|
| Status |
Public on Sep 26, 2019 |
| Title |
Bap1MO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bap1MO_whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
Sex: female
animal id#: 1
embryonic stage: stage 12
frog type: pigmented
tissue: whole embryo
sequence of mo injected per embryo - ng: AGCCTTTATTCATGTTGCCTCCTCC-15
genotype/variation: Bap1 depleted
|
| Treatment protocol |
Embryos were injected at the 1-cell stage with 15 ng of control MO or MO targeting Bap1 and maintained at 22oC until they reached stage 12.
|
| Growth protocol |
the embryos were obtained by in vitro fertilization
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Trizol/Chloroform, and yolk and pigment were further removed from samples using RNeasy MinElute Cleanup Kit
Libraries were prepared using the NEBNext® Ultra™ kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
02_F1_MO2BAP1
|
| Data processing |
Next generation sequencing quality was assessed using FastQC (v0.11.3).
Reads were trimmed (if required) and aligned to the Xenopus laevis 9.1 genome (available on Xenbase.org) using STAR (v2.5.2a)
Read counts of RNA-seq data were obtained using HTSeq
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Feb 14, 2019 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Michael Durante |
| E-mail(s) |
mdurante@med.miami.edu
|
| Phone |
2393575338
|
| Organization name |
University of Miami Miller School of Medicine
|
| Department |
Ophthalmology
|
| Lab |
Harbour
|
| Street address |
1501 NW 10th Ave., Ste 832
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL21248 |
| Series (2) |
| GSE126597 |
Bap1 loss leads to decreased expression of lineage specific commitment genes, and increased expression of pluripotency genes [RNA-seq] |
| GSE126599 |
Loss of Bap1 in Xenopus laevis embryos |
|
| Relations |
| BioSample |
SAMN10941057 |
| SRA |
SRX5381418 |
