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Sample GSM517060 Query DataSets for GSM517060
Status Public on Apr 19, 2010
Title 100ng_S2_2.5ng_ERCC_phaseV_pool15_mRNA-seq
Sample type SRA
Source name Drosophila S2 cell and 2.5ng ERCC RNA controls
Organisms Drosophila melanogaster; synthetic construct
Characteristics cell line: S2
external rna control: ERCC phase V pool 15
s2 treatment: msl2 RNAi
rna quantity (s2): 100ng
rna quantity (ercc): 2.5ng
Treatment protocol S2 cells were mock or RNAi treated with 10ng dsRNA using standard procedure. See Zhang et al., PLoS Biology 2010 for details.
Growth protocol Drosophila S2 cells ("SL2" originally obtained from the Drosophila RNAi Screening Center, Boston MA) were grown at 25°C in Schneider's Drosophila Medium (Invitrogen, Carlsbad, CA) supplemented with 10% Fetal Bovine serum (SAFC Biosciences, Lenexa, KS) and Penicillin-Streptomycin.
Extracted molecule total RNA
Extraction protocol Libraries were made with 100ng S2 mRNA or 100ng mRNA from S2 RNAi-treated cells with 5ng, 2.5ng or 1ng ERCC mRNAs and with 50ng ERCC mRNAs only following the standard procedure. See Zhang et al. PLoS Biology 2010 for details.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Description Sequences and abundance information of ERCC phase V pool 15 used in this study were provided separately with the supplementary files:
Data processing We retained reads that passed default quality filtering parameters in the Illumina pipeline (v1.4.0). We aligned reads passing quality filtering using Bowtie (v0.10.0; parameter -m 1 -v 2). Sequences of the ERCC RNAs (*ERCC_map.txt) were used as the alignment reference. Additionally, Drosophila genome sequence (BDGP release 5, dm3) and ERCC RNA sequences were combined into a reference (*ERCC_dm3_map.txt). We used unique mapped reads with less than 2 mismatches for analysis.
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
Platform ID GPL10119
Series (1)
GSE20579 RNA-Seq on libraries made from ERCC external RNA controls, and a mixture of D. melanogaster S2 cell mRNA and ERCC mRNAs
Reanalyzed by GSM3274609
SRA SRX019235
BioSample SAMN00011329

Supplementary file Size Download File type/resource
GSM517060_run29_s_3_ERCC_dm3_map.txt.gz 357.8 Mb (ftp)(http) TXT
GSM517060_run29_s_3_ERCC_map.txt.gz 9.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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