|
| Status |
Public on Jan 31, 2024 |
| Title |
explants, control, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic tissue explants
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: embryonic tissue explants
developmental stage: 11.5 NF
genotype: wild type
treatment: control explants
|
| Treatment protocol |
At the stage 11.5 NF, neuroectodermal explants were cut off, combined in pairs, inner sides to each other (head to head), pinned them to an agarose substrate by thin glass needles and stretched within 3 hours. The procedure was adopted from (Beloussov et al., 1999). Control explants were pinned to agarose, but not stretched.
|
| Growth protocol |
Xenopus laevis embryos were obtained, fertilized in vitro and dejellied in 2% cysteine in 0.1xMMR solution. Intact and treated embryos were grown up to stage 11.5 NF in 0.1xMMR solution.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
All RNA purifications and RNA-seq analysis were made by Genoanalytica (Moscow, Russia). Briefly, total RNA was extracted from the samples with Trizol reagent according to the manufacturer’s protocol. Quality of RNA was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A) RNA was purified using Dynabeads® mRNA Purification Kit (Ambion).
Illumina library was made from poly(A) NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
fastq files were aligned to Xenopus laevis reference genome Xenla9.1 using TopHat2.
Non-normalized counts were obtained using HTseq software.
Statistics of differential expression (stretched vs control explants) were caluclated via DEseq R package.
Assembly: Xenla9.1
Supplementary files format and content: excel file (.xlsx) containing output from edgeR (for each transcript (gene))
|
| |
|
| Submission date |
Oct 23, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Fedor M Eroshkin |
| E-mail(s) |
Xenopus.FE@gmail.com
|
| Organization name |
IBCH RAS
|
| Street address |
16/10 Miklukho-Maklaya str.
|
| City |
Moscow |
| ZIP/Postal code |
117997 |
| Country |
Russia |
| |
|
| Platform ID |
GPL21046 |
| Series (1) |
| GSE246027 |
Identification of genes regulated by mechanical tension in Xenopus laevis explants by transcriptome comparison |
|
| Relations |
| BioSample |
SAMN37928471 |
| SRA |
SRX22176066 |
