GEO DataSets

(Submitter supplied) Here we modified a single cell whole transcriptome amplification method to make it capable of amplifying cDNAs as long as 3kb efficiently and unbiasedly. We combined this modified single cell cDNA amplification method with Applied Biosystems next generation sequencing SOLiD™ System to set up a single cell whole transcriptome assay. The modified amplification strategy allows us to amplify full-length cDNAs for most of the expressed genes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9318

24 Samples

Download data: SRF

(Submitter supplied) Upon 2-cell embryo splitting, individual blastomeres were compared and contrasted with each other respecting pair associations (e.g. blastomere '1a' and '1b' of embryo 1, '2a' and '2b' of embryo 2, and so forth) Transcriptome analysis followed by cluster analysis (Ward) was able to match a minority of the blastomeres with the correct sister blastomere

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL20775

20 Samples

Download data: CEL, TXT

(Submitter supplied) Upon 2-cell embryo splitting, individual blastomeres were cultured in KSOM(aa) medium and developed into blastocysts, which were compared and contrasted with each other respecting pair associations (e.g. twin vs cotwin) Transcriptome analysis revelaled minimal differences between twins and unmanipulated controls, in contrast to larger differences between twins and cotwins; these differences are mainly related to the epiblast lineage

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL20775

25 Samples

Download data: CEL, TXT

(Submitter supplied) Mammalian preimplantation development involves highly conserved genetic programs across species. However, temporal differences in gene network activation and membership differences in gene modules are also observed. In this study, we focus on understanding the activation of crucial gene networks in trophoectoderm (TE) and inner cell mass across species using human, monkey, and mouse models. By single cell RNA sequencing analysis in cynomolgus monkey early embryos, we find relatively late major embryonic genome activation occurring at early morula stages. more...

Organism:

Homo sapiens; Mus musculus; Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18648 GPL13112 GPL11154

195 Samples

Download data: TXT

(Submitter supplied) Find the casual relationship between gene expression network and cellular phenotype at single cell resolution. We collected donated human pre-implatation embryos, and the embryonic stem cells derived from them, isolate individual cells, prepared single cell cDNAs, and sequenced them by HiSeq2000. Then we analyzed the expression of known RefSeq genes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

124 Samples

Download data: BED, TDF, TXT

(Submitter supplied) The aberrant gene expression of early bovine embryos are a major cause for developemtal arrest. Therefore our aim was to detect transcriptomic fingerprints which correlate with the subsequent developmental competence of a two cell stage embryo.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

12 Samples

Download data: GPR

(Submitter supplied) H3.3-mediated paternal chromatin remodeling is essential for the development of preimplantation embryos and the activation of the paternal genome during embryogenesis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: FPKM_TRACKING

(Submitter supplied) We have examined whether twin blastomeres from 2-cell stage mouse embryos differ in mRNA content. Amplified mRNA from 12 blastomeres derived from six embryos approximately mid-way through their second cell cycle was analyzed. Probes displaying normalized values greater than 0.25 were selected and examined for consistent bias in expression within blastomere pairs. Although transcript content varied both between individual embryos and twin blastomeres, no consistent asymmetries were observed for the majority of genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

12 Samples

Download data: TXT

(Submitter supplied) In multicellular organisms, heterogametes of oocytes and sperms are fertilized and resulting zygotes give rise to new individuals. The ability of zygotes that produce a fully formed individual from single cell when placed in a supportive environment is defined as totipotency. Given that totipotent cells are the source of all multicellular organisms, better understanding of totipotency has a profound effect on not only biology but also our society. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

2 Samples

Download data: CSV, TXT

(Submitter supplied) Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple (UCSFB1-10). Versus numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns, in part, indicative of trophoblast competence. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL6947 GPL13534 GPL10558

383 Samples

Download data: TXT

(Submitter supplied) Duplication of the genome in mammalian cells occurs in a defined temporal order referred as its replication-timing program (RT). RT is regulated in units of 400-800 Kb referred as replication domains (RDs) and changes dynamically during development. Changes in RT are generally coordinated with transcriptional competence and changes in sub-nuclear position. We generated genome-wide RT profiles for 29 distinct human cell types including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm and neural crest (NC) development. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

64 Samples

Download data: TXT

(Submitter supplied) Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. Through single-cell RNA-sequencing (RNA-seq), we report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos. Based on single nucleotide variants (SNVs) in blastomere mRNAs and paternal-specific SNPs, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25-53%). more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL11154

47 Samples

Download data: TXT, WIG

(Submitter supplied) Much of posttranscriptional mRNA regulation occurs through cis-acting sequences in mRNA 3´ untranslated regions (UTRs), which interact with specific proteins and ribonucleoprotein complexes that modulate translation, mRNA stability and subcellular localization. Studies in Caenorhabditis elegans have revealed indispensable roles for 3´UTR-mediated gene regulation, yet most C. elegans genes have lacked annotated 3´UTRs. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9269

10 Samples

Download data: BED, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28352 GPL24676

83 Samples

Download data

(Submitter supplied) Human preimplantation development is a complex process involving extensive remodeling of gene expression. However, the preimplantation embryo transcriptome has only been annotated using short-read sequencing, which fails to capture full-length mRNAs and associated isoform diversity. We present a novel human embryo transcriptome using integrated long- and short-read RNA sequencing data. Our analysis reveals a total of 110,212 novel isoforms transcribed from known genes containing either a novel combination of known splice sites or at least one novel splice site, and 17,964 isoforms transcribed from completely novel genes located either in antisense direction of known genes or in intergenic space.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28352

10 Samples

Download data: GTF

(Submitter supplied) Human preimplantation development is a complex process involving extensive remodeling of gene expression. However, the preimplantation embryo transcriptome has only been annotated using short-read sequencing, which fails to capture full-length mRNAs and associated isoform diversity. We present a novel human embryo transcriptome using integrated long- and short-read RNA sequencing data. Our analysis reveals a total of 110,212 novel isoforms transcribed from known genes containing either a novel combination of known splice sites or at least one novel splice site, and 17,964 isoforms transcribed from completely novel genes located either in antisense direction of known genes or in intergenic space.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

73 Samples

Download data: TSV

(Submitter supplied) Pathological cardiac hypertrophy was induced by pressure overload on the heart. We performed genome-wide exon array experiments with left ventricles of mice with 1 week and 4 week of transverse aortic constriction (TAC). The exon level analysis revealed widespread regulation of alternative splicing and alternative polyadenylation during hypertrophy.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

6 Samples

Download data: CEL

(Submitter supplied) We hypothesized that LincGET/CARM1 complex activates ICM-specific genes at the 8-cell stage. And we examined chromatin accessibility of these genes by preforming an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

3 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19129 GPL24522

256 Samples

Download data

(Submitter supplied) To explore the dynamic change of transcriptome in pre-implantation of rhesus monkey, we collected single cells for RNA-sequencing.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24522

161 Samples

Download data: TXT