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Sample GSM814838 Query DataSets for GSM814838
Status Public on May 03, 2012
Title Nucleoplasmic_15min
Sample type SRA
Source name Macrophage
Organism Mus musculus
Characteristics strain: C57BL/6
subcellular fraction: Nucleoplasmic
stimulation time: 15 minutes
stimulation type: Lipid A
Treatment protocol Lipid A was added at a concentration of 100ng/ml to each 25 cm plate for the times indicated.
Growth protocol Bone marrow from mixed sex mice were plated at a density of 7x10^5 cells/ml into DMEM containing 20% FBS supplemented with sodium pyruvate, L-glutamine and M-CSF. Media was changed on day three of differentiation. Adherent cells were scraped and replated at a density of 1x10^6 cells/mL into 15 cm plates on day five of differentiation. Cells were stimulated on day six.
Extracted molecule total RNA
Extraction protocol Cells were fractionated according to the protocol described in Pandya-Jones and Black, RNA 2009. Briefly, cells were lysed in 0.15% NP40 buffer and spun over a sucrose cushion to obtain nuclei. Nuclei were lysed in buffer containing 1% NP40 and 1M urea. RNA from the cytoplasmic and nucleoplasmic lysates as well as the chromatin pellet was purified using Qiagen RNeasy columns according to manufacturer protocol. 10 ug of RNA from each sample was depleted of ribosomal RNA using the Invitrogen Human/Mouse Ribominus kit. Libraries were constructed from 500 ng of rRNA-depleted RNA using the dUTP method described in Levin et al, Nat Methods 2010 was used to generate strand-specific sequencing libraries.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing BAM: Sequence reads were obtained and mapped to the mouse mm9 genome using Tophat. Uniquely mapping reads with two or fewer mismatches were retained.
Submission date Oct 12, 2011
Last update date Jan 25, 2024
Contact name Allison Daly
Organization name UCLA
Department MIMG
Lab Smale Lab
Street address 6-730 MRL 675 Charles E. Young Drive South
City Los Angeles
State/province Ca
ZIP/Postal code 90024
Country USA
Platform ID GPL13112
Series (1)
GSE32916 Analysis of Pro-Inflammatory Gene Activation and RNA Processing by RNAseq of Nascent Transcripts I
SRA SRX100833
BioSample SAMN00738690

Supplementary file Size Download File type/resource
GSM814838_N2.bam 1.4 Gb (ftp)(http) BAM
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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