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Sample GSM2150847 Query DataSets for GSM2150847
Status Public on Jun 29, 2017
Title Untreated replicate 2
Sample type SRA
 
Source name Untreated, HeLa
Organism Homo sapiens
Characteristics cell line: HeLa
transfection: Untreated
Treatment protocol The RNA and Lipofectamine 2000 were diluted and mixed in Opti-MEM (Invitrogen, 31985-088), incubated for 5 min at rt, the nucleic acids and Lipofectamine 2000 were mixed together, incubated for 15 min at rt and then the nucleic acids-Lipofectamine 2000 complexes were applied to the monolayer cultures. (500 ng of nucleic acids was transfected into one well of a 24-well plate.)
Growth protocol Hela cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, 11995-073) supplemented with 100 units/ml penicillin-streptomycin (Gibco, 15140-163), 10% (v/v) fetal bovine serum
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol reagent, according to manufacturer’s instructions. Total RNA was subjected to rRNA depletion with Ribo Minus Kit.
RNA sequencing libraries were prepared as decribed in Flynn et al., 2015
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequenced reads were collapsed for PCR duplicates and trimmed for adaptor sequence. Reads mapping to rRNA and transfected RNA were removed. Remaining reads were mapped to hg19 genome assembly whole genome using sequence aligner STAR with parameters FilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4
Reads matching each gene were calculated using HTSeq. Differential gene expression was calculated with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: counts.txt files include counts calculated by HTSeq, and DGE.txt includes fold change and p-value calculated by DESeq2.
Supplementary_files_format_and_content: MolCell2017_DNA_plasmidseq.docx includes plasmid insert sequences.
 
Submission date May 11, 2016
Last update date Apr 21, 2024
Contact name Howard Y Chang
Organization name Stanford University
Department Dermatology
Lab Chang lab
Street address CCSR 2130, 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL18573
Series (1)
GSE81345 Sensing self and nonself circular RNAs
Relations
BioSample SAMN04990196
SRA SRX1756865

Supplementary file Size Download File type/resource
GSM2150847_Neg2A.counts.txt.gz 96.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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