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Sample GSM2425183 Query DataSets for GSM2425183
Status Public on Mar 07, 2017
Title Nugen, replicate 1, hour 10
Sample type SRA
 
Source name Cells developing on nitrocellulose filters
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
Growth protocol Dictyostelium discoideum cells were grown in nutrient media (HL-5) to mid-log phase prior to collection for development.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description rRNA-depleted total RNA
Nu_rep1_hr10
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.
 
Submission date Dec 12, 2016
Last update date May 15, 2019
Contact name Rafael Rosengarten
E-mail(s) rafael@genialis.com
Phone 8439913407
Organization name Genialis, Inc
Street address 2520 Robinhood St #603
City Houston
State/province Texas
ZIP/Postal code 77005
Country USA
 
Platform ID GPL22784
Series (1)
GSE90829 The long non-coding RNA transcriptome of Dictyostelium discoideum development
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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