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pmid:31909123

RNA sequencing data of mouse 2-cell embryos treated with DMSO.

Min-Hee Kang · Seong-Yeob You · Kwonho Hong · Jin-Hoi Kim

Data in brief · 2020 doi:10.1016/j.dib.2019.105025

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:31909123
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title
RNA sequencing data of mouse 2-cell embryos treated with DMSO.
doi
10.1016/j.dib.2019.105025
pmid
31909123
authors array · 4 items
[0]
Min-Hee Kang
[1]
Seong-Yeob You
[2]
Kwonho Hong
[3]
Jin-Hoi Kim
journal
Data in brief
year
2020
abstract
To understand the effect of DMSO in preimplantation embryos, we have treated mouse 1 cell zygotes with DMSO and found that DMSO treatment caused 2 or 4 cell embryonic arrest and altered the acetylation levels of mouse preimplantation embryos To illustrate the mechanism of DMSO in mouse preimplantation embryos, fertilized zygotes have been treated with 2% of DMSO and then performed RNA-seq analyses. Differentially expressed genes were identified using DESeq2 after adjustment for false discovery rate (FDR q value < 0.05). Gene Set Enrichment Analysis (GSEA) was also performed to identify biological pathways significantly modulated by DMSO. Raw and processed RNA-seq data were deposited and made publicly available on the Gene Expression Omnibus (GEO; GSE124598). The data presented in this article are related to the research paper entitled "DMSO impairs the transcriptional program for maternal-to-embryonic transition by altering histone acetylation", available in Biomaterials [1].
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Differentially expressed gene (DEG) were analyzed by DESeq2 [4] in R/Bioconductor with the parameters (baseMean counts >14; false discovery rate (FDR) < 0.05).
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sections[7] "RNA-seq data analysis" paragraph 2
quote
Differentially expressed gene (DEG) were analyzed by DESeq2 [4] in R/Bioconductor with the parameters (baseMean counts >14; false discovery rate (FDR) < 0.05).
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The raw data generated from Illumina sequencing were deposited on the Gene Expression Omnibus (GEO) with the reference number GSE124598 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124598).
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sections[3] "Data" paragraph 2
quote
The raw data generated from Illumina sequencing were deposited on the Gene Expression Omnibus (GEO) with the reference number GSE124598 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124598).
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Differentially expressed genes by DMSO in mouse 2-cell embryos identified by RNA sequencing
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KEGG and REACTOME pathway analysis in DMSO-treated 2-cell embryos.
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Data
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Table 1
caption
KEGG and REACTOME pathway analysis in DMSO-treated 2-cell embryos.
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[0]
[1]
Pathway ID
[2]
Pathway Term
[3]
adj_pvalue
[4]
No. of Genes
[5]
% Genes
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1
[1]
R-MMU:2262752
[2]
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0.00107233
[4]
92
[5]
24.02
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[1]
R-MMU:72702
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41.07
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[0]
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[1]
R-MMU:1234176
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Oxygen-dependent proline hydroxylation of Hyposia-inducible factor alpha
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[4]
24
[5]
40.00
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4
[1]
R-MMU:72689
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0.00117991
[4]
20
[5]
44.44
[5] array · 6 items
[0]
5
[1]
R-MMU:8948751
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0.00118317
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[5]
39.06
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[0]
6
[1]
R-MMU:373076
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Class A/1 (Rhodopsin-like receptors)
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0.00134226
[4]
20
[5]
6.25
[7] array · 6 items
[0]
7
[1]
R-MMU:4641258
[2]
Degradation of DVL
[3]
0.00147675
[4]
22
[5]
41.51
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[0]
8
[1]
R-MMU:74158
[2]
RNA Polymerase III Transcription
[3]
0.00154192
[4]
17
[5]
48.57
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[0]
9
[1]
R-MMU:76046
[2]
RNA Polymerase III Transcription Initiation
[3]
0.00154192
[4]
17
[5]
48.57
[10] array · 6 items
[0]
10
[1]
R-MMU:6807505
[2]
RNA polymerase II transcribes snRNA genes
[3]
0.00160451
[4]
27
[5]
36.99
[11] array · 6 items
[0]
11
[1]
R-MMU:69275
[2]
G2/M Transition
[3]
0.00170795
[4]
50
[5]
28.57
[12] array · 6 items
[0]
12
[1]
R-MMU:212436
[2]
Generic Transcription Pathway
[3]
0.00209786
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135
[5]
21.63
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[0]
13
[1]
R-MMU:453274
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Mitotic G2-G2/M phases
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0.00214072
[4]
50
[5]
28.25
[14] array · 6 items
