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| Status |
Public on May 28, 2018 |
| Title |
SPLEEN_LT4_EE_6_29 |
| Sample type |
SRA |
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| Source name |
SPLEEN_LT4_EE_6_29
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| Organism |
Mus musculus |
| Characteristics |
cell type: LT4
environment (se: standard; ee=enriched): EE
tissue: spleen
animal id: 6
number of cells: 29
strain: C57BL6/J
Sex: female
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| Treatment protocol |
Mice were exposed to an enriched environment (EE) starting 4 weeks after birth (i.e. at weaning) for a 4 weeks period. 12-15 age-matched mice were housed in large-sized cages (9120 cm2; L x l x h: 120 x 76 x 21 cm) with nesting material, houses, running wheels, hammocks, scales, plastic toys and tunnels. Objects were changed twice a week. Mice in standard conditions (SE) were housed in medium sized cages (666 cm2; L x l x h: 36 x 18.5 x 14 cm) with 5-6 mice/cage without objects. All mice had access to tap water and standard lab chow (diet SAFE A04, 2900 kcal/kg) ad libitum and were housed on a 12 hr light/12 hr dark cycle at 22-23°C with 40-60% humidity. The animals analyzed for each experiment raised either in SE or EE came from the same cage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted cells were directly collected into 0.2ml tube stripes in a lysis reaction with a final volume of 13.5 µl according to Arguel et al (Arguel, NAR 2017).
Template switching oligonucleotide (TSO) was design as in Picelli et al., with a LNA in 3 prime extremity 5’-GCA ATG AAG TCG CAG GGT TGN NNN HHH HrGrG lnG-3’.
Barcoded cDNA were pooled and 20 ng used as template for Ion Proton sequencer tagmentation protocol as described in Arguel et al (Arguel et al., 2017).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
EE6.LT4.29
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| Data processing |
Adaptators were removed using cutadapt, then reads which did not have the proper UMI construction (N4H4 followed by GGG) or with less than 50 bases were discarded.
Mapping was performed with STAR_2.4.0a versus mm10
UMI counts were obtained using the Dropseq Core Computational Protocol version 1.0.1 (dropseq.jar) from McCarrol (Macosko et al., 2015) using GTF gene model from Ensembl release GRCm38.83. DigitalExpression function of dropseq.jar was called with default parameters (edit distance=1) to produce matrix of molecule counts which was used in subsequent statistical analysis.
Low UMI count genes were filtered out.
Normalisation was performed using R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of normalized UMI counts for genes in row, and samples in columns.
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| Submission date |
Jun 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
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| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
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| Street address |
660 route des lucioles
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| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE100584 |
Comparison of CD4+ and CD8+ T cells from spleen of mice raised in standard or in enriched environment. |
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| Relations |
| BioSample |
SAMN07286000 |
| SRA |
SRX2962824 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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