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Series GSE110684 Query DataSets for GSE110684
Status Public on Feb 15, 2019
Title Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We investigate the role of resident memory T cells in protective immunity in HIV infection

Funding sources:

Michael R. Betts: NIH/NIAID R01 AI076066 and R01 AI118694

Marcus Buggert: Swedish Research Council (Dnr 537-2014-6829), Karolinska Institutet, Magnus Bergvall and Lars Hiertas Stiftelse

 
Overall design Examination of resident memory T cell transcriptome and chromatin accessibility in lymph nodes. Examination of single-cell transcriptome and T cell receptor sequences of HIV-specific resident memory CD8+ T cells in lymph nodes.
Bulk RNASeq and ATAC-Seq were performed on CD69+ and CD69- CD8+ T cells from human lymph nodes. Single cell RNASeq was performed on CD69+ and CD69- CD8+ T cells from human mesenteric lymph nodes.

 
Contributor(s) Betts M
Citation(s) 29858286, 31852798
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AI076066 T cell functionality and control of HIV infection UNIVERSITY OF PENNSYLVANIA Michael R. Betts
R01 AI118694 Viral control mechanisms of HIV-specific T cells in HIV-infected lymph node UNIVERSITY OF PENNSYLVANIA Michael R. Betts
Submission date Feb 15, 2018
Last update date Jun 08, 2020
Contact name Marcus Buggert
E-mail(s) marcus.buggert@ki.se
Organization name Karolinska Institutet
Department Microbiology
Street address C2:94; Karolinska Universitetssjukhuset Huddinge
City Stockholm
State/province PA
ZIP/Postal code 141 86
Country Sweden
 
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (217)
GSM3011764 A8: LN1 CD69+ RNA-seq
GSM3011765 A9: LN1 CD69- RNA-seq
GSM3011766 B8: LN2 CD69+ RNA-seq
Relations
BioProject PRJNA434272
SRA SRP132938

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
GSE110684_CD69_RNAseq_counts.txt.gz 419.2 Kb (ftp)(http) TXT
GSE110684_EC_CD69_count.csv.gz 704.0 Kb (ftp)(http) CSV
GSE110684_Normalized_LN_EC_CP.csv.gz 1.5 Mb (ftp)(http) CSV
GSE110684_RAW.tar 1.1 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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