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Sample GSM4795814 Query DataSets for GSM4795814
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

Supplementary file Size Download File type/resource
GSM4795814_03_htseqEXON_cts.txt.gz 167.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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