[0]
14
[1]
R-MMU:4608870
[2]
Asymmetric localization of PCP proteins
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0.00222022
[4]
23
[5]
39.66
[15] array · 6 items
[0]
15
[1]
R-MMU:5689603
[2]
UCH proteinases
[3]
0.00278995
[4]
32
[5]
33.33
[16] array · 6 items
[0]
16
[1]
R-MMU:174113
[2]
SCF-beta-TrCP mediated degradation of Emi1
[3]
0.00288664
[4]
21
[5]
41.18
[17] array · 6 items
[0]
17
[1]
R-MMU:8854050
[2]
FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
[3]
0.00288664
[4]
21
[5]
41.18
[18] array · 6 items
[0]
18
[1]
R-MMU:5687128
[2]
MAPK6/MAPK4 signaling
[3]
0.00300873
[4]
26
[5]
36.62
[19] array · 6 items
[0]
19
[1]
R-MMU:174154
[2]
APC/C:Cdc20 mediated degradation of Securin
[3]
0.00312854
[4]
24
[5]
38.10
[20] array · 6 items
[0]
20
[1]
R-MMU:5621481
[2]
C-type lectin receptors (CLRs)
[3]
0.003421
[4]
35
[5]
31.82
[21] array · 6 items
[0]
21
[1]
R-MMU:73863
[2]
RNA Polymerase I Transcription Termination
[3]
0.00380234
[4]
15
[5]
50.00
[22] array · 6 items
[0]
22
[1]
R-MMU:1236978
[2]
Cross-presentation of soluble exogenous antigens (endosomes)
[3]
0.00388676
[4]
20
[5]
41.67
[23] array · 6 items
[0]
23
[1]
R-MMU:174178
[2]
APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
[3]
0.00417739
[4]
25
[5]
36.76
[24] array · 6 items
[0]
24
[1]
R-MMU:174184
[2]
Cdc20:Phospho-APC/C mediated degradation of Cyclin A
[3]
0.00417739
[4]
25
[5]
36.76
[25] array · 6 items
[0]
25
[1]
R-MMU:351202
[2]
Metabolism of polyamines
[3]
0.0042154
[4]
29
[5]
34.52
[26] array · 6 items
[0]
26
[1]
R-MMU:68882
[2]
Mitotic Anaphase
[3]
0.00531307
[4]
52
[5]
27.08
[27] array · 6 items
[0]
27
[1]
KEGG:03008
[2]
Ribosome biogenesis in eukaryotes
[3]
0.00545287
[4]
36
[5]
31.03
[28] array · 6 items
[0]
28
[1]
R-MMU:179419
[2]
APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfaction of the cell cycle checkpoint
[3]
0.00560289
[4]
25
[5]
36.23
[29] array · 6 items
[0]
29
[1]
R-MMU:1234174
[2]
Regulation of Hypoxia-inducible Factor (HIF) by oxygen
[3]
0.00579829
[4]
24
[5]
36.92
[30] array · 6 items
[0]
30
[1]
R-MMU:2262749
[2]
Cellular response to hypoxia
[3]
0.00579829
[4]
24
[5]
36.92
[31] array · 6 items
[0]
31
[1]
R-MMU:5610780
[2]
Degradation of GLI1 by the proteasome
[3]
0.00584049
[4]
21
[5]
39.62
[32] array · 6 items
[0]
32
[1]
R-MMU:72086
[2]
mRNA Capping
[3]
0.00770714
[4]
14
[5]
50.00
[33] array · 6 items
[0]
33
[1]
R-MMU:112382
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Formation of RNA Pol II elongation complex
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0.00820743
[4]
21
[5]
38.89
[34] array · 6 items
[0]
34
[1]
R-MMU:75955
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RNA Polymerase II Transcription Elongation
[3]
0.00820743
[4]
21
[5]
38.89
[35] array · 6 items
[0]
35
[1]
R-MMU:2555396
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Mitotic Metaphase and Anaphase
[3]
0.00834028
[4]
52
[5]
26.94
[36] array · 6 items
[0]
36
[1]
R-MMU:6807070
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PTEN Regulation
[3]
0.00889033
[4]
34
[5]
31.48
[37] array · 6 items
[0]
37
[1]
R-MMU:3858494
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Beta-catenin independent WNT signaling
[3]
0.01005271
[4]
37
[5]
30.08
[38] array · 6 items
[0]
38
[1]
R-MMU:2871837
[2]
FCERI mediated NF-kB activation
[3]
0.01119674
[4]
26
[5]
35.14
[39] array · 6 items
[0]
39
[1]
R-MMU:5358346
[2]
Hedgehog ligand biogenesis
[3]
0.01121237
[4]
22
[5]
37.29
[40] array · 6 items
[0]
40
[1]
R-MMU:5607761
[2]
Dectin-1 mediated noncanonical NF-kB signaling
[3]
0.01133035
[4]
21
[5]
38.18
[41] array · 6 items
[0]
41
[1]
R-MMU:5610785
[2]
GLI3 is processed to GLI3R by the proteasome
[3]
0.01133035
[4]
21
[5]
38.18
[42] array · 6 items
[0]
42
[1]
R-MMU:5676590
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NIK-->noncanonical NF-kB signaling
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0.01133035
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21
[5]
38.18
[43] array · 6 items
[0]
43
[1]
R-MMU:68827
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CDT1 association with the CDC6:ORC:origin complex
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0.01133035
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21
[5]
38.18
[44] array · 6 items
[0]
44
[1]
R-MMU:73772
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RNA Polymerase I Promoter Escape
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0.01271169
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14
[5]
48.28
[45] array · 6 items
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45
[1]
KEGG:03013
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RNA transport
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0.01396122
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[5]
27.54
[46] array · 6 items
[0]
46
[1]
R-MMU:2454202
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Fc epsilon receptor (FCERI) signaling
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0.01424613
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36
[5]
30.00
[47] array · 6 items
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47
[1]
R-MMU:5658442
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Regulation of RAS by GAPs
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0.01448249
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23
[5]
35.94
[48] array · 6 items
[0]
48
[1]
R-MMU:68867
