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Series GSE107672 Query DataSets for GSE107672
Status Public on Apr 21, 2020
Title Transcriptional responses to RTS,S induced vaccination in controlled human malaria infection studies
Sample organism Homo sapiens
Experiment type Expression profiling by array
Expression profiling by high throughput sequencing
Other
Summary Identification of host responses that are induced by RTS,S vaccination in controlled malaria infection
 
Overall design In order to examine host responses induced in response to RTS,S-based malaria vaccine, expression profiles from both RNAseq and Microarrays platforms were pulled together from a number of RTS,S-based malaria trials. Mixed effects regression models and various filtering strategies were then applied to identify 6 protection-associated gene pairs that were induced by RTS,S vaccination and common in the RTS,S trials. Lastly, these 6 gene pairs were carefully examined and investigate if they were associated with protection in other RTS,S-related trials.
 
Contributor(s) Du Y, Thompson E, Zak DE, Shankar S
Citation(s) 32411130
Submission date Dec 04, 2017
Last update date May 18, 2020
Contact name Daniel Zak
E-mail(s) danielzak000@gmail.com
Organization name 2Seventy Bio
Lab Data Sciences
Street address 188 East Blaine Street, Suite 300
City Seattle
State/province WA
ZIP/Postal code 98102
Country USA
 

Data table header descriptions
GEO Sample accession
Sample name
STUDY
source name
organism
characteristics: patient ID
characteristics: ARM
characteristics: TREATMENT
characteristics: PROTECTION
characteristics: TIME POINTS
characteristics: TIME DESCRIPTION
processed data file
BioSample
SRA Experiment
CEL file name

