NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4082957 Query DataSets for GSM4082957
Status Public on Apr 21, 2021
Title Vegetative stage replicate 1 (RNA-Seq)
Sample type SRA
 
Source name Vegetative cells
Organism Dictyostelium discoideum
Characteristics developmental stage: Vegetative
strain: AX4
Growth protocol We cultured te strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin
Extracted molecule total RNA
Extraction protocol mRNA was extracted from D. Discoedium cells using Dynabeads mRNA direct micro purification kit (Invitrogen)
8 groups were prepared for RNA-seq libraries using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Real-Time Analysis (RTA) software
sequencing reads were aligned to the AX4 genome by Bowtie2(2.2.9)
The analysis pipeline started with pseudo-alignment of the reads using kallisto, followed by building an index and quantification process, which generated h5 files containing the raw binary files for preliminary differential analysis in sleuth.
Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05.
Genome_build: AX4
Supplementary_files_format_and_content: Data matrix was generated by sleuth
 
Submission date Sep 17, 2019
Last update date Apr 21, 2021
Contact name Eric Greer
E-mail(s) Eric.Greer@childrens.harvard.edu
Organization name Boston Children's Hospital/Harvard Medical School
Department Newborn Medicine/Department of Pediatrics
Lab Greer Lab
Street address 320 Longwood Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL26360
Series (2)
GSE137602 Transcriptome analysis in D. discoideium (AX2) in different developmental stages
GSE137604 Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium
Relations
BioSample SAMN12775763
SRA SRX6862335

Supplementary file Size Download File type/resource
GSM4082957_LIB13.abundance.h5 4.3 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap