|
| Status |
Public on Jan 14, 2020 |
| Title |
noPGpolysome_1 |
| Sample type |
SRA |
| |
|
| Source name |
polysome fraction from sucrose density gradient
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: oocyte
developmental stage: Stage VI oocyte
|
| Treatment protocol |
oocyte extracts were separated using sucrose density gradients. PG90 = 90 minutes after progesterone addition.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol, Zymo clean and concentrate, Exiqon LNA dT kit.
NEB
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
polysome fraction from sucrose density gradient
SupplementalTable2.txt
SupplementalTable3.txt
|
| Data processing |
Base calls were generated using Illumina software
reads were collapsed to unique using a custom Perl script (Schwart and Blower. JCB. 2014)
reads were aligned to X. laevis transcripts using Bowtie and counted using a custom Perl script or reads were aligned to X. laevis 9.2 genome sequence using Tophat2 and counted agains gene models using Cufflinks.
PAS-seq 5' linker sequences (CGG TCT CGG CAT TCC TGC TGA ACC GCT CTT CCG ATC TGG G) were trimmed form all reads using the fasx toolkit. Trimmed sequences longer than 30nts were retained for analysis.
PAS-Seq Reads were aligned to the Xl9_2 genome using Bowtie2. Alignments were filtered to retain only reads with two nonteplated As.
Genome_build: Xl9_2
Supplementary_files_format_and_content: Supplemental Table 2: Measures of RNA stability during oocyte maturation derived from sucrose density gradient sequencing.
Supplemental Table 3: Fraction of each mRNA present in polyribosome fraction of sucrose density gradient during oocyte maturation.
Supplemental Table 5: Genomic locations of polyadenylation sites derived from PAS-seq experiment.
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Jan 14, 2020 |
| Contact name |
Michael Demian Blower |
| E-mail(s) |
blower@molbio.mgh.harvard.edu
|
| Phone |
617 643 0777
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Molecular Biology
|
| Street address |
185 Cambridge St CPZN-7250
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL17682 |
| Series (1) |
| GSE134537 |
Genome-wide analysis of mRNA polyadenylation and translation during vertebrate oocyte maturation |
|
| Relations |
| BioSample |
SAMN12321573 |
| SRA |
SRX6473710 |
