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Sample GSM3554175 Query DataSets for GSM3554175
Status Public on Feb 11, 2019
Title BM_CD69pos_2
Sample type SRA
 
Source name Isolated from BM of LCMV-primed C57BL/6 mice, 60 days after last immunization
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: male
age: 8 weeks
tissue: bone marrow
cell type: CD69+ LCMV-specific CD4 memory T cells
Growth protocol Eight week old C57BL/6 male mice were immunized intraperitoneally (i.p.) with 100 μg poly(I:C) and LCMV GP61-80 coupled to murine serum albumin (MSA) and 4-Hydroxy-3-nitrophenylacetyl (NP) . Two weeks after priming, mice were immunized i.p. again with 100 μg poly(I:C) and 100 μg uncoupled LCMV GP61-80. 60 days after the last immunization, cells were isolated from BM and spleen.
Extracted molecule total RNA
Extraction protocol Total RNA was purified with miRNeasy Micro Kit (Qiagen) from FACS sorted LCMV-specific CD4 memory T cells isolated from spleen and bone marrow. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
For poly-A dependent cDNA synthesis and a first amplification step the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) was used. After quality control (High sensitivity DNA Kit, Agilent) and concentration measurement (Qubit dsDNA HS Assay Kit, Invitrogen), 150 pg of the purified cDNA was used for tagmentation and library completion with the Nextera XT library preparation kit (Illumina). In the following, 2x75 nucleotides paired-end sequencing was performed on a NextSeq 500 using a mid-output flow cell.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description F_S6
CD69+ LCMV-specific CD4 memory T cells, isolated from BM of LCMV-primed C57BL/6 mice, 60 days after last immunization
Data processing Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.
 
Submission date Jan 08, 2019
Last update date Feb 11, 2019
Contact name Pawel Durek
E-mail(s) pawel.durek@drfz.de
Organization name Deutsches Rheuma-Forschungszentrum
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL19057
Series (2)
GSE124794 Whole-transcriptome profiling of LCMV.GP66-77 specific CD4 T cells isolated from bone marrow (BM) and spleen, 60 days after last immunization [RNA-seq]
GSE124796 CD69+ memory T lymphocytes of the bone marrow and spleen express the signature transcripts of tissue-resident memory T lymphocytes
Relations
BioSample SAMN10713682
SRA SRX5227087

Supplementary file Size Download File type/resource
GSM3554175_BM_CD69pos_2.txt.gz 134.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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