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Status |
Public on Mar 07, 2017 |
Title |
Nugen, replicate 1, hour 10 |
Sample type |
SRA |
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Source name |
Cells developing on nitrocellulose filters
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Organism |
Dictyostelium discoideum |
Characteristics |
strain: AX4 growth media: HL-5 treatment: Development on 5 cm nitrocellulose filters, InDA-C rRNA depletion time point (hour): 10 replicate: 1
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Growth protocol |
Dictyostelium discoideum cells were grown in nutrient media (HL-5) to mid-log phase prior to collection for development.
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Extracted molecule |
total RNA |
Extraction protocol |
TriZol (Life Sciences) -- Cells were scraped (filter) or pelleted (suspension) and disrupted in TriZol. Total RNA was extracted by phenol/chloroform as per manufacturer's instructions. Ribosomal RNA was depleted using either the InDA-C method (Ovation, Nugen) or RiboZero "Plant root & seed" reagents, following manufacturer's instructions.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
rRNA-depleted total RNA Nu_rep1_hr10
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Data processing |
The data was mapped to the D. discoideum genome using TopHat version 2.0.13. Only uniquely mapped reads were permitted and the reference transcript annotation was supplied (--GTF --report-secondary-alignments --max-multihits 1 --mate-inner-dist 100). Transcripts were assembled using Cufflinks (v2.2.1) with the option --GTF-guide to guide the reference annotation based transcript (RABT) assembly. The transcript annotation files from cufflinks were then merged using Cuffmerge (v2.2.1) to obtain a final transcriptome assembly. Raw expression values were computed as the number of reads that were uniquely mapped to gene exons. Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the reads mapped to the chrR (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable). Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked. All DDB_G* IDs will be available on dictybase.org and dictyexpress.org although are not present on these websites at the time of accessioning these data in GEO. Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names (DDB_G ids, CUFF ids) and the second its expression. Files ending with "_raw.txt" contain raw expression values while files ending with "_nor.txt" contain normalized expression values. Supplementary_files_format_and_content: File_S3 contains the entire set of of CUFF models (and previously defined coding genes) with their genomic coordinates. This file also contains the normalized expression values for all samples. Supplementary_files_format_and_content: File_S4 contains the DDB_G assignments to the confident subset of those CUFF models.
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Submission date |
Dec 12, 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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Platform ID |
GPL22784 |
Series (1) |
GSE90829 |
The long non-coding RNA transcriptome of Dictyostelium discoideum development |
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Relations |
BioSample |
SAMN06132935 |
SRA |
SRX2416403 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2425183_Nu_rep1_hr10_nor.txt.gz |
149.7 Kb |
(ftp)(http) |
TXT |
GSM2425183_Nu_rep1_hr10_raw.txt.gz |
70.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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