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Series GSE20555 Query DataSets for GSE20555
Status Public on Apr 19, 2010
Title RNA-Seq on libraries made from serial dilutions of Drosophila melanogaster S2 cell mRNA and ERCC external RNA controls
Organisms Drosophila melanogaster; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Summary RNA-Seq on libraries made from serial dilutions of mRNA from Drosophila melanogaster S2 cell and the External RNA Controls Consortium (ERCC) external RNA controls.

We evaluated performance of RNA-Seq by serially diluting a complex pool of known synthetic PolyA+ mRNAs from the External RNA Controls Consortium (ERCC) and 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 with 100ng to 10pg of input mRNA. Our data shows an outstanding linear fit between RNA-Seq read density and known input amounts.
Overall design We performed RNA-Seq from libraries made with 0.01ng to 100ng mRNA (mixture of mRNA from Drosophila melanogaster S2 cells and ERCC RNA controls). One RNA-Seq library was prepared with 100ng mRNA and six libraries were made with serial dilutions of mRNA using a modified protocol (see Sample 'extraction protocol'). One lane was sequenced for each library and all seven libraries were run on the same flow cell.
Contributor(s) Zhang Y, Jiang L, Oliver B
Citation(s) 21816910
Submission date Feb 27, 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 (1)
GPL10119 Illumina Genome Analyzer II (Drosophila melanogaster; synthetic construct)
Samples (7)
GSM516588 100ng_library_methA_S2_2.5%ERCC_phaseV_pool15mRNA
GSM516589 100ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA
GSM516590 50ng_library_methB_S2_2.5%ERCC_phaseV_pool15_mRNA
SRA SRP002255
BioProject PRJNA125199

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
GSE20555_ERCC_pool12_to_pool15_concentration.txt.gz 2.7 Kb (ftp)(http) TXT
GSE20555_ERCC_sequence.txt.gz 27.1 Kb (ftp)(http) TXT
GSE20555_RAW.tar 1.1 Gb (http)(custom) TAR (of TXT)
GSE20555_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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