NCBI GEO Search & Collection
| ID | Species | Cell | Data type | Pubmed | Description |
|---|---|---|---|---|---|
|
GSE76973
|
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) ChIP-seq |
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 |
|
GSE64825 SRP051966 |
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 GSM958501 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 | ||
|
GSE42629 SRP017350 |
Mus musculus (C57BL/6) | Sperm/RS nucleosome, H3 variants, K4me3, K27me3 |
RNA-seq, MNase-seq, ChIP-seq (GAIIx, HiSeq 2000) |
Erkek et al. (2013) 23770822 | CpGs define histone variant specific retention |
|
GSE55471 MNase-seq is same with GSE42629 SRP039082 |
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 |
|
GSE58101 SRP042377 |
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 SRP060661 |
Mus musculus | RS (round spermatids) | TF ChIP-seq (HiSeq 2000) | Pugacheva et al. (2015) 26268681 | CTCF and BORIS occupancy |
|
GSE55060 SRP037992 |
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) GSE43719 SRP018126 |
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 |
|
GSE43717 SRP018124 Whole Brain,Liver,Testes GSE43721 SRP018127 |
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 |
|
GSE75544 SRP066841 |
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 |
|
GSE21749 GSE4193 GSE23119 GSE21447 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 |
