NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE80297 Query DataSets for GSE80297
Status Public on May 01, 2016
Title mRNA expression of breast cancer cell lines across different densities [SCRB-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary mRNA expression profiles for 3 breast cancer cell lines seeded at different density and grown for different duration
 
Overall design This experiment is part of a study fo the effect of cell density on drug sensitivity [1]. Cells plated at different densities in 384-well plates were harvested at the indicated times and RNA was extracted using the RNeasy mini kit (Qiagen). To ensure sufficient RNA amounts wells with low cell numbers were pooled. Some conditions have been tested in biollogical replicates grown at the same time. Libraries were prepared by the Broad Technology Labs (BTL) following the protocol for SCRB-Seq described in [2]. Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1 [3]. [1] Hafner, M., Niepel, M., Chung, M., Sorger, P.K., Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. DOI:10.1038/NMETH.3853 [2] Soumillon, M., Cacchiarelli, D., Semrau, S., van Oudenaarden, A. & Mikkelsen, T.S. Characterization of directed differentiation by high-throughput single-cell RNA-Seq http://biorxiv.org/content/early/2014/03/05/003236 [3] Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L. & Pachter, L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat. Protoc. 7, 562-578 (2012).
Web link http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3853.html
 
Contributor(s) Hafner M, Niepel M, Chung M, Soumillon M, Sorger P
Citation(s) 27135972
Submission date Apr 14, 2016
Last update date May 15, 2019
Contact name Marc Hafner
E-mail(s) Marc_Hafner@hms.harvard.edu
Organization name Harvard Medical School
Department Systems Biology
Lab Sorger Lab
Street address WAB 438, 200 Longwood Av.
City Boston
State/province MASSACHUSETTS
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (87)
GSM2123895 P3_A1 - MCF10A_625_day0
GSM2123896 P3_B1 - MCF10A_625_day0
GSM2123897 P3_C1 - MCF10A_1250_day0
Relations
BioProject PRJNA318513
SRA SRP073318

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
GSE80297_SSF102_PS1.refseq.umi.dat.gz 1.1 Mb (ftp)(http) DAT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap