|
| Status |
Public on Aug 04, 2022 |
| Title |
foxh1MO_AC_RNAseq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Xenopus tropicalis animal cap explant, Foxh1 MO, st10.5
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: animal cap explant
Stage: 10.5
genotype: wildtype
treatment: Foxh1 morpholino injection
|
| Treatment protocol |
For Foxh1 morpholino (MO) experiments, injections were performed at the 1-cell stage. A total of 22.5 ng of foxh1 MO (Chiu et al., 2014) or standard control MO (Genetools) was used.
|
| Growth protocol |
All embryos were cultured in 1/9X Marc’s modified Ringers (MMR) at 25C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, total RNA from dissected animal cap explants was extracted using Trizol as described (Amin et al., 2014). mRNA was then isolated using NEBNext PolyA mRNA Magnetic Isolation Module (NEB E7490S).
Sequencing libraries were prepared using NEBNext Ultra II RNA library prep kit (NEB E7770S)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The multiplexed libraries were sequenced on the Novaseq 6000. The version of Novaseq control software was NVCS ver 1.7.0 with real time analysis software, RTA 3.4.4.
reads were aligned to Xenopus tropicalis v10.0 genome (Xenbase) using STAR v2.7.3a
RSEM v1.3.3 was used to calculate raw counts and expression values in transcripts per million (TPM)
differential expression analysis was performed using edgeR v3.36.0 in R v4.1.2
Assembly: Xenopus tropicalis v10.0 genome
Supplementary files format and content: raw count values and TPM values for each sample is included
Supplementary files format and content: output file for differential gene expression analysis using edgeR is included
|
| |
|
| Submission date |
May 27, 2022 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Ken Cho |
| E-mail(s) |
kwcho@uci.edu
|
| Organization name |
University of California, Irvine
|
| Street address |
University of California, Irvine
|
| City |
Irvine |
| ZIP/Postal code |
92617 |
| Country |
USA |
| |
|
| Platform ID |
GPL30018 |
| Series (1) |
| GSE204990 |
Engagement of Foxh1 in chromatin regulation revealed by protein interactome analyses |
|
| Relations |
| BioSample |
SAMN28698624 |
| SRA |
SRX15483850 |
