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Series GSE89403 Query DataSets for GSE89403
Status Public on Nov 01, 2017
Title A blood RNA signature for predicting the treatment outcome in the Tuberculosis Treatment Response Cohort
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Identification of blood biomarkers that prospectively predict Mycobacterium tuberculosis treatment response.
 
Overall design There are a total of 914 samples used in this design. This involves samples from 100 cases and 38 controls. Most of the samples have 2 technical replicates where as 2 samples have 4. Samples from the TB cases have been collected on the start day of TB treatment and on 1,4 and 24 weeks after treatment as well. For some subjects we also have samples after the subject has been cured. The case or TB Subjects have been categorized by the nature of their response as definite,probable or possible cure. The day of cure is presented in the time to negativity column. Also provided in the metadata are the MGIT -Mycobacteria Growth Indicator Tube and XPERT (cartridge based nucleic acid amplification test, automated diagnostic test that can identify Mycobacterium tuberculosis (MTB)) values at the various times of sample collection for all TB Subjects.
 
Contributor(s) Zak DE, Thompson E, Shankar S
Citation(s) 29050771
Submission date Nov 01, 2016
Last update date May 15, 2019
Contact name Daniel Zak
E-mail(s) danielzak000@gmail.com
Organization name Center for Infectious Disease Research
Lab Zak Lab
Street address 307 Westlake Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (914)
GSM2369703 S100_day_7-TB Subjects-140805_I272_FCC4MTNACXX_L6_RHUMjlxTAAHBRABPEI-227
GSM2369704 S100_day_7-TB Subjects-140805_I272_FCC4MTNACXX_L7_RHUMjlxTAAHBRABPEI-227
GSM2369705 S100_DX-TB Subjects-140805_I272_FCC4MTNACXX_L6_RHUMjlxTAAHARABPEI-225
Relations
BioProject PRJNA352062
SRA SRP092402

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
GSE89403_TBCatalysis_juncCounts_raw_Star.txt.gz 85.7 Mb (ftp)(http) TXT
GSE89403_log2ExpGeneNames_AllSamples.csv.gz 56.1 Mb (ftp)(http) CSV
GSE89403_rawCounts_GeneNames_AllSamples.csv.gz 12.6 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
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