|
| Antibodies |
|
|
|
| anti-Afp |
R&D Systems |
AF1369; RRID:AB_354758 |
| anti-Pax6 |
BioLegend |
901301; RRID:AB_2565003 |
| J2 anti-dsRNA |
Scicons |
10010200; RRID:AB_2651015 |
| anti-(gag/pol)HERVK |
Austrial Biological |
HERM18315; RRID:AB_10890594 |
| anti-Pan Corona FIPV3-70 |
Life Technologies |
MA1-82189; RRID:AB_930177 |
| anti-Oct3/4-AF488 |
Santa Cruz |
sc-5279-AF488; RRID:AB_628051 |
| anti-Brachyury |
R&D Systems |
IC2085G;RRID:AB_2933975 |
| anti-Otx2 |
R&D Systems |
AF1979; RRID:AB_2157172 |
| anti-Zic2 |
Abcam |
ab150404; RRID:AB_2868423 |
| anti-Tfe3 |
Sigma Aldrich |
HPA023881; RID:AB_1857931 |
| anti-Tfcp2l1 |
R&D Systems |
AF5726; RRID:AB_2202564 |
| anti-Cdx2 |
Invitrogen |
PA5-20891; RRID:AB_11155394 |
| Donkey anti-chicken-Cy3 |
Millipore |
AP194C; RRID:AB_92679 |
| Goat anti-chicken-AF488 |
Invitrogen |
A-11039; RRID:AB_2534096 |
| Donkey anti-rabbit-AF647 |
Invitrogen |
A-31573; RRID:AB_2536183 |
| Goat anti-rabbit-AF488 |
Invitrogen |
A-10034; RRID:AB_2576217 |
| Goat anti-mouse-AF488 |
Invitrogen |
A-11029; RRID:AB_2534088 |
| Abberior Star 635P |
Abberior |
ST635P; RRID:AB_2893232 |
| H3K4me3 |
Active Motif |
39159; RRID:AB_2615077 |
| H3K27me3 |
Active Motif |
39155; RRID:AB_2561020 |
| anti-mouse-HRP |
Promega |
W4021; RRID:AB_430834 |
|
| Bacterial and virus strains |
|
|
|
| SARS-CoV-2, isolate USA-WA1/2020 |
BEI Resources |
NR-52281 |
| Human Metapneumovirus MPV-GFP1 |
ViraTree |
M121 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| DPBS (Life Technologies, 14190144), |
Gibco |
14190144 |
| DPBS |
Biowest |
L0615-500 |
| 0.05% Trypsin |
Gibco |
25300054 |
| DMEM |
Gibco |
10569010 |
| DMEM |
Gibco |
11995065 |
| Fetal bovine serum, FBS |
Sigma-Aldrich |
F4135 |
| Fetal bovine serum, FBS |
Gibco |
10500064 |
| MEM Non-essential amino |
Gibco |
11140050 |
| GlutaMax Supplement |
Gibco |
35050061 |
| Penicillin-Streptomycin solution |
Gibco |
15140122 |
| Gelatin |
Millipore |
ES006B |
| Antibiotic-Antimycotic (100X) |
Gibco |
15240096 |
| Collagenase type II |
Gibco |
17101015 |
| Gentle Cell Dissociation Reagent |
StemCell Technologies |
07174 |
| DMEM/F-12 |
Gibco |
11330057 |
| Knockout serum replacement |
Gibco |
10828-028 |
| DMSO |
Sigma-Aldrich |
D8418-100ML |
| 2-mercaptoethanol |
Fluka |
63689 |
| FGF2 |
R&D Systems |
233-FB |
| Leukemia inhibitory factor |
Millipore |
ESG1107 |
| SCF |
R&D Systems |
PHC2111 |
| Forskolin |
Sigma-Aldrich |
F6886 |
| KaryoMAX Colcemid Solution in HBSS |
Gibco |
15210040 |
| Sodium Pyruvate, 100 mM |
Gibco |
11360070 |
| Potassium chloride |
Sigma-Aldrich |
P9327 |
| Glacial acetic |
Fisher Scientific |
A38-212 |
| Methanol |
Sigma-Aldrich |
A412-4 |
| KaryoMax Giemsa staining solution |
Gibco |
10092013 |
| Gurr buffer tablets |
Gibcco |
10582013 |
| Cytoseal 60 |
Thermo Scientific |
23-244257 |
| SuperScript IV VILO™ Master Mix |
Invitrogen |
11756050 |
| GoTaq Green Polymerase |
Promega |
M7123 |
| Cytofix/Cytoperm solution |
Becton Dickinson |
BDB554714 |
| NucBlue Dapi stain |
Invitrogen |
R37606 |
| Prolong Dimond antifade mounting medium |
Invitrogen |
P36965 |
| DyeCycle Violet stain |
