NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1470725 Query DataSets for GSM1470725
Status Public on Dec 07, 2016
Title Clone 34 hF Replicate 2
Sample type SRA
 
Source name Limiting dilution of TERT-immortalised NHDF17914 fibroblast
Organism Homo sapiens
Characteristics cell type: human fibroblast clones derived from TERT-immortalised NHDF17914 (Lonza)
time point: before fusion with mouse ESC
Treatment protocol hF clones were fused with mESC by PEG (Roche)
Growth protocol Human fibroblast (hF) clones were maintainedat 3% O2 in DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine and antibiotics (10 µg/ml penicillin and streptomycin). After hF x mESC fusion, heterokaryons and hybrids were cultured in mouse ESC medium (KO-DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine, 50μM β-mercaptoethanol, antibiotics (10 µg/ml penicillin and streptomycin) and LIF) and selected 12hrs after by adding puromycin (1.5 μg/ml) and HAT (20μM hypoxantine, 0.08 mM aminopterin, and 3.2 mM thymidine; Sigma).
Extracted molecule total RNA
Extraction protocol Total RNA was exacted by RNABee (Amsbio) accordingly to manifacturer instructions
RNA-seq libraries were prepared from 0.6μg total RNA accordingly to Illumina True-seq RNA sample preparation v2 guide (Illumina). Libraries were amplified 14 cycles before deep-sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Clone_34_hF_2
Data processing Human fibroblast RNA-seq reads were aliged to the Human genome (hg19) using Tophat v2.0.8 using Ensembl gene v72 as gene model.
RNA-Seq reads from hF x mESC fusion were aligned independently to Human (hg19, Ensembl v72) and Mouse (mm9, Ensembl v67) using Tophat v2.0.8. Reads aligned to both Human and Mouse were excluded from the further anlaysis.
Reads overlapping with each gene was counted using HTSeq and differentially expressed genes were identified using edgeR
FPKM values were estimated using R script
Genome_build: hg19; mm9
Supplementary_files_format_and_content: hg19 FPKM values
 
Submission date Aug 11, 2014
Last update date May 15, 2019
Contact name Gopuraja Dharmalingam
Organization name MRC London Institute of Medical Sciences
Department Epigenetics section
Street address Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
 
Platform ID GPL16791
Series (1)
GSE60308 Selective reactivation of human X-linked genes in female fibroblasts reprogrammed by cell fusion
Relations
BioSample SAMN02981713
SRA SRX674540

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