Database of Transcriptome in Mouse Early Embryos

NCBI GEO Search & Collection

NCBI SRA Search: 

NCBI GEO Search: 


IDSpeciesCellData typePubmedDescription
Mouse E10.5, E11.5, E12.5, E14.5
PGC-to-gonocyte transition
NGS data (RNA-seq, RRBS, WGBS, AbaSeq) Hill et al. (2018) 29513657
SRP004904 (Histone ChIP)
SRP005409 (Histone ChIP)
SRP056573 (ATAC-seq, ESC,iPSC)
SRP090208 (RNA-seq)
SRX969061 (RNA-seq)
Mouse MEF NGS data Sangrithi et al. (2017) 28132849 NGS data from MEF that can be used as a control data of germ/embryo development
SRP071781  (GSE79230) Mouse Mature sperms ATAC-seq, Hi-C, ChIP-seq (CTCF, H3, Protamine, Smc1), BS-seq by HiSeq2000 Jung et al. (2017) 28178516 Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes
E-MTAB-4616  (ERP015330 Mouse EGFP-positive/negative germ cells/somatic cells (E9.5, E11.5, E12.5, E14.5, E15.5, E16.5 and E18.5) RNA-seq (HiSeq2500) Sangrithi et al. (2017) 28132849 Distinct and sexually dimorphic X dosage compensation states in the mammalian germline
DRA002477  DRA002402 (Sperm Bisulfite-seq) Mouse E16.5, P0.5, P7.5 (kit-, kit+), Sperm RNA-seq (GAIIx, HiSeq 1500, HiSeq2000), WGBS Kubo et al. (2015) 26290333 DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis
SRP016882  (GSE41908) Mouse (C57BL/6) PGC (E9.5, E13.5) RNA-seq (Smart-Seq, Illumina HiSeq 2500) Yamaguchi et al. (2013) 23151479 Transcriptome profiling of wild type primordial germ cells (PGC) by RNAseq
SRP066097  (GSE74938) Mouse PGC (Dnmt1 -/-, WT, male/female E10.5, E11.5, E13.5) RNA-seq (Illumina HiSeq 2500) Hargan-Calvopina J et al. (2016) 27618282 Demethylation in Primordial Germ Cells Safeguards against Precocious Differentiation
DRP002863 Mouse (C57BL/6N) PGC (E13.5, H3K27, male/femail, single cell) single cell RNA-seq (Illumina HiSeq 2500)
Sakashita et al. (2015) 26700643 Sex Specification and Heterogeneity of Primordial Germ Cells in Mice
SRP072248 Human, Mouse Epiblast, PGC, Heart (E6.5, E11.5, E13.5, E16.5 26 weeks) RNA-seq (Illumina HiSeq 2500) Guo et al. (2017) 27824029 DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
E-MTAB-2950, E-MTAB-4775 Mus musculus (C57BL/6) MII Oocyte, 2C, zygote, blastocyst, Morula RNA-seq (Illumina GA IIx) Karlic et al. (2017) 28087610 Long non-coding RNA exchange during the oocyte-to-embryo transition in mice
GSE71257 Mus musculus (C57BL/6) GV, MII Oocytes, Zygote, 2C RNA-seq (Illumina HiSeq 2500) Yu et al. (2016) 27065194 BTG4 is a meiotic cell cycle-coupled maternal-zygotic-transition licensing factor in oocytes
GSE80006 Homo sapiens, Mus musculus (C57BL/6) K562, Oocyte, Pronucleus (male, female) Hi-C (Illumina HiSeq 2500) Ilya et al., 2016 Single-cell Hi-C
GSE16893 Mus musculus (C57BL/6) ES (H3K36me3, H3K4me1, NPII, H3.3-HA,
H3.3B, H3.2, H3K27me3)
ChIP-seq (Illumina GAII) Goldberg et al. (2010) 20211137 Distinct factors control histone variant H3.3 localization
Mus musculus (46C (129/Ola strain)) ES (normal/knockdown Chd1,2,4,6,8,9, Ep400, Brg1) MNase-seq, ChIP-seq,
FAIRE-seq, RNA-seq, ChIP-exo, ATAC-seq
(Illumina GA/GAIIx, HiSeq2000/2500, NextSeq500
Hmitou et al. (2016) 26814966 Genome-wide distribution and function of ATP-dependent chromatin remodelers
GSM359413 Brg1
GSM359413 DNase-seq
GSM1014154 DNase-seq
GSM590132 Ezh2
GSM665994 GRO-seq
DRP001103 H2A.Z
GSM1386359 H3.3
GSM594578 H3K27ac
GSM590115 H3K27me3
GSM590119 H3K36me3
GSM590111 H3K4me3
GSM560347 Med1
GSM687284 Mi2b (Chd4)
GSM1004653 MNase-seq
GSM1082340 Oct4, Sox2, Nanog
GSM515662 Pol II S5ph
GSM958503 TBP
Mus musculus ES Hmitou et al. (2016) 26814966
Mus musculus (C57BL/6) Sperm/RS nucleosome, H3 variants, K4me3, K27me3 RNA-seq,
ChIP-seq (GAIIx, HiSeq 2000)
Erkek et al. (2013) 23770822 CpGs define histone variant specific retention
MNase-seq is same with GSE42629
Mus musculus (C57BL/6) Sperm nucleosome, H3K4me2 (WT, TG of KDM1A) MNase-seq, ChIP-seq (HiSeq 2000) Siklenka et al. (2015) 26449473 histone methylation homeostasis during spermatogenesis
Mus musculus (129 X Ola,C57/B6J) ES, Sperm nucleosome MNase-seq (HiSeq 2000) Carone et al. (2014) 24998598 High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm
GSE45489 Mus musculus (C57BL/6) Spermatids Sfmbt1, LSD1(Kdm1a), POL2 ChIP-seq (HiSeq 2000) 23592795 regulation of canonical histone genes by SFMBT1 & LSD1
ENCODE Mus musculus (C57BL/6) Testes ChIP-seq (HiSeq 2000) H3K4me1/3, K27ac, K27me3, K36me3, CTCF, Pol2
GSE63130 RNA-seq, ChIP-seq
SRP057695 Rfx2-binding
Mus musculus
(C57BL/6|129/Sv|FVB/N Mixed BKG)
RFX2 KO/WT Testes ChIP-seq (HiSeq 2000/2500) Kistler et al. (2015) 25142466 RFX2 in spermiogenesis
GSE60207 Mus musculus H3K4me3 KO/WT Testes ChIP-seq (HiSeq 2000) Yuen et al. (2014) 25142466 H3K4me3 KO/WT
GSM1817673 CTCF
GSM1817674 BORIS
GSM1817675 Input
Mus musculus RS (round spermatids) TF ChIP-seq (HiSeq 2000) Pugacheva et al. (2015) 26268681 CTCF and BORIS occupancy
Mus musculus (CD1xC57BL/6) GS (germline stem) cells:
mitotically active undiff. spermatogonia

