|
Status |
Public on Sep 20, 2020 |
Title |
hnRNPab 1 |
Sample type |
SRA |
|
|
Source name |
Oocyte lysate enriched for L-bodies
|
Organism |
Xenopus laevis |
Characteristics |
rna ip antibody: hnRNPab oocyte stage: Pool stage II-III
|
Extracted molecule |
total RNA |
Extraction protocol |
Oocyte lysate was passed over a size exclusion chromatography column and fractions enriched for L-bodies were pooled. RNA in the pool was then immunoprecipitated with one of three antibodies, then extracted with Trizol and precipitated. 150bp Paired-end RNA-seq conducted by Genewiz on Illumina Hi-Seq (model # not provided)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Aligned raw data to Xenopus 9.2 genome with STAR 2.6.1b; Genome FASTA and .GTF file were downloaded from Xenbase.org (trimming reads was not found to have significant effect) Generated counts files using HTSeq-count 0.9.1, again using the .GTF file from Xenbase Differential expression analysis conducted with EdgeR Final analysis and Q-value/logFC filtering conducted in R Genome_build: XENLA_9.2_genome.fasta.gz Supplementary_files_format_and_content: Each processed data file generated using htseq-count 0.9.1, contains count information for one replicate indexed to gene IDs used by Xenbase
|
|
|
Submission date |
Sep 19, 2020 |
Last update date |
Sep 20, 2020 |
Contact name |
Kimberly Mowry |
E-mail(s) |
kimberly_mowry@brown.edu
|
Organization name |
Brown University
|
Department |
MCB
|
Lab |
269
|
Street address |
185 Meeting Street
|
City |
Providence |
State/province |
RI |
ZIP/Postal code |
02912 |
Country |
USA |
|
|
Platform ID |
GPL18936 |
Series (1) |
GSE158246 |
L-bodies are novel RNA-protein condensates driving RNA transport in Xenopus oocytes |
|
Relations |
BioSample |
SAMN16221282 |
SRA |
SRX9156830 |