|
| Status |
Public on Nov 06, 2015 |
| Title |
Xla_J_strain_NF33_PolyA |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
strain: J strain
developmental stage: 33
|
| Treatment protocol |
embryos were snap frozen in liquid nitrogen at the desired stage, and stored at -80 until extraction
|
| Growth protocol |
embryos were raised in 0.1 X MMR containing gentamycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using TRIzol and phase-lock tubes
libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Casava version 1.8.2 was used for base calling
samples were adapter/quality trimmed using Trimmomatic
Ribosomal reads were removed and remaining high quality paired reads were aligned to reference set using Bowtie, using default parameters except setting k_min_coverage=2 to minimize noise
RSEM package was used to determine abundance estimates for all transcripts, transcripts with little read support were filtered out
Genome_build: JGI v6.1
|
| |
|
| Submission date |
Oct 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Esther Jane Pearl |
| Organization name |
Marine Biological Laboratory
|
| Department |
National Xenopus Resource
|
| Street address |
7 MBL Street
|
| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
| |
|
| Platform ID |
GPL20998 |
| Series (2) |
| GSE73870 |
On the relationship of protein and mRNA dynamics in vertebrate embryonic development [polyA] |
| GSE73905 |
On the relationship of protein and mRNA dynamics in vertebrate embryonic development |
|
| Relations |
| BioSample |
SAMN04157067 |
| SRA |
SRX1319047 |
