GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2310070 Query DataSets for GSM2310070
Status Public on Oct 12, 2017
Title siControl NXF1 RIP Rep-2
Sample type SRA
Source name HeLa transfected with control siRNA
Organism Homo sapiens
Characteristics cell line: HeLa
culture media: DMEM
antibody: Abcam ab129160 Anti-NXF1 antibody [EPR8009]
strain: ATCC CCL-2
Treatment protocol Transfections were carried out using Lipofectamine RNAiMAX according to manufacturers protocol in the absence of antibiotics.
Growth protocol HeLa cells (ATCC CCL-2) were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep.
Extracted molecule total RNA
Extraction protocol RIP was performed according to literature procedure (Peritz et al., 2006) using polyA selected RNA following treatment with two uique siRNA sequences as biological replicates.
RIP-seq and subcellular RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA kit.
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
Description RIP NXF1 Poly(A)
Data processing After adaptor trimming with Cutadapt (v1.4.1) and quality control, 50 bp sequence reads were mapped to the human genome (hg19) using TopHat (v.2.0.11) and Bowtie (v1.0.1).
RIP-seq and RNA-seq differential expression was quantified between replicate experiments using Cufflinks (v.2.2.1)
Genome_build: hg19 (human)
Supplementary_files_format_and_content: Differential enrichment in siControl vs siYTHDC1 was assessed in repliacte using Cufflinks (v.2.2.1), including normalization to input samples under each condition.
Submission date Sep 13, 2016
Last update date May 15, 2019
Contact name Ian Roundtree
Organization name University of Chicago
Department Department of Chemistry
Lab Chuan He Lab
Street address 929 E 57th Street E307
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platform ID GPL11154
Series (1)
GSE74397 N6-methyladenosine-Mediated Nuclear Export of Messenger RNA
BioSample SAMN05770400
SRA SRX2162600

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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