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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 09, 2014 |
| Title |
Mel MRE-seq |
| Sample type |
SRA |
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| Source name |
Mel, mouse leukemia cell line
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| Organism |
Mus musculus |
| Characteristics |
cell line: Mel
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For MRE: DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100–300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 µl used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 μl used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.
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| Library strategy |
MRE-Seq |
| Library source |
genomic |
| Library selection |
Restriction Digest |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
Sequencing reads were aligned to human hg19 or mouse mm9 with BWA
For MeDIP-seq, redandunt reads were discard
For MRE-seq, reads were filtered by MRE recognization site in genome.
Aligned results were further processed by methylQA (http://methylqa.sourceforge.net/) to get bigWig files
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bigWig
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| Submission date |
Apr 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
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| Phone |
(314) 286-0866
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| Organization name |
Washington University in St. Louis
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| Department |
Genetics
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| Lab |
Ting Wang Lab
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| Street address |
4515 McKinley Avenue
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| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL15103 |
| Series (1) |
| GSE57230 |
Widespread contribution of transposable elements to the innovation of gene regulatory networks [mouse ENCODE] |
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| Relations |
| BioSample |
SAMN02727257 |
| SRA |
SRX534889 |
| Named Annotation |
GSM1368912_TW232_Mel_MRE.CpG.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1368912_TW232_Mel_MRE.CpG.bigWig |
9.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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