|
| 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 |
| E-mail(s) |
jim.hughes@imm.ox.ac.uk
|
| 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 |
|
| Relations |
| BioSample |
SAMN05388846 |
| SRA |
SRX1942827 |
