|
| Status |
Public on Nov 06, 2015 |
| Title |
Xla_J_strain_NF14_RiboZero |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
strain: J
developmental stage: 14
tissue: whole embryo
|
| 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 rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 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
Supplementary_files_format_and_content: tsv (showing TPM counts)
|
| |
|
| Submission date |
Oct 10, 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) |
| GSE73904 |
On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero] |
| GSE73905 |
On the relationship of protein and mRNA dynamics in vertebrate embryonic development |
|
| Relations |
| BioSample |
SAMN04158984 |
| SRA |
SRX1325674 |
