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| Status |
Public on Apr 21, 2015 |
| Title |
Filter development, replicate 2, hour 12 |
| 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: HL-5
treatment: Development on 5 cm nitrocellulose filters
time point (hour): 12
replicate: 2
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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 |
polyA 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.
mRNA was enriched by 2x polyA bead selection (Ambion, Life Sciences). Multiplexed libraries were constructed as outlined in Miranda et al (2013), PMID #23494306.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Sample 32
FDrep2_hr12
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| Data processing |
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
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 non-polyadenylated genes (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.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names (DDB_G 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.
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| Submission date |
Sep 30, 2014 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Gad Shaulsky |
| E-mail(s) |
gadi@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular and Human Genetics
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| Street address |
One Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL9379 |
| Series (1) |
| GSE61914 |
Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum |
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| Relations |
| Reanalyzed by |
GSM5145743 |
| BioSample |
SAMN03084991 |
| SRA |
SRX717779 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1517252_FDrep2_hr12_nor.txt.gz |
109.1 Kb |
(ftp)(http) |
TXT |
| GSM1517252_FDrep2_hr12_raw.txt.gz |
48.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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