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Sample GSM1048201 Query DataSets for GSM1048201
Status Public on Sep 27, 2013
Title Resting B cells Replicate 1
Sample type SRA
Source name CD43 negative mouse resting B cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: wild type
developmental stage: adult
tissue: Spleen
cell type: CD43 negative mouse resting B cells
Treatment protocol Resting B cells were isolated from the spleens of adult mice. The spleens were dissected and minced on sieves and the single-cell suspensions were centrifuged on a Ficoll-Paque cushion to remove erythrocytes and dead cells. The resulting splenocytes were resuspended at a concentration of 10^7 cells/ml in 0.1% BSA/HBSS supplemented with 5% goat serum and anti-CD16 antibody. The cells were firstly incubated with biotinylated anti-CD43 antibody and then with Dynabeads Biotin Binder beads to capture CD43+ cells. Bound CD43+ cells were removed by 4 sequential magnetic separations. The remaining population of CD43- cells was cultured at a concentration of 2-5x10^6 cells/ml.
Growth protocol RPMI, 15% foetal calf serum, 0.1 U/mL penicillin, 0.1 μg/mL streptomycin, 2 mM L-Glutamine, 50 μM beta-mercaptoethanol, 6 ng/ml IL-4
Extracted molecule total RNA
Extraction protocol Cell lysates were homogenized using QIAshredder spin columns (Qiagen). Total RNA was purified with RNeasy Mini Kit (Qiagen), eluted in 30 μl of DEPC-treated water and quantified on an ND-1000 spectrophotometer. mRNA-seq libraries were prepared using 2 μg of total RNA purified as previously described. A total of four libraries were prepared for four independent biological replicates. Libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina) according to the manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Expression profiling of Quiescent B-cells
Data processing RNA-seq sequencing reads were aligned to mm9 using Tophat version 1.4.1 with default parameters. Gene coordinates from Ensembl version 64 was used as known gene model
FPKM values for each sample was estimated using Cufflinks version 1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values
Submission date Dec 04, 2012
Last update date May 15, 2019
Contact name Gopuraja Dharmalingam
Organization name MRC London Institute of Medical Sciences
Department Epigenetics section
Street address Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
Platform ID GPL13112
Series (2)
GSE42704 The Aurora B kinase and the polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes [RNA-Seq]
GSE42706 The Aurora B kinase and the polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes
SRA SRX208219
BioSample SAMN01822817

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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