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| Status |
Public on Feb 05, 2024 |
| Title |
Pol II pausing is a milestone on the road to complex animals |
| Organisms |
Escherichia coli; Haloferax mediterranei; Daphnia pulex; Strongylocentrotus purpuratus; Mus musculus; Perkinsus marinus; Dryas iulia; Dictyostelium discoideum; Nematostella vectensis; Sphaeroforma arctica; Capsaspora owczarzaki; Creolimax fragrantissima |
| Experiment type |
Other
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| Summary |
PRO-seq experiments in multiple organisms. Also, PRO-seq experiment of Nelfb and Nelfe degron mESC in serum/LIF with or without dTAG-13.
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| Overall design |
We used Precision Run-On and Sequencing (PRO-seq) to study transcription in 20 extant organisms that represent very diverse branches on the tree of life, including multiple species near the base of the Metazoa phylogeny and the transition between plants and animals. We also used PRO-seq to study mESCs after degrading NELF-B or NELF-E.
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| Contributor(s) |
Chivu AG, Lewis JJ, Lis JT, Danko CG |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jan 28, 2023 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Alexandra Georgiana Chivu |
| E-mail(s) |
agc94@cornell.edu
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| Phone |
6072624972
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| Organization name |
Cornell University
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| Department |
Molecular Biology and Genetics
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| Lab |
Danko and Lis labs
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| Street address |
215 Tower Rd
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platforms (12)
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| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
| GPL23029 |
Illumina NextSeq 500 (Nematostella vectensis) |
| GPL23218 |
Illumina NextSeq 500 (Strongylocentrotus purpuratus) |
| GPL24021 |
Illumina NextSeq 500 (Daphnia pulex) |
| GPL26360 |
Illumina NextSeq 500 (Dictyostelium discoideum) |
| GPL27022 |
Illumina NextSeq 500 (Capsaspora owczarzaki) |
| GPL33064 |
Illumina NextSeq 500 (Haloferax mediterranei) |
| GPL33065 |
Illumina NextSeq 500 (Sphaeroforma arctica) |
| GPL33066 |
Illumina NextSeq 500 (Creolimax fragrantissima) |
| GPL33067 |
Illumina NextSeq 500 (Dryas iulia) |
| GPL33068 |
Illumina NextSeq 500 (Perkinsus marinus) |
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| Samples (46)
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| GSM7000651 |
Haloferax_mediterranei_1 |
| GSM7000652 |
Haloferax_mediterranei_2 |
| GSM7000653 |
Haloferax_mediterranei_3 |
| GSM7000655 |
Dictyostelium_discoideum_1 |
| GSM7000656 |
Dictyostelium_discoideum_2 |
| GSM7000657 |
Capsaspora_owczarzaki_1 |
| GSM7000658 |
Capsaspora_owczarzaki_2 |
| GSM7000659 |
Sphaeroforma_arctica_1 |
| GSM7000660 |
Sphaeroforma_arctica_2 |
| GSM7000662 |
Creolimax_fragrantissima_1 |
| GSM7000663 |
Nematostella_vectensis_1 |
| GSM7000664 |
Nematostella_vectensis_2 |
| GSM7000665 |
Daphnia_pulex_1 |
| GSM7000666 |
Daphnia_pulex_2 |
| GSM7000668 |
Dryas_iulia_F1 |
| GSM7000669 |
Dryas_iulia_H1 |
| GSM7000670 |
Strongylocentrotus_purpuratus |
| GSM7000671 |
Perkinsus_marinus_1 |
| GSM7000672 |
Perkinsus_marinus_2 |
| GSM7000674 |
mESCs NELFb, 1 -- S/L |
| GSM7000675 |
mESCs NELFb, 2 -- S/L |
| GSM7000676 |
mESCs NELFb, 3 -- S/L |
| GSM7000678 |
mESCs NELFb, 22 -- S/L + 1 hr dTAG |
| GSM7000679 |
mESCs NELFb, 23 -- S/L + 1 hr dTAG |
| GSM7000680 |
mESCs NELFb, 24 -- S/L + 1 hr dTAG |
| GSM7000682 |
mESCs NELFb, 25 -- 30 mins HS at 42 |
| GSM7000683 |
mESCs NELFb, 26 -- 30 mins HS at 42 |
| GSM7000684 |
mESCs NELFb, 27 -- 30 mins HS at 42 |
| GSM7000686 |
mESCs NELFb, 28 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG |
| GSM7000687 |
mESCs NELFb, 29 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG |
| GSM7000688 |
mESCs NELFb, 30 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG |
| GSM7000690 |
mESCs NELFe, 1 -- 30 mins HS at 42 |
| GSM7000691 |
mESCs NELFe, 2 -- 30 mins HS at 42 |
| GSM7000692 |
mESCs NELFe, 3 -- 30 mins HS at 42 |
| GSM7000694 |
mESCs NELFe, 4 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG |
| GSM7000695 |
mESCs NELFe, 5 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG |
| GSM7000696 |
mESCs NELFe, 6 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG |
| GSM7000698 |
mESCs NELFe, 13 -- S/L |
| GSM7000700 |
mESCs NELFe, 14 -- S/L |
| GSM7000702 |
mESCs NELFe, 15 -- S/L |
| GSM7000704 |
mESCs NELFe, 16 -- S/L + 30 mins dTAG |
| GSM7000705 |
mESCs NELFe, 17 -- S/L + 30 mins dTAG |
| GSM7000707 |
mESCs NELFe, 18 -- S/L + 30 mins dTAG |
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| Relations |
| BioProject |
PRJNA929029 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE223913_Extant_bigwig.tar.gz |
229.1 Mb |
(ftp)(http) |
TAR |
| GSE223913_mESCs_NELF-B_bigwig.tar.gz |
510.8 Mb |
(ftp)(http) |
TAR |
| GSE223913_mESCs_NELF-E_bigwig.tar.gz |
530.0 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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