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| Status |
Public on Aug 22, 2022 |
| Title |
Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf |
| Organism |
Xenopus laevis |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To characterize the effect of cell cyle elongation on nascent transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and treated the embryos with 0.2 mg/ml of cycloheximide (CHX) to arrest them in interphase from 5 hpf to 7.5 hpf. Control and CHX-arrested embryos were collected for isolating total RNAs, followed by biotinylation using disulfide biotin azide via click reaction and purification of nascent transcripts using streptavidin beads. Libraries were constructed and sequenced on illumina NextSeq 500.
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| Overall design |
Two replicates of embryos from one clutch were treated with CHX from 5 hpf to 7.5 hpf. EU labeled nascent RNAs from both replicates of control and CHX-arrested embryos were sequenced.
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| Contributor(s) |
Chen H, Good MC |
| Citation(s) |
36007528 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R35 GM128748 |
Regulation of the Timing and Spatial Patterning of Zygotic Genome Activation During Embryogenesis |
UNIVERSITY OF PENNSYLVANIA |
Matthew Charlton Good |
| R03 HD105802 |
Hierarchical Onset of Germ Layer Specification |
UNIVERSITY OF PENNSYLVANIA |
Hui Chen |
|
| Submission date |
Apr 28, 2022 |
| Last update date |
Nov 21, 2022 |
| Contact name |
Matthew C Good |
| E-mail(s) |
mattgood@pennmedicine.upenn.edu
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| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Good Lab
|
| Street address |
Room 1140, 421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL21248 |
Illumina NextSeq 500 (Xenopus laevis) |
|
| Samples (6)
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| GSM6076934 |
Xenopus laevis Embryos, Control, 5 hpf, Rep 1 [Control_5hpf_rep1] |
| GSM6076935 |
Xenopus laevis Embryos, Control, 5 hpf, Rep 2 [Control_5hpf_rep2] |
| GSM6076936 |
Xenopus laevis Embryos, Control, 7.5 hpf, Rep 1 [Control_7.5hpf_rep1] |
| GSM6076937 |
Xenopus laevis Embryos, Control, 7.5 hpf, Rep 2 [Control_7.5hpf_rep2] |
| GSM6076938 |
Xenopus laevis Embryos, CHX, 7.5 hpf, Rep 1 [CHX_7.5hpf_rep1] |
| GSM6076939 |
Xenopus laevis Embryos, CHX, 7.5 hpf, Rep 2 [CHX_7.5hpf_rep2] |
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| This SubSeries is part of SuperSeries: |
| GSE201874 |
Timing of Germ Layer Initiation Linked to Spatially Patterned Onset of Genome Activation |
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| Relations |
| BioProject |
PRJNA833148 |
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