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Sample GSM1440297 Query DataSets for GSM1440297
Status Public on Dec 30, 2016
Title control_exp2
Sample type SRA
 
Source name Daoy cell line
Organism Homo sapiens
Characteristics tissue: brain/cerebellum
cell type: cerebellar medulloblastoma
cell line: Daoy
genotype/variation: control
Treatment protocol Daoy cells were cultured in DMEM supplemented with 10% fetal bovine serum. Daoy cells were flow sorted after infected with virus for 5days.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent. mRNA were purified with Dynabeads® mRNA Purification Kit (Cat#61006).
RNA libraries were prepared for sequencing using strand specific dUTP protocols.(nature methods 2010, 7(9): 709-715)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Sample 2
Data processing Illumina CASAVA-1.8.2 software used for basecalling.
Reads were aligned to the hg19 genome assembly using STAR version 2.3.1f with parameters --genomeDir hg19 –runThreadN 8 …
Reads of genes were counted using HOMER software (Mol Cell 2010, 38(4):576-589) followed analysis with edgeR package in R
for bedGraph file, reads were mapped to hg19 using STAR 2.3.1f, and the bed files were made based on the mapping information with HOMER software command “makeTagDirectory” with -flip option and followed by “makeUCSCfile”.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file reports Total Tags
 
Submission date Jul 18, 2014
Last update date May 15, 2019
Contact name Bruce Hamilton
E-mail(s) bah@ucsd.edu
Phone 8588222298
Organization name UC San Diego
Department Medicine
Lab CMM
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL16791
Series (1)
GSE59598 mRNA expression in human DAOY cells
Relations
BioSample SAMN02927659
SRA SRX657418

Supplementary file Size Download File type/resource
GSM1440297_Daoy2ctl.ucsc.bedGraph.gz 14.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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