|
| Status |
Public on Apr 19, 2010 |
| Title |
50ng_ERCC_phaseV_pool15_mRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
ERCC RNA controls only
|
| Organism |
synthetic construct |
| Characteristics |
external rna control: ERCC phase V pool 15
rna quantity (s2): 0ng
rna quantity (ercc): 50ng
|
| 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 |
polyA 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:
ERCC_phaseV_pool15_sequence.txt
ERCC_phaseV_pool15_abundance.txt
|
| 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 |
| E-mail(s) |
[email protected]
|
| 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 |
GPL9423 |
| 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 |
|
| Relations |
| SRA |
SRX019237 |
| BioSample |
SAMN00011331 |
