|
| Status |
Public on Aug 22, 2022 |
| Title |
Xenopus laevis Embryos, EU-RNA, 8 hpf, Rep 2 [Bead_8hpf_rep2] |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: Embryo
developmental stage: Blastula
time: 8 hpf
genotype: Wildtype
treatment: EU microinjected
batch: Experiment 1
|
| Treatment protocol |
Embryos at 1-cell stage were microinjected with 10 nl of 50 mM EU. The final concentration of EU is at ~ 0.5 mM. Embryos developed to blasula stages at 5-9 hpf were collected for RNA extraction.
|
| Growth protocol |
Xenopus laevis embryos were cultured in 0.1× Marc’s Modified Ringer’s (MMR) medium. All embryo experiments were performed at room temperature (22℃ ± 0.5 ℃)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using the RNeasy Mini Kit (Qiagen), following the instructions provided by the manufacturer. Nascent EU-RNAs were biotinylated using bisulfide biotin azide via click reaction and purified using streptavidin beads following the instructions provided by the Click-iTTM Nascent RNA Capture Kit (Thermo Fisher Scientific, Cat# C10365).
The cDNA libraries for 'All' (Total RNA), 'Bead' (Nascent transcripts), 'FL' (Flowthrough RNA) and 'Egg' (Maternal RNA) were prepared using the Universal RNA-seq with NuQuant® kit (NuGEN, Cat# 0364), following the manual provided by the manufacturer. Ribosomal RNAs were depleted using the custom designed AnyDeplete Probe Mix for Xenopus laevis provided by the kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files were aligned to transcripts annotated in Xenopus laevis genome build 9.2 (xenbase.org) using salmon v0.12.0 yeilding raw counts per transcript.
Raw counts quantified from salmon were normalized to library size using DESeq2.
Assembly: Xenopus laevis genome build 9.2 (xenbase.org)
Supplementary files format and content: DESeq2 normalized reads per transcript, comma separated values text file
|
| |
|
| Submission date |
Apr 28, 2022 |
| Last update date |
Aug 22, 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 |
| |
|
| Platform ID |
GPL21248 |
| Series (2) |
| GSE201835 |
Total and Nascent Transcriptome of Xenopus laevis Embryos at 5-9 hpf (stage 7-9) |
| GSE201874 |
Timing of Germ Layer Initiation Linked to Spatially Patterned Onset of Genome Activation |
|
| Relations |
| BioSample |
SAMN27962915 |
| SRA |
SRX15045258 |
