Homo sapiens	Placenta	M	RNA-seq	Placenta-related	14
GSE206042	Homo sapiens	Placenta	M	ncRNA-seq	Placenta-related	6
GSE213799	Homo sapiens	Placenta	O	ncRNA-seq	Placenta-related	14
GSE112168	Homo sapiens	Chorionic villi	M	ncRNA-seq	Placenta-related	12
GSE154415	Homo sapiens	Placenta	M	Multi-omics	Placenta-related	24
GSE206041	Homo sapiens	Placenta	M	ncRNA-seq	Placenta-related	6
GSE2956	Homo sapiens	Placenta	M	Microarray	Placenta-related	1
GSE19649	Homo sapiens	Blood, placenta	M	Microarray	Placenta-related	5
GSE103552	Homo sapiens	Placenta	O	Microarray	Placenta-related	37
GSE51546	Homo sapiens	Umbilical cord	O	Microarray	Placenta-related	12
GSE154413	Homo sapiens	Placenta	M	ncRNA-seq	Placenta-related	16
GSE89497	Homo sapiens	Placenta	M	RNA-seq	Placenta-related	764
GSE200983	Homo sapiens	Placenta	M	RNA-seq	Placenta-related	6
GSE49524	Homo sapiens	Umbilical cord blood	O	Microarray	Placenta-related	6
GSE250374	Homo sapiens	Placenta	M	ncRNA-seq	Placenta-related	12
GSE236335	Mus musculus	Uterus, vagina	M	RNA-seq	Placenta-related	16
GSE87295	Homo sapiens	Umbilical cord	O	Microarray	Placenta-related	10
GSE150621	Homo sapiens	Amniocytes	O	RNA-seq	Circulating biomarkers	14
GSE70494	Homo sapiens	Placenta	M	Multi-omics	Circulating biomarkers	145
GSE70493	Homo sapiens	Placenta	M	Microarray	Circulating biomarkers	63
GSE267259	Homo sapiens	Serum	M	RNA-seq	Circulating biomarkers	8
GSE284329	Homo sapiens	PBMCs	M	RNA-seq	Circulating biomarkers	17
GSE212309	Homo sapiens	Umbilical cord blood	O	scRNA-seq	Circulating biomarkers	7
GSE228990	Homo sapiens	Umbilical cord blood	O	RNA-seq	Circulating biomarkers	60
GSE192813	Homo sapiens	Plasma sEVs	M	ncRNA-seq	Circulating biomarkers	24
GSE216997	Homo sapiens	Plasma	M	ncRNA-seq	Circulating biomarkers	328
GSE203346	Homo sapiens	Umbilical cord blood	B	RNA-seq	Circulating biomarkers	84
GSE243374	Homo sapiens	Serum maternal exosomes, serum placental exosomes	M	Microarray	Circulating biomarkers	28
GSE154377	Homo sapiens	Plasma	M	RNA-seq	Circulating biomarkers	134
GSE92772	Homo sapiens	Blood	M	Multi-omics	Circulating biomarkers	32
GSE98043	Homo sapiens	Plasma	M	Microarray	Circulating biomarkers	4
GSE65737	Homo sapiens	Umbilical cord vein blood	O	Microarray	Circulating biomarkers	6
E-MEXP-3382	Homo sapiens	Blood	M	Microarray	Circulating biomarkers	6
E-MEXP-3966	Homo sapiens	Blood	M	Microarray	Circulating biomarkers	3
E-MEXP-3349	Homo sapiens	Blood	M	Microarray	Circulating biomarkers	17
GSE241770	Mus musculus	Pancreatic islets	M	scRNA-seq	β-cell/islet function	7899
GSE278861	Mus musculus	Pancreatic islets	O	scRNA-seq	β-cell/islet function	9
GSE234741	Mus musculus	Pancreatic islets	M	scRNA-seq	β-cell/islet function	2
GSE289077	Mus musculus	Pancreatic islets	M	RNA-seq	β-cell/islet function	15
GSE237149	Mus musculus	Liver	B	RNA-seq	β-cell/islet function	40
GSE234740	Mus musculus	Pancreatic islets	M	RNA-seq	β-cell/islet function	11
GSE116663	Rattus norvegicus	Pancreatic islets	O	RNA-seq	β-cell/islet function	12
GSE118323	Rattus norvegicus	Pancreatic islets	O	RNA-seq	β-cell/islet function	6
GSE104017	Rattus norvegicus	Pancreatic islets	O	RNA-seq	β-cell/islet function	12
GSE90022	Ovis aries	Pancreatic islets	O	RNA-seq	β-cell/islet function	8
GSE21860	Mus musculus	Pancreatic islets	M	RNA-seq	β-cell/islet function	6
GSE130997	Mus musculus	Pancreatic islets	M	RNA-seq	β-cell/islet function	6
GSE36067	Rattus norvegicus	Pancreatic islets	M	Microarray	β-cell/islet function	14
GSE100645	Mus musculus	Pancreatic islets	M	Microarray	β-cell/islet function	6
GSE255246	Mus musculus	Skeletal muscle	O	RNA-Seq	β-cell/islet function	10
GSE136737	Rattus norvegicus	Cardiac	O	RNA-seq	β-cell/islet function	12
GSE147039	Mus musculus	Hippocampus	O	Microarray	β-cell/islet function	15
GSE194119	Homo sapiens	Blood exosomes	M	Multi-omics	Predictive models	6
GSE182737	Homo sapiens	PBMCs	M	Microarray	Predictive models	12
GSE114860	Homo sapiens	Exosomes	M	ncRNA-seq	Predictive models	28

M: Maternal; O: Offspring; B: Both; PBMCs: Peripheral blood mononuclear cells; sEVs: Secreted extracellular vesicles; RNA-seq: RNA-sequencing; scRNA-seq: Single-cell RNA-sequencing; ncRNA-seq: Non-coding RNA-sequencing.

Table 2 Overview of RNA sequencing and expression profiling platforms used in gestational diabetes mellitus transcriptomic studies

Platform	Read configuration/probe architecture	Data output capacity	Advantages	Disadvantages	Frequency	Category
NovaSeq 6000	2 × 50 ~ 2 × 250 bp (2 × 150 bp common)	Ultra-high	High-throughput, good cost/data ratio	Expensive, best for large projects	11	NGS, short-read (Illumina)
HiSeq 4000	2 × 50 ~ 2 × 150 bp	High	Mainstream, reliable	Being replaced by NovaSeq	10	NGS, short-read (Illumina)
HiSeq 2000	2 × 100 bp	Moderate	Stable, classical platform	Older, limited throughput	4	NGS, short-read (Illumina)
HiSeq 2500	2 × 50 ~ 2 × 125 bp (rapid)	Moderate	Flexible (rapid/high modes)	Phasing out	6	NGS, short-read (Illumina)
NextSeq 500	2 × 75 ~ 2 × 150 bp	Middle	Fast run time, flexible	Limited throughput, costlier	4	NGS, short-read (Illumina)
NextSeq 2000	2 × 50 ~ 2 × 150 bp	Middle-high	Improved chemistry, higher quality	Still relatively costly	1	NGS, short-read (Illumina)
Illumina BeadChip	48 k/24 k fixed probes	Ultra-high	Mature, low cost	Lower sensitivity, cannot detect novel transcripts	5	DNA microarray
Affymetrix	3’-biased or whole-transcript probes	High	Mature database support	Lower resolution, narrow dynamic range	4	DNA microarray
Agilent	8 × 60 k format, 20638 genes	High	Cost-effective, widely used	Limited depth of analysis	4	DNA microarray

NGS: Next-generation sequencing.