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| Status |
Public on Jul 27, 2016 |
| Title |
End Sequence Analysis ToolKit (ESAT) expands the extractable information from single cell RNA-Seq data |
| Organisms |
Mus musculus; Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Test data used for the evaluation of ESAT performance and results files for data from 3' and 5' end-sequencing RNA-Seq protocols and droplet-based single-cell RNA-Seq.
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| |
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| Overall design |
Quantification and analysis of Tophat-aligned (v2.0.9) samples from mouse bone-marrow derived dendritic cells (mBMDC) timecourse (0, 2, 4 and 6 hours) post LPS stimulation and non-diabetic BBDR rat pancreatic islet cells.
Since end-sequencing (3' or 5') is used for all samples, alignments are only required for the R2 (sequence-containing) read.
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| |
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| Contributor(s) |
Derr AG, Yang C, Zilionis R, Redick S, Artyomov M, Garber M |
| Citation(s) |
27470110 |
| |
| Submission date |
Mar 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alan G Derr |
| E-mail(s) |
alan.derr@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Bioinformatics and Integrative Biology
|
| Lab |
Garber Lab
|
| Street address |
55 Lake Ave North
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01655 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
| GPL15103 |
Illumina HiSeq 1000 (Mus musculus) |
|
| Samples (14)
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| Relations |
| BioProject |
PRJNA316604 |
| SRA |
SRP072449 |
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