THY1+ undiff. spermatogonia
PS(pachytene spermatocytes)
RS(round spermatids)
RNA-seq, ChIP-seq, MNase-seq (HiSeq 2000) Hasegawa et al. (2015) 25703348 Scml2 WT/KO, ubH2A, Rnf2, Bmi1,
RRBS,H3K4me2 (Whole Brain,Liver,Testes)
RRBS,H3K4me2 (Spermatocytes,Spermatids)
Mus musculus (C57BL/6) Spermatocytes, Spermatids RRBS,ChIP-seq (GA IIx) Soumillon et al. (2013) 23791531 high transcriptome complexity in the mammalian testis
GSE73382 Mus musculus (C57BL/6) MII oocytes RNA-seq (HiSeq 2500) Nashun et al. (2015) 26549683 Single cell RNA-Seq of Hira-KO and control MII oocytes
Hira (floxed/floxed), Gdf9-Cre+, Zp3-Cre+
GSE75765  (single embryo)
GSE75769  (ICSI)
GSE75902  (IVF)
Mus musculus (FVB/NJ) Sperm, Zygotes, F1 RNA-seq (NextSeq 500) Chen et al. (2016) 26721680
Sharma et al. (2016) 26721685
Biogenesis and function of sperm tRNA fragments

Whole Brain,Liver,Testes
Mus musculus (C57BL/6) Sertoli, Spermatogonia,
Spermatocytes, Spermatids and Spermatozoa
RNA-seq (GA IIx) Soumillon et al. (2013) 23791531
Margolin et al. (2014) 24438502
GSE55009 Mus musculus (129SVE) 2-Cell embryos RNA-seq (HiSeq2000) Ihara et al. (2014) 24810616 Poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones
Mus musculus (C57BL/6) Sperm, 8C, Blastocyst (nc)RNA-seq (HiSeq2000/2500) Chen et al. (2016) 26721680 Non-coding RNA profiling
GSE47843 Homo sapiens; Bos taurus Sperm nucleosome MNase-seq (GA IIx) 24998597 Nucleosome retention in sperm at repetitive DNA regions
GSE59252 Mus musculus (CD-1) PGC, Spermatids, Testes
small non-coding RNAs
MI Ready Array 49K Garcia-Lopez et al. (2015) 25805854 sncRNAs in male germ cell diff. and fertlization.
GSE71478 Mus musculus (BDF1) PGC, Spermatids Expression (Affymetrix) 26923202 In vitro meiosis from murine ESC-derived PGCLCs
resulting in the formation of male spermatid-like cells
GSE35303 H3f3b null/WT
Mus musculus Spermatogenesis Expression (Affymetrix, Illumina MouseWG-6) Yuen et al. (2014) 25142466 H3.3 (H3f3b null/WT) regulation during spermatogenesis
GSE19542 Mus musculus (C57BL/6) ES rep1,2,3; Cl34 ES rep 1,2,3; Expression (Affymetrix) Goldberg et al. (2010) 20211137 Distinct factors control histone variant H3.3 localization