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Sample GSM2232663 Query DataSets for GSM2232663
Status Public on Aug 10, 2017
Title RHBDF1-P_CAPseq
Sample type SRA
Source name mES derived embryoid bodies day 7
Organisms Homo sapiens; Mus musculus
Characteristics strain: E14-TG2a.IV
cell type: ES derived embryoid bodies
stage of differentiation: day 7
Growth protocol ES-cell derived EB were obtained by culturing ES cells in the absence of LIF and the presence of transferrin and ascorbic acid as described in Tufarelli et al., 2003 (PMID 12730694)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRI Reagent (Sigma-Aldrich, T9424) and then fragmented using the NEBNext Magnesium RNA Fragmentation Module.
Fragmented RNA was cleaned up using RiboMinus Concentration Module (Life Technologies) and the 3’ adapters were ligated using a modified version of the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). Samples were subjected to a second round of clean up using RiboMinus Concentration Module and then subsequently treated with Calf Intestinal Phosphatase (CIP) and Tobacco Acid Phosphatase (TAP). The reaction was cleaned up using the RiboMinus Concentration Module (Life Technologies) as before, and annealing of the SR RT (reverse transcription) primer and ligation of the 5’ adapter was performed. Reverse transcription was carried out using the Superscript III First Strand Synthesis system, followed by library amplification and cleaned up using a QIAquick PCR Purification kit (Qiagen, 28104).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Contains human sequence chr16: 47,911 - 60,819; hg18
Data processing Data was aligned with STAR align (default parameters) to the human hg19 genome to map transcription initiation sites within the human gene sequence of the RHBDF1 with (chr16: 47,861 - 63,210; hg18) and without its promoter (chr16: 47,911 - 60,819; hg18), that was targeted into the RMCE system within the mouse α-globin locus (Lynch et al., 2012, DOI: 10.1038/emboj.2011.399).
downsampling bam files to smallest sample, using all mapped, properly paired reads as the reference count
generating raw coverage bigwig of the above counts
Genome_build: hg19
Supplementary_files_format_and_content: downsampled coverage bigwig
Submission date Jul 13, 2016
Last update date May 15, 2019
Contact name Jim Hughes
Phone 1865222113
Organization name University of Oxford
Department MHU
Lab Genome Biology Group
Street address Weatherall Institute Of Molecular Me
City oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platform ID GPL19415
Series (2)
GSE84353 Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [CAP-Seq]
GSE84355 Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs
BioSample SAMN05388846
SRA SRX1942827

Supplementary file Size Download File type/resource 1.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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