Invitrogen |
V35003 |
| DNase |
Qiagen |
79254 |
| Formaldehyde |
Sigma-Aldrich |
F8775 |
| Sodium chloride solution, 5M |
Sigma-Aldrich |
S5150 |
| EDTA (0.5 M), pH 8.0, RNase-free |
Invitrogen |
AM9260G |
| HEPES, 1M |
Invitrogen |
15630080 |
| Glycine |
Sigma-Aldrich |
G8898 |
| Igepal |
Sigma-Aldrich |
I3021 |
| PMSF |
Sigma-Aldrich |
P7626 |
| mTeSR medium |
StemCell Technologies |
85850 |
| Vitronectin |
StemCell Technologies |
07180 |
| BMP4 |
R&D Systems |
314-BP-010 |
| Versene |
Gibco |
15040066 |
| 10% Formalin |
Fisher Scientific |
SF1004 |
| RIPA lysis and extraction buffer |
Fisher Scientific |
89900 |
| Proteinase Inhibitor |
Roche |
45582400 |
| BCA Protein assay kit |
Pierce |
23252 |
| 12% TGX Precast gel |
Bio-Rad |
4561044 |
| TGS buffer |
Bio-Rad |
1610772 |
| the Precision Plus Kaleidoscope Protein standard |
Bio-Rad |
161-3075 |
| EveryBlot blocking buffer |
Bio-Rad |
12010020 |
| Tris-buffered saline |
Fisher Scientific |
BP2471500 |
| Tween 20 |
Bio-Rad |
161-0781 |
| Clarity Western ECL Substrate |
Bio-Rad |
170-5060 |
| Paraformaldehyde |
Electron Microscopy Sciences |
19200 |
| Glutaraldehyde |
Electron Microscopy Sciences |
16220 |
| Sodium Cacodylate Buffer |
Electron Microscopy Sciences |
11652 |
| Aqueous osmium tetroxide |
Sigma-Aldrich |
75633-2ML |
| 2% aqueous uranyl acetate |
Electron Microscopy Sciences |
22400-2 |
| Ethanol |
Electron Microscopy Sciences |
15055 |
| Epoxy resin EMbed 812 |
Electron Microscopy Sciences |
14900 |
| Toluidine Blue |
Electron Microscopy Sciences |
26074-15 |
| Lead citrate |
Electron Microscopy Sciences |
22410 |
| Minimum Essential Medium |
Gibco |
11935046 |
| 4 mM L-glutamine |
Gibco |
25030081 |
| 0.7% agar |
Fisher Scientific |
AAJ1090722 |
| TrueBlue substrate |
Seracare |
5510-0030 |
| Trizol reagent |
Invitrogen |
15596018 |
| Bovine Serum Albumin |
Sigma-Aldrich |
A2153-50G |
|
| Critical commercial assays |
|
|
|
| CytoTune iPS2.0, Invitrogen, A16517 |
Life Technologies |
A16517 |
| STEMdiff Trilineage differentiation kit |
StemCell Technologies |
05230 |
| QuickTiter Retrovirus Quantitation Kit |
Cell Biolabs |
VPK-120 |
| Colorimetric reverse transcriptase kit |
Roche |
11468120910 |
| SMART-Seq v4 Ultra Low Input kit |
Takara Bio |
634888 |
| Total RNA with Ribo-Zero Plus kit |
Illumina |
20040529 |
| AllPrep DNA/RNA Mini Kit |
Qiagen |
80204 |
| SMRTbell Express Template Preparation Kit v2.0 |
PacBio |
100-938-900 |
| NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module |
New England Biolabs |
E6421L |
| SMRTbell Enzyme Clean Up Kit |
PacBio |
101-746-400 |
| RNeasy Mini Kit |
Qiagen |
74104 |
|
| Deposited data |
|
|
|
|
Rhinolophus ferrumequinum assembled and annotated by the Vertebrate Genomes Project |
Vertebrate Genome Project |
GCF_004115265.1 |
|
Rhinolophus ferrumequinum genome assembled and annotated by the Bat1K project |
Bat1K |
GCA_014108255.1 |
|
Rhinolophus ferrumequinum genome, Ensembl annotation version 102 |
Ensembl |
GCA_004115265.2 |
| Bat1K annotation of known endogenous retroviruses (ERVs) for R. ferrumequinum
|
https://genome.senckenberg.de/) |
N/A |
