|
| Status |
Public on Oct 25, 2017 |
| Title |
17_NC_B100T3 |
| Sample type |
SRA |
| |
|
| Source name |
Neural Crest
|
| Organism |
Xenopus laevis |
| Characteristics |
developmental stage: 17
tissue: Neural Crest
genotype: wild type
|
| Growth protocol |
Xenopus laevis embryos were obtained by in vitro fertilization using standard procedures and grown until the desired stage (12.5, 14, or 17) according to Nieuwkoop and Faber developmental table.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ectodermal explant were microdissected, RNA was harvested using Trizol Reagent, RNA-seq libraries were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina) starting with 40-300 ng of total RNA, and sequenced on a HiSeq 2000 (Illumina) with a target of 15-20 million 100 bp paired reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
B100T3
|
| Data processing |
Reads were mapped on the X. laevis genome (9.1), using tophat 2.0.14 with the following parameters (--rg-library Illumina --rg-platform Illumina --keep-fasta-order -N 6 --read-gap-length 6 --read-edit-dist 6 --segment-mismatches 3 -i 5 -I 500000 -r 155 --mate-std-dev 80 --no-coverage-search -p 6 --library-type fr-firststrand -g 2).
Read counts were computed using HTSeq with the gene models v1.8.0 of the Xenopus laevis 9.1 genome annotation.
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample.
|
| |
|
| Submission date |
Aug 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anne-Helene Monsoro-Burq |
| E-mail(s) |
Anne-Helene.Monsoro-Burq@curie.fr
|
| Organization name |
Institut Curie
|
| Department |
Université Paris Sud
|
| Lab |
U1021 - UMR3347
|
| Street address |
Bat 110
|
| City |
Orsay |
| ZIP/Postal code |
91405 |
| Country |
France |
| |
|
| Platform ID |
GPL17682 |
| Series (1) |
| GSE103240 |
A Molecular Atlas of the Developing Ectoderm Defines Neural, Neural Crest, Placode and Non-Neural Progenitor Identity in Vertebrates. |
|
| Relations |
| BioSample |
SAMN07571746 |
| SRA |
SRX3144221 |
