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Series GSE90829 Query DataSets for GSE90829
Status Public on Mar 07, 2017
Title The long non-coding RNA transcriptome of Dictyostelium discoideum development
Organism Dictyostelium discoideum
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary This study details the content and dynamics of the long non-coding transcriptome during D. discoideum development, providing an important compendium to the well-characterized protein coding transcriptome. Applying a novel sample preparation method, we isolated antisense and long intergenic non-coding RNAs in addition to mRNAs. We describe the behavior of these different classes of RNAs that have been shown to play important regulatory roles in numerous model systems. Our analyses contribute a wholly different perspective to the most widely appreciated and compelling aspect of Dictyostelium biology—the change in life style from solitary amoebae to differentiated multicellular organisms.
Overall design RNA-sequencing of rRNA-depleted (Ovation, Nugen) libraries from Dictyosteloium discoideum developmental time course. Samples were collected every 2 hours during the 24-hour development cycle. Biological replicate 1 consists of all 13 time points. Bio rep 2 consists of 11 time points, with hours 16 and 22 failing to sequence properly. Additionally, hours 0, 4, 8, 12, 16, and 22 were reprocessed with a different rRNA-depletion method (RiboZero, Epictentre) and sequenced.
Contributor(s) Rosengarten RD, Santhanam B, Kokosar J, Shaulsky G
Citation(s) 27932387
Submission date Dec 02, 2016
Last update date May 15, 2019
Contact name Rafael Rosengarten
Phone 8439913407
Organization name Genialis, Inc
Street address 2520 Robinhood St #603
City Houston
State/province Texas
ZIP/Postal code 77005
Country USA
Platforms (1)
GPL22784 Illumina HiSeq 2500 (Dictyostelium discoideum)
Samples (23)
GSM2425178 Nugen, replicate 1, hour 00
GSM2425179 Nugen, replicate 1, hour 02
GSM2425180 Nugen, replicate 1, hour 04
BioProject PRJNA357088
SRA SRP094967

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE90829_File_S3.xlsx 6.0 Mb (ftp)(http) XLSX
GSE90829_File_S4.xlsx 99.3 Kb (ftp)(http) XLSX
GSE90829_RAW.tar 5.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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