| Bat1K annotation of known endogenous retroviruses (ERVs) for Myotis myotis
|
https://genome.senckenberg.de/) |
N/A |
| RFe_BEF-R1_RNA: R. ferrumequinum fibroblasts RNA-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BEF-R2_RNA: R. ferrumequinum fibroblasts RNA-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BEF-R3_RNA: R. ferrumequinum fibroblasts RNA-seq replicate 3 |
This paper |
GEO: GSE221965
|
| RFe_BiPS1-R1_RNA: R. ferrumequinum iPS#1 RNA-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS1-R2_RNA: R. ferrumequinum iPS#1 RNA-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS1-R3_RNA: R. ferrumequinum iPS#1 RNA-seq replicate 3 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-R1_RNA: R. ferrumequinum iPS#2 RNA-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-R2_RNA: R. ferrumequinum iPS#2 RNA-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-R3_RNA: R. ferrumequinum iPS#2 RNA-seq replicate 3 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EB-R1_RNA: R. ferrumequinum EB RNA-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EB-R2_RNA: R. ferrumequinum EB RNA-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EB-R3_RNA: R. ferrumequinum EB RNA-seq replicate 3 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EN-R1_RNA: R. ferrumequinum Endoderm RNA-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EN-R2_RNA: R. ferrumequinum Endoderm RNA-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EN-R3_RNA: R. ferrumequinum Endoderm RNA-seq replicate 3 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-ME-R1_RNA: R. ferrumequinum Mesoderm RNA-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-MS-R2_RNA: R. ferrumequinum Mesoderm RNA-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-MS-R3_RNA: R. ferrumequinum Mesoderm RNA-seq replicate 3 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EC-R1_RNA: R. ferrumequinum Ectoderm RNA-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EC-R2_RNA: R. ferrumequinum Ectoderm RNA-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-EC-R3_RNA: R. ferrumequinum Ectoderm RNA-seq replicate 3 |
This paper |
GEO: GSE221965
|
| RFe_BEF-R1_ATAC: R. ferrumequinum fibroblasts ATAC-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BEF-R2_ATAC: R. ferrumequinum fibroblasts ATAC-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-R1_ATAC: R. ferrumequinum iPS#2 ATAC-seq replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-R2_ATAC: R. ferrumequinum iPS #2 ATAC-seq replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BEF_H3K4: R. ferrumequinum fibroblasts H3K4me3 ChIP-seq |
This paper |
GEO: GSE221965
|
| RFe_BiPS2_H3K4: R. ferrumequinum iPS H3K4me3 ChIP-seq |
This paper |
GEO: GSE221965
|
| RFe_BEF_H3K27: R. ferrumequinum fibroblasts H3K4me3 ChIP-seq |
This paper |
GEO: GSE221965
|
| RFe_BiPS2_H3K27: R. ferrumequinum iPS#2 H3K4me3 ChIP-seq |
This paper |
GEO: GSE221965
|
| RFe_BEF-R1: RRBS: R. ferrumequinum fibroblasts RRBS replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BEF-R2: RRBS: R. ferrumequinum fibroblasts RRBS replicate 2 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-R1_RRBS: R. ferrumequinum iPS#2 RRBS replicate 1 |
