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Status |
Public on Feb 11, 2019 |
Title |
BM_CD69pos_3 |
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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
H_S8 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.
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|
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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 |
SAMN10713680 |
SRA |
SRX5227089 |