Data table
GEO Sample accession Sample name STUDY source name organism characteristics: patient ID characteristics: ARM characteristics: TREATMENT characteristics: PROTECTION characteristics: TIME POINTS characteristics: TIME DESCRIPTION processed data file BioSample SRA Experiment CEL file name
GSM2769951 RNAseq-A-41_D2 Mal68.RNAseq Blood Homo sapiens A-41 ARR ARR: Ad35.CS+RTS,S/AS01 01 NOT PROTECTED D2 Day 2 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596860 SRX3154671
GSM2769952 RNAseq-A-180_D2 Mal68.RNAseq Blood Homo sapiens A-180 ARR ARR: Ad35.CS+RTS,S/AS01 01 NOT PROTECTED D2 Day 2 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596859 SRX3154672
GSM2769953 RNAseq-R-37_D78 Mal68.RNAseq Blood Homo sapiens R-37 RRR RRR: RTS,S/AS01 012 NOT PROTECTED D78 Day 1 post Challenge Malaria_ExpressionData_RNAseqData.txt SAMN07596858 SRX3154673
GSM2769954 RNAseq-R-23_D1 Mal68.RNAseq Blood Homo sapiens R-23 RRR RRR: RTS,S/AS01 012 NOT PROTECTED D1 Day 1 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596857 SRX3154674
GSM2769955 RNAseq-A-83_D56 Mal68.RNAseq Blood Homo sapiens A-83 ARR ARR: Ad35.CS+RTS,S/AS01 01 NOT PROTECTED D56 Day 0 post VAC3/Day 28 post VAC2 Malaria_ExpressionData_RNAseqData.txt SAMN07596942 SRX3154675
GSM2769956 RNAseq-A-117_D28 Mal68.RNAseq Blood Homo sapiens A-117 ARR ARR: Ad35.CS+RTS,S/AS01 01 PROTECTED D28 Day 0 of VAC2/Day 28 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596941 SRX3154676
GSM2769957 RNAseq-R-23_D14 Mal68.RNAseq Blood Homo sapiens R-23 RRR RRR: RTS,S/AS01 012 NOT PROTECTED D14 Day 14 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596940 SRX3154677
GSM2769958 RNAseq-R-81_D6 Mal68.RNAseq Blood Homo sapiens R-81 RRR RRR: RTS,S/AS01 012 NOT PROTECTED D6 Day 6 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596939 SRX3154678
GSM2769959 RNAseq-A-135_D77 Mal68.RNAseq Blood Homo sapiens A-135 ARR ARR: Ad35.CS+RTS,S/AS01 01 PROTECTED D77 Day of Challenge/Day 21 post VAC3 Malaria_ExpressionData_RNAseqData.txt SAMN07596938 SRX3154679
GSM2769960 RNAseq-A-104_D14 Mal68.RNAseq Blood Homo sapiens A-104 ARR ARR: Ad35.CS+RTS,S/AS01 01 PROTECTED D14 Day 14 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596937 SRX3154680
GSM2769961 RNAseq-A-47_D14 Mal68.RNAseq Blood Homo sapiens A-47 ARR ARR: Ad35.CS+RTS,S/AS01 01 PROTECTED D14 Day 14 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596936 SRX3154681
GSM2769963 RNAseq-A-104_D56 Mal68.RNAseq Blood Homo sapiens A-104 ARR ARR: Ad35.CS+RTS,S/AS01 01 PROTECTED D56 Day 0 post VAC3/Day 28 post VAC2 Malaria_ExpressionData_RNAseqData.txt SAMN07596934 SRX3154683
GSM2769964 RNAseq-A-39_D57 Mal68.RNAseq Blood Homo sapiens A-39 ARR ARR: Ad35.CS+RTS,S/AS01 01 PROTECTED D57 Day 1 post VAC3 Malaria_ExpressionData_RNAseqData.txt SAMN07596933 SRX3154684
GSM2769965 RNAseq-A-139_D62 Mal68.RNAseq Blood Homo sapiens A-139 ARR ARR: Ad35.CS+RTS,S/AS01 01 NOT PROTECTED D62 Day 6 post VAC3 Malaria_ExpressionData_RNAseqData.txt SAMN07596932 SRX3154685
GSM2769967 RNAseq-R-140_D1 Mal68.RNAseq Blood Homo sapiens R-140 RRR RRR: RTS,S/AS01 012 NOT PROTECTED D1 Day 1 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596930 SRX3154687
GSM2769968 RNAseq-R-151_D56 Mal68.RNAseq Blood Homo sapiens R-151 RRR RRR: RTS,S/AS01 012 PROTECTED D56 Day 0 post VAC3/Day 28 post VAC2 Malaria_ExpressionData_RNAseqData.txt SAMN07596929 SRX3154688
GSM2769969 RNAseq-R-151_D28 Mal68.RNAseq Blood Homo sapiens R-151 RRR RRR: RTS,S/AS01 012 PROTECTED D28 Day 0 of VAC2/Day 28 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596928 SRX3154689
GSM2769970 RNAseq-A-83_D2 Mal68.RNAseq Blood Homo sapiens A-83 ARR ARR: Ad35.CS+RTS,S/AS01 01 NOT PROTECTED D2 Day 2 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596927 SRX3154690
GSM2769971 RNAseq-R-136_D28 Mal68.RNAseq Blood Homo sapiens R-136 RRR RRR: RTS,S/AS01 012 PROTECTED D28 Day 0 of VAC2/Day 28 post VAC1 Malaria_ExpressionData_RNAseqData.txt SAMN07596926 SRX3154691
GSM2769972 RNAseq-A-35_D0 Mal68.RNAseq Blood Homo sapiens A-35 ARR ARR: Ad35.CS+RTS,S/AS01 01 NOT PROTECTED D0 PreVAC Malaria_ExpressionData_RNAseqData.txt SAMN07596925 SRX3154692

Total number of rows: 2130

Table truncated, full table size 375 Kbytes.




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
GSE107672_CEL_files.tar.gz 2.4 Gb (ftp)(http) TAR
GSE107672_Malaria_ExpressionData_ArrayData.txt.gz 96.8 Mb (ftp)(http) TXT
GSE107672_Malaria_ExpressionData_RNAseqData.txt.gz 44.6 Mb (ftp)(http) TXT
Processed data are available on Series record
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