This paper |
GEO: GSE221965
|
| RFe_BiPS2-R2_RRBS: R. ferrumequinum iPS#2 RRBS replicate 2 |
This paper |
GEO: GSE221965
|
| Dog iPS RNAseq: K9_1_iPS_P9 |
GSE15249395
|
GEO: GSM4616525
|
| Dog iPS RNAseq: K9_2_iPS_P8 |
GSE15249395
|
GEO: GSM4616526
|
| Dog iPS RNAseq: K9_3_iPS_P8 |
GSE15249395
|
GEO: GSM4616527
|
| Marmoset iPS RNAseq: CM421F_B0_12_iPS_P11 |
GSE15249395
|
GEO: GSM4617887
|
| Marmoset iPS RNAseq: CTXNS1_B1_iPS_P7 |
GSE15249395
|
GEO: GSM4617889
|
| Marmoset iPS RNAseq: CTXNS2_B1_iPS_P5 |
GSE15249395
|
GEO: GSM4617890
|
| Marmoset iPS RNAseq: E01F_A2_2_iPS_P10 |
GSE15249395
|
GEO: GSM4617891
|
| Marmoset iPS RNAseq: E02M_B0_7_iPS_P13 |
GSE15249395
|
GEO: GSM4617895
|
| Marmoset iPS RNAseq: I5061F_B3_15_iPS_P10 |
GSE15249395
|
GEO: GSM4617900
|
| Marmoset iPS RNAseq: I5061F_B3_3_iPS_P11 |
GSE15249395
|
GEO: GSM4617901
|
| Human iPS RNA-seq: BjiPS_P3 |
GSE15249395
|
GEO: GSM4616532
|
| Pig iPS cell RNA-seq: N01F_N1_iPS_P3 |
GSE15249395
|
GEO: GSM4616535
|
| Pig iPS cell RNA-seq: N01F_N2_iPS_P3 |
GSE15249395
|
GEO: GSM4616536
|
| Mouse ES cell RNA-seq: WT ESC -1 |
GSE5321296
|
GEO: GSM1287734
|
| Mouse ES cell RNA-seq: WT ESC -2 |
GSE5321296
|
GEO: GSM1287735
|
| Mouse ES cell RNA-seq: WT ESC -3 |
GSE5321296
|
GEO: GSM1287745
|
| Mouse ES cell RNA-seq: WT ESC -4 |
GSE5321296
|
GEO: GSM1287746
|
| Mouse ES cell RNA-seq: iPSC -1 |
GSE5321296
|
GEO: GSM1287736
|
| Mouse iPS cell RNA-seq: WT iPSC -2 |
GSE5321296
|
GEO: GSM1287747
|
| Mouse iPS cell RNA-seq: WT iPSC -3 |
GSE5321296
|
GEO: GSM1287748
|
| Mouse fibroblasts RNA-seq: WT MEFs -1 |
GSE5321296
|
GEO: GSM1287749
|
| Mouse fibroblasts RNA-seq: WT MEFs -2 |
GSE5321296
|
GEO: GSM1287750
|
| Human naive ES cell RNA-seq: Naive_Ex1 |
GSE14499497
|
GEO: GSM4303994
|
| Human naive ES cell RNA-seq: Naive_Ex2 |
GSE14499497
|
GEO: GSM4303995
|
| Human primed ES cell RNA-seq: Primed_Ex1 |
GSE14499497
|
GEO: GSM4304018
|
| Human primed ES cell RNA-seq: Primed_Ex2 |
GSE14499497
|
GEO: GSM4304019
|
| Human H9 ES cells RNA-seq: H9.WT.1.1 _RNA-seq |
GSE14099798
|
GEO: GSM4192140
|
| Human H9 ES cells RNA-seq: H9.WT.1.2_RNA-seq |
GSE14099798
|
GEO: GSM4192141
|
|
| Experimental models: Cell lines |
|
|
|
|
Rhinolophus ferrumequinum embryonic fibroblasts
|
This paper |
BEF |
|
Rhinolophus ferrumequinum induced |
This paper |
RFe.iPS#1(BiPS1) |
| pluripotent stem cells clone 1 |
|
|
|
Rhinolophus ferrumequinum induced |
This paper |
RFe.iPS2 (BiPS#2) |
| pluripotent stem cells clone 2 |
|
|
|
Myotis myotis uropatagium fibroblasts |
This paper |
MMy.BUF |
|
Myotis myotis induced pluripotent stem cells |
This paper |
MMy.iPS |
| 293FT cells |
Life Technologies |
R700-07 |
| NIH/3T3 cells |
ATCC |
CRL-1658 |
| R1 mouse ES cells |
ATCC |
SCRC-1011 |
| H9 human ES cells |
WiCell |
WA09 |
| Vero-E6 |
ATCC |
CRL-1587 |
| Irradiated CF1 mouse fibroblasts |
Gibco |
A34181 |
|
| Experimental models: Organisms/strains |
|
|
|
| 8-week-old male Fox Chase SCID Beige Mice |
Charles River |
250 |
|
| Oligonucleotides |
|
|
|
| SeV-F: GGATCACTAGGTGATATCGAGC |
CytoTune 2.0 |
