 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 22, 2022 |
| Title |
Nascent Transcriptome of AP and VP from Xenopus laevis Embryos at 5-9 hpf (stage 7-9) |
| Organism |
Xenopus laevis |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To characterize the spatial patterns of zygtoic transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and isolated total RNAs from whole embryos at 5, 6, 7, 8 and 9 hours post-fertilization (hpf) at room temperature, respectively, covering the stages of pre-ZGA to widespread ZGA (stage 7-9). The animal pole (AP, ~ 1/3 at the top region of embryo) and the vegetal pole (VP,~ 1/3 at the bottom region of embryo) regions were dissected and used for total RNA isolation. To purify nascent transcripts, total RNAs were biotinylated using disulfide biotin azide via click reaction and biotinylated nascent transcripts were purified using streptavidin beads. Libraries were constructed from using the nascent transcripts. All libraries were sequenced on illumina NextSeq 500.
|
| |
|
| Overall design |
Two experiments were conducted. In the first experiment, the AP and VP regions from three clutches of embryos at 5-9 hpf (three biological replicates) were used for sequecing the nascent transcripts. In the second experiment, the AP and VP regions from one clutch of embryos at 6-9 hpf (one biological replicate, two technical replicates) were used for sequencing the nascent transcripts.
|
| |
|
| 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
|
| 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 |
| |
|
| Platforms (1) |
| GPL21248 |
Illumina NextSeq 500 (Xenopus laevis) |
|
| Samples (46)
|
| GSM6076888 |
Xenopus laevis Embryos, Animal Pole (AP), 5 hpf, Rep 1 [AP_5hpf_rep1] |
| GSM6076889 |
Xenopus laevis Embryos, Animal Pole (AP), 5 hpf, Rep 2 [AP_5hpf_rep2] |
| GSM6076890 |
Xenopus laevis Embryos, Animal Pole (AP), 5 hpf, Rep 3 [AP_5hpf_rep3] |
| GSM6076891 |
Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 1 [AP_6hpf_rep1] |
| GSM6076892 |
Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 2 [AP_6hpf_rep2] |
| GSM6076893 |
Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 3 [AP_6hpf_rep3] |
| GSM6076894 |
Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 1 [AP_7hpf_rep1] |
| GSM6076895 |
Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 2 [AP_7hpf_rep2] |
| GSM6076896 |
Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 3 [AP_7hpf_rep3] |
| GSM6076897 |
Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 1 [AP_8hpf_rep1] |
| GSM6076898 |
Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 2 [AP_8hpf_rep2] |
| GSM6076899 |
Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 3 [AP_8hpf_rep3] |
| GSM6076900 |
Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 1 [AP_9hpf_rep1] |
| GSM6076901 |
Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 2 [AP_9hpf_rep2] |
| GSM6076902 |
Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 3 [AP_9hpf_rep3] |
| GSM6076903 |
Xenopus laevis Embryos, Vegetal Pole (VP), 5 hpf, Rep 1 [VP_5hpf_rep1] |
| GSM6076904 |
Xenopus laevis Embryos, Vegetal Pole (VP), 5 hpf, Rep 2 [VP_5hpf_rep2] |
| GSM6076905 |
Xenopus laevis Embryos, Vegetal Pole (VP), 5 hpf, Rep 3 [VP_5hpf_rep3] |
| GSM6076906 |
Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 1 [VP_6hpf_rep1] |
| GSM6076907 |
Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 2 [VP_6hpf_rep2] |
| GSM6076908 |
Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 3 [VP_6hpf_rep3] |
| GSM6076909 |
Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 1 [VP_7hpf_rep1] |
| GSM6076910 |
Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 2 [VP_7hpf_rep2] |
| GSM6076911 |
Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 3 [VP_7hpf_rep3] |
| GSM6076912 |
Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 1 [VP_8hpf_rep1] |
| GSM6076913 |
Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 2 [VP_8hpf_rep2] |
| GSM6076914 |
Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 3 [VP_8hpf_rep3] |
| GSM6076915 |
Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 1 [VP_9hpf_rep1] |
| GSM6076916 |
Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 2 [VP_9hpf_rep2] |
| GSM6076917 |
Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 3 [VP_9hpf_rep3] |
| GSM6076918 |
Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 4 [AP_6hpf_rep4] |
| GSM6076919 |
Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 5 [AP_6hpf_rep5] |
| GSM6076920 |
Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 4 [AP_7hpf_rep4] |
| GSM6076921 |
Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 5 [AP_7hpf_rep5] |
| GSM6076922 |
Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 4 [AP_8hpf_rep4] |
| GSM6076923 |
Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 5 [AP_8hpf_rep5] |
| GSM6076924 |
Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 4 [AP_9hpf_rep4] |
| GSM6076925 |
Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 5 [AP_9hpf_rep5] |
| GSM6076926 |
Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 4 [VP_6hpf_rep4] |
| GSM6076927 |
Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 5 [VP_6hpf_rep5] |
| GSM6076928 |
Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 4 [VP_7hpf_rep4] |
| GSM6076929 |
Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 5 [VP_7hpf_rep5] |
| GSM6076930 |
Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 4 [VP_8hpf_rep4] |
| GSM6076931 |
Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 5 [VP_8hpf_rep5] |
| GSM6076932 |
Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 4 [VP_9hpf_rep4] |
| GSM6076933 |
Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 5 [VP_9hpf_rep5] |
|
| This SubSeries is part of SuperSeries: |
| GSE201874 |
Timing of Germ Layer Initiation Linked to Spatially Patterned Onset of Genome Activation |
|
| Relations |
| BioProject |
PRJNA833149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE201833_AP_VP_DESeq2_reads.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...