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Assembly of the pre-replicative complex
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0.01448249
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23
[5]
35.94
[49] array · 6 items
[0]
49
[1]
R-MMU:73762
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RNA Polymerase I Transcription Initiation
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0.01479977
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18
[5]
40.91
[50] array · 6 items
[0]
50
[1]
R-MMU:5205647
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Mitophagy
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0.01554993
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13
[5]
50.00
[51] array · 6 items
[0]
51
[1]
R-MMU:77075
[2]
RNA Pol II CTD phosphorylation and interaction with CE
[3]
0.01554993
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13
[5]
50.00
[52] array · 6 items
[0]
52
[1]
R-MMU:176409
[2]
APC/C:Cdc20 mediated degradation of mitotic proteins
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0.01645248
[4]
25
[5]
35.21
[53] array · 6 items
[0]
53
[1]
R-MMU:176814
[2]
Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins
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0.01850655
[4]
25
[5]
34.72
[54] array · 6 items
[0]
54
[1]
R-MMU:113418
[2]
Formation of the Early Elongation Complex
[3]
0.0203327
[4]
14
[5]
46.67
[55] array · 6 items
[0]
55
[1]
R-MMU:9006925
[2]
Intracellular signaling by second messengers
[3]
0.02051725
[4]
62
[5]
24.60
[56] array · 6 items
[0]
56
[1]
R-MMU:2467813
[2]
Separation of Sister Chromatids
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0.02055007
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48
[5]
26.52
[57] array · 6 items
[0]
57
[1]
R-MMU:176408
[2]
Regulation of APC/C activators between G1/S and early anaphase
[3]
0.02193502
[4]
26
[5]
33.33
[58] array · 6 items
[0]
58
[1]
KEGG:05206
[2]
MicroRNAs in cancer
[3]
0.02406351
[4]
19
[5]
6.76
[59] array · 6 items
[0]
59
[1]
R-MMU:76061
[2]
RNA Polymerase III Transcription Initiation From Type 1 Promoter
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0.02559861
[4]
13
[5]
48.15
[60] array · 6 items
[0]
60
[1]
R-MMU:76066
[2]
RNA Polymerase III Transcription Initiation From Type 2 Promoter
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0.02559861
[4]
13
[5]
48.15
[61] array · 6 items
[0]
61
[1]
R-MMU:202424
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Downstream TCR signaling
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0.02570574
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28
[5]
32.56
[62] array · 6 items
[0]
62
[1]
R-MMU:72731
[2]
Recycling of eIF2:GDP
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0.02607639
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7
[5]
77.78
[63] array · 6 items
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63
[1]
R-MMU:71291
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Metabolism of amino acids and derivatives
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0.0304537
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60
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24.69
[64] array · 6 items
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64
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R-MMU:76071
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RNA Polymerase III Transcription Initiation From Type 3 Promoter
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0.04105632
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13
[5]
46.43
[65] array · 6 items
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65
[1]
R-MMU:202403
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TCR signaling
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0.04107335
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31
[5]
30.10
[66] array · 6 items
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66
[1]
R-MMU:174143
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APC/C-mediated degradation of cell cycle proteins
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0.04146255
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27
[5]
32.14
[67] array · 6 items
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67
[1]
R-MMU:453276
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Regulation of mitotic cell cycle
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0.04146255
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27
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32.14
[68] array · 6 items
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68
[1]
R-MMU:69304
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Regulation of DNA replication
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0.04440004
[4]
24
[5]
33.33
[69] array · 6 items
[0]
69
[1]
R-MMU:68949
[2]
Orc1 removal from chromatin
[3]
0.04507583
[4]
23
[5]
34.33
[70] array · 6 items
[0]
70
[1]
R-MMU:69052
[2]
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RNA sequencing data of mouse 2-cell embryos treated with DMSO.
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in preimplantation embryos, we have treated mouse 1 cell zygotes with DMSO and found that DMSO
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arrest and altered the acetylation levels of mouse preimplantation embryos To illustrate the me
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