|
| Status |
Public on Mar 15, 2017 |
| Title |
WE_St9_3 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
strain: Nasco
tissue: whole embryo
developmental stage: 9
|
| Treatment protocol |
MO and mRNAs were injected at 2-4 cell stage; Embryos were treated with LiCl at 32 cell stage; Dorsal and ventral halves were dissected at stage 8 in 1x Barth’s solution and cultured to stage 10.5 in 0.3 x Barth's solution.
|
| Growth protocol |
The embryos were cultured in 0.1x Marc's Modified Ringers (MMR) and staged according to Nieuwkoop and Faber (1967).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from whole embryos or dorsal halves or ventrla halves was isolated with an Absolutely RNA miniprep Kit (Agilent).
Libraries were constructed with the Illumina TruSeq RNA Library Preparation Kit V2 according to manufacturer’s protocol. Briefly, 1 µg total RNA from whole embryos, dorsal halves or ventral halves was used for input RNA. Then mRNA was purified through polyA+ selection. After fragmentation of the mRNA, first strand and second strand synthesis, double strand cDNA (ds cDNA) was obtained. The ds cDNA was then further processed for A-tailing, end repair and ligation of appropriate adaptors. Finally, the ds cDNA with adaptors was amplified by PCR to generate libraries. After measurement of the length and concentration of the libraries by Bioanalyser and Qubit, the libraries were sent for sequencing on Illumina Hi-Seq 2000 using standard methods to generate 100-bp single end reads by the Broad Stem Cell Research Center at UCLA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
After sequencing, adaptors were first trimmed from the RNA reads and RNA reads of low quality filtered. The clean RNA reads were mapped using Tophat (Version 2.09, default parameters) against the Xenopus laevis JGI9.1 (Xenbase) transcript sequences.
Transcripts counts were normalized using DESeq package in R . RPKM (Reads Per Kilobase per Million mapped reads) for transcripts was calculated in R.
Human gene names were assigned to transcripts using an annotation file obtained by blasting the JGI9.1 peptide sequences to human reference protein sequences.
Genome_build: Xenopus Laevis J-strain Version 9.1
Supplementary_files_format_and_content: Excel tables that include RPKM and fold induction values of genes for each sample
Supplementary_files_format_and_content: Supplemental Table S1 - Complete table of all sequenced libraries (~43000 transcripts) (correct names, new order to match figures).xlsx
Supplementary_files_format_and_content: Supplemental Table S2 - Early dorsal bCatenin Signature (123 genes) expression values (in RPKM) throughout all libraries sequenced.xlsx
Supplementary_files_format_and_content: Supplemental Table S3 - Complete table of all stage 9 sequenced libraries.xlsx
|
| |
|
| Submission date |
Jan 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Edward M De Robertis |
| E-mail(s) |
ederobertis@mednet.ucla.edu
|
| Organization name |
HHMI/UCLA
|
| Department |
Biological chemistry
|
| Lab |
De Robertis lab
|
| Street address |
615 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL17682 |
| Series (1) |
| GSE93195 |
Spemann organizer transcriptome induction by early β-Catenin, Wnt, Nodal and Siamois signals in Xenopus laevis |
|
| Relations |
| BioSample |
SAMN06205999 |
| SRA |
SRX2464732 |
