GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2537509 Query DataSets for GSM2537509
Status Public on Mar 15, 2018
Title ZT56.CLKkd.1 (ns500)
Sample type SRA
Source name Neural progenitor cells
Organism Homo sapiens
Characteristics cell type: Neural progenitor cells
line: OF4106
Sex: F
age: --
Treatment protocol Tissue culture was performed as previously described (PMID: 21647150). Lentivirus was delivered via pZIP shRNA constructs (Transomics).
Growth protocol Differentiated human neural progenitor cell lines were used.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Qiagen’s miRNeasy kit according to the manufacturer’s instructions. All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. 2ug of total RNA were enriched for mRNA with poly-A selection beads. Libraries were prepared using previously published methods (PMID: 25662462)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Single-end reads were aligned in a staged manner. Reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
RNA-seq Counts values were quantified using HTSeq python suite, providing gene definitions (hg38, Gencode v.24). HiSeq 2500 and NextSeq 500 counts per gene were further added into a final count to calculate RPKM values and downstream analysis.
RNA-seq RPKM values were then quantified using in-home scripts, providing gene definitions (hg38, Gencode v.24).
Gene-level RPKMs quantifications were used for all downstream processing.
tab-delimited text file include RPKM values for each Sample.
Genome_build: Human hg38
Submission date Mar 15, 2017
Last update date May 15, 2019
Contact name Genevieve Konopka
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
Platform ID GPL18573
Series (1)
GSE96659 Novel transcriptional networks regulated by CLOCK in human neurons
BioSample SAMN06604857
SRA SRX2642571

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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