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| Status |
Public on Jul 25, 2012 |
| Title |
RNA-seq from ENCODE/Stanford/Yale |
| Project |
Mouse ENCODE
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| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Philip Cayting mailto:pcayting@stanford.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).
The tracks show enrichment of RNA sequence tags mapped to the mouse genome generated by high throughput sequencing (RNA-Seq). Double stranded cDNA was synthesized from enriched RNA that was obtained after depletion of ribosomal RNA. Pieces of cDNA, 300-350 nucleotides in length, were PCR amplified, adapter ligated, and sequenced on an Illumina HiSeq sequencer.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). Total RNA was extracted using RNeasy Mini Kit (74104, Aiagen), following the manufacturer's protocol. Ribosomal RNA was removed from total RNA using the Ribo-ZeroTM Gold Kits (MRZG126, Epicentre). Double-stranded cDNA synthesis was performed on the rRNA depleted RNA using random primers and the SuperScript double-stranded cDNA synthesis kit (11917-010, Life Tech). After first strand cDNA synthesis, NucAway Spin Column (Ambion cat. 100070-30) was used to remove dNTPs. In the second strand cDNA synthesis reaction, dTTP in the dNTP mix was substituted with dUTP. After end repair and addition of 'A' base to 3' end, illumina paired-end adapter was ligated to Double-stranded cDNA library. After gel size selection of adapter ligated cDNA (300-350), Uracil-N-Glycosylase (UNG: Applied Biosystems) was used to digest the second strand cDNA (Parkhomchuk et al. , 2009). PCR amplified adapter ligated cDNA was sequenced using Illumina HiSeq. Sequence reads of 2x101 nt long with 0-2 mismatches were mapped to the mouse genome (version mm9) using the BWA aligner, version 0.5.7. The signal height corresponds to the number of overlapping fragments at each nucleotide position in the genome.
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| Web link |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhRnaSeq
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| Contributor(s) |
Snyder M, Cayting P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA66167 |
| Submission date |
Jul 24, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
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| Organization name |
ENCODE DCC
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| Street address |
300 Pasteur Dr
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (4)
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| GSM973232 |
Stanford_RnaSeq_MEL (superseded by GSE90278) |
| GSM973233 |
Stanford_RnaSeq_MEL_DMSO_2.0pct (superseded by GSE90279) |
| GSM973234 |
Stanford_RnaSeq_CH12 (superseded by GSE78620) |
| GSM973235 |
Stanford_RnaSeq_ES-E14 (superseded by GSE90277) |
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| Relations |
| SRA |
SRP014631 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE39619_RAW.tar |
2.9 Gb |
(http)(custom) |
TAR (of BIGWIG) |
| GSE39619_run_info_with_UCSC_objects.txt.gz |
821 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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