 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 04, 2014 |
| Title |
DP Input BGT GLIB-Seq |
| Sample type |
SRA |
| |
|
| Source name |
DP T cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: thymus
strain: C57/BL6
developmental stage: DP T cells
|
| Growth protocol |
Mouse embryonic stem cells V6.5 were cultured in Knockout D-MEM with 15% ES-qualified FBS (Gemini Bio-products), 2 mM L-glutamine with 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 units/ml penicillin/streptomycin and 1000 U/ml ESGRO® (LIF; Chemicon)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared by lysing ES or DP T cells, followed by treatment with RNase A (Qiagen) for 1 hour at 37 0C and then overnight treatment with proteinase K (Roche) at 550C with vigorous shaking. DNA was purified after sequential treatment with phenol, phenol/chlorophorm/isoamyl alcohol, chlorophorm/isoamyl alcohol (all obtained from Sigma) and then ethanol (Sigma) precipitation. DNA was resuspended in 10 mM Tris-Cl pH 8.0, 0.1mM EDTA .Biotin-glucosyl tagging and enrichment of 5hmC (Biotin-gmC, a variant of GLIB (Song C.-X. et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nature Biotechnology 29, 68–72 (2011))): For specific biotinylation of 5hmC in DP T cells and ES cells, we used the Hydroxymethyl Collector kit (Active Motif, Carlsbad, CA) to selectively label 5hmC bases with glucose and biotin moieties to form biotin-N3-5-gmC as previously described(Song C.-X. et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nature Biotechnology 29, 68–72 (2011)). To ensure efficient biotinylation, 2 µg of genomic DNA were biotinylated per reaction. In this case we used the 5500 SoliD fragment library preparation kit from Applied Biosystems in order to prepare the library and the 5500 SOLiD Library indexed adaptors 1-16 according to the manufacturer’s instructions. The samples were sequenced using the SOLiD 5500 platform.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Data processing |
The GLIB and input reads were mapped against mm9 in color-space using Bowtie.
The coverage tracks (RPM normalized) were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: The RPM normalized coverage tracks (bigWig)
|
| |
|
| Submission date |
Jul 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tarmo Äijö |
| Organization name |
Flatiron Institute
|
| Department |
Center for Computational Biology
|
| Street address |
162 5th Avenue
|
| City |
New York |
| ZIP/Postal code |
10010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16790 |
| Series (2) |
| GSE59122 |
Dissecting the dynamic changes of 5-hydroxymethylcytosine in T cell development and differentiation [MeDIP-Seq] |
| GSE59213 |
Dissecting the dynamic changes of 5-hydroxymethylcytosine in T cell development and differentiation |
|
| Relations |
| BioSample |
SAMN02905035 |
| SRA |
SRX648172 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1428951_DP_Input_BGT_tags.ucsc.bigWig |
556.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
