GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1282339 Query DataSets for GSM1282339
Status Public on Mar 06, 2014
Title ARN_cl1_RA_12h_rep3
Sample type SRA
Source name TAF4-/- immortalized mouse embryonic fibroblasts.
Organism Mus musculus
Characteristics genotype: TAF4-/-
cell type: immortalized mouse embryonic fibroblasts
treatment: retinoic acid
time: 12 h
genetic background: C57BL/6
Extracted molecule polyA RNA
Extraction protocol Sequencing libraries were prepared from 1 µg of total RNA using reagents from the DpnII Digital Gene Expression Tag Profiling kit (Part # 1003803 Rev. B protocol, Illumina). mRNA was captured on magnetic oligo(dT) beads and reverse transcribed into single-strand cDNA and double-stranded cDNA was then synthesized. The cDNA attached to the beads was digested using the restriction enzyme DpnII. A DpnII adapter was ligated to the DpnII cleavage sites. The adapter-ligated cDNA was then digested with MmeI to release 17bp fragments of cDNA from the magnetic bead. The fragments were dephosphorylated and purified by phenol-chloroform. A second adapter was ligated at the MmeI cleavage sites. The adapter-ligated cDNA fragments were amplified by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 15 sec at 72°C] x 15 cycles; 10 min at 72°C) and the PCR products were purified on a 6% TBE PAGE gel. The 85 bp PCR products were excised from the gel and eluted overnight, followed by ethanol precipitation. DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).The libraries were loaded in the flowcell at 8pM concentration and clusters were generated following Illumina’s instructions. Libraries were sequenced on the Illumina Genome Analyzer II as single read 18 bases reads, following the manufacturer's protocols.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina Genome Analyzer IIx
Data processing Illumina Pipeline v1.4 software was used for image analysis and basecalling.
The 16-base long reads (excluding the 4-base DpnII recognition site) were aligned to DpnII tag tables generated by Stowers Institute using Eland.
Genome_build: mm9
Supplementary_files_format_and_content: The NormalizedTagCountPerGenes.tsv file is a tab separated text file containing the normalized number of reads for each Ensembl Gene (Annotations from Ensembl Core v53_37f) .
Submission date Dec 06, 2013
Last update date May 15, 2019
Contact name Igor Martianov
Phone 0033388653440
Organization name IGBMC
Street address 1 rue Laurent Fries
City Illkirch
ZIP/Postal code 67400
Country France
Platform ID GPL11002
Series (1)
GSE53097 Retinoic acid induced changes in gene expression in TAF4 knock out fibroblasts
BioSample SAMN02438051
SRA SRX388719

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