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| 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
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| 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.
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| 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.
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| Contributor(s) |
Rosengarten RD, Santhanam B, Kokosar J, Shaulsky G |
| Citation(s) |
27932387 |
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| Submission date |
Dec 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rafael Rosengarten |
| E-mail(s) |
rafael@genialis.com
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| Phone |
8439913407
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| Organization name |
Genialis, Inc
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| Street address |
2520 Robinhood St #603
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77005 |
| Country |
USA |
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| Platforms (1) |
| GPL22784 |
Illumina HiSeq 2500 (Dictyostelium discoideum) |
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| Samples (23)
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| GSM2425181 |
Nugen, replicate 1, hour 06 |
| GSM2425182 |
Nugen, replicate 1, hour 08 |
| GSM2425183 |
Nugen, replicate 1, hour 10 |
| GSM2425184 |
Nugen, replicate 1, hour 12 |
| GSM2425185 |
Nugen, replicate 1, hour 14 |
| GSM2425186 |
Nugen, replicate 1, hour 16 |
| GSM2425187 |
Nugen, replicate 1, hour 18 |
| GSM2425188 |
Nugen, replicate 1, hour 20 |
| GSM2425189 |
Nugen, replicate 1, hour 22 |
| GSM2425190 |
Nugen, replicate 1, hour 24 |
| GSM2425191 |
Nugen, replicate 2, hour 00 |
| GSM2425192 |
Nugen, replicate 2, hour 02 |
| GSM2425193 |
Nugen, replicate 2, hour 04 |
| GSM2425194 |
Nugen, replicate 2, hour 06 |
| GSM2425195 |
Nugen, replicate 2, hour 08 |
| GSM2425196 |
Nugen, replicate 2, hour 10 |
| GSM2425197 |
Nugen, replicate 2, hour 14 |
| GSM2425198 |
Nugen, replicate 2, hour 18 |
| GSM2425199 |
Nugen, replicate 2, hour 20 |
| GSM2425200 |
Nugen, replicate 2, hour 24 |
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| Relations |
| BioProject |
PRJNA357088 |
| SRA |
SRP094967 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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