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Series GSE20579 Query DataSets for GSE20579
Status Public on Apr 19, 2010
Title RNA-Seq on libraries made from ERCC external RNA controls, and a mixture of D. melanogaster S2 cell mRNA and ERCC mRNAs
Organisms Drosophila melanogaster; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Summary RNA-Seq on libraries made from External RNA Controls Consortium (ERCC) external RNA controls, and a mixture of mRNA from Drosophila melanogaster S2 cell and ERCC mRNAs.

We evaluated performance of RNA-Seq on known synthetic PolyA+ mRNAs from the External RNA Controls Consortium (ERCC) alone and in mixtures with PolyA+ mRNA from Drosophila S2 cells. ERCC mRNAs were obtained under Phase V testing from the National Institutes of Standards and Technology (NIST). The ERCC pool contained 96 species of mRNA of various lengths and GC content covering a 2^20 concentration range. Libraries were constructed using 100ng S2 mRNA with 5ng, 2.5ng, or 1ng ERCC mRNAs, and using 50ng ERCC mRNA without S2 cell mRNA. Our data shows an outstanding linear fit between RNA-Seq read density and known input amounts.
Overall design We made libraries with 100ng S2 mRNA with 5ng, 2.5ng or 1ng ERCC mRNAs and with 50ng ERCC mRNAs only. For each library, one lane was sequenced for a 36bp run and around 15 million reads were obtained for each lane.
Contributor(s) Zhang Y, Jiang L, Oliver B
Citation(s) 21816910
Submission date Mar 01, 2010
Last update date May 15, 2019
Contact name Brian Oliver
Phone 301-204-9463
Organization name NIDDK, NIH
Department LBG
Lab Developmental Genomics
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL9423 Illumina Genome Analyzer II (synthetic construct)
GPL10119 Illumina Genome Analyzer II (Drosophila melanogaster; synthetic construct)
Samples (4)
GSM517059 100ng_S2_5ng_ERCC_phaseV_pool15_mRNA-seq
GSM517060 100ng_S2_2.5ng_ERCC_phaseV_pool15_mRNA-seq
GSM517061 100ng_S2_1ng_ERCC_phaseV_pool15_mRNA
SRA SRP002315
BioProject PRJNA125273

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE20579_ERCC_pool12_to_pool15_concentration.txt.gz 2.7 Kb (ftp)(http) TXT
GSE20579_ERCC_sequence.txt.gz 27.1 Kb (ftp)(http) TXT
GSE20579_RAW.tar 1.6 Gb (http)(custom) TAR (of TXT)
GSE20579_readme.txt 2.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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