N/A |
| SeV-R: |
CytoTune 2.0 |
N/A |
| ACCAGACAAGAGTTTAAGAGATATGTATC |
|
|
| KOS-F: ATGCACCGCTACGACGTGAGCGC |
CytoTune 2.0 |
N/A |
| KOS-R: ACCTTGACAATCCTGATGTGG |
CytoTune 2.0 |
N/A |
| Klf4-F TTCCTGCATGCCAGAGGAGCCC |
CytoTune 2.0 |
N/A |
| Klf4-R: AATGTATCGAAGGTGCTCAA |
CytoTune 2.0 |
N/A |
| cMyc-F: TAACTGACTAGCAGGCTTGTCG |
CytoTune 2.0 |
N/A |
| cMyc-R: TCCACATACAGTCCTGGATGATGATG |
CytoTune 2.0 |
N/A |
| GAPDH_F1_GHB: TGGTGAAGGTCGGAGTGAAC |
This paper |
Z25-132 |
| GAPDH_R1_GHB: GAAGGGGTCATTGATGGCGA |
This paper |
Z25-133 |
|
| Software and algorithms |
|
|
|
| FastQC vO.11.9 |
Andrews et al.99
|
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
| Trimmomatic v0.39 |
Bolger et al.100
|
http://www.usadellab.org/cms/?page=trimmomatic
|
| HISAT2 v2.2.1 |
Kim et al.101
|
http://daehwankimlab.github.io/hisat2/
|
| SAMtools v1.10 |
Li et al.102
|
https://github.com/samtools/samtools/releases/
|
| featureCounts v2.0.1 |
Liao et al.103
|
https://subread.sourceforge.net/
|
| deepTools |
Rami’rez et al.104
|
https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
|
| DESeq2 v1.10.1 |
Love et al.105
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| ClustVis (Beta) |
Metsalu and Vilo106
|
https://biit.cs.ut.ee/clustvis/
|
| R package ggpubr |
Wickham and Grolemund107
|
https://cran.r-project.org/web/packages/ggpubr/index.html
|
| ggplot2 |
Wickham and Grolemund107
|
cran.r-project.org/web/packages/ggplot2/index.html
|
| ggmaplot |
Wickham and Grolemund107
|
https://rpkgs.datanovia.com/ggpubr/reference/ggmaplot.html
|
| ggscatter |
Wickham and Grolemund107
|
https://rpkgs.datanovia.com/ggpubr/reference/ggscatter.html
|
| codeml package of the PAML suite software |
Yang et al.108
|
http://abacus.gene.ucl.ac.uk/software/paml.html
|
| bedGraphToBigWig v4 |
Kent et al.109
|
https://www.encodeproject.org/software/bedgraphtobigwig/
|
| Enrichr |
Xie et al.110
|
maayanlab.cloud/Enrichr/
|
| Cytoscape Version 3.8.2 |
Shannon et al.111
|
https://cytoscape.org
|
| SMRTLink version 10.1 |
PacBio |
https://www.pacb.com/support/software-downloads/
|
| Kraken2 v2.1.2 |
Wood et al.112
|
https://github.com/DerrickWood/kraken2
|
| gmap/gsnap |
Wu et al.113
|
http://research-pub.gene.com/gmap
|
| Trimmgalore v.0.6.6 |
Github, Open Source |
https://github.com/FelixKrueger/TrimGalore
|
| Cutadapt |
Krueger n.d. Andrews114
|
https://github.com/marcelm/cut adapt
|
| stringTie v2.2.1 |
Pertea et al.115
|
http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
|
| Seqtk v1.3 |
Github, Open Source |
https://github.com/lh3/seqtk
|
| Trinity v2.12 |
Grabbherr et al.116
|
https://github.com/trinityrnaseq/trinityrnaseq/releases/tag/v2.12.0
|
| BLAST |
Altschul et al.117 Camacho118
|
https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
| SQUID |
Eddy Lab, Harvard University |
http://eddylab.org/software.html
|
| INSPIRE 2.0 |
Luminex |
https://www.luminexcorp.com
|
| IDEAS 6.2 |
Luminex |
https://www.luminexcorp.com
|
|
| Other |
|
|
|
| ATAC-seq service |
Active Motif |
25079 |
| RRBS Service, Active Motif, |
Active Motif |
25069 |
| HistoPath ChIP-seq service, |
Active Motif |
25001 |
