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Sample GSM1190811 Query DataSets for GSM1190811
Status Public on Jun 11, 2014
Title Tnfr_KO_LPS_4h_S18
Sample type SRA
 
Source name BMDC (Tnfrsf1a-/- x Tnfrsf1b-/-, 4h LPS stimulation)
Organism Mus musculus
Characteristics strain: B6;129S
cell type: BMDC
stimulation: Tnfrsf1a-/- x Tnfrsf1b-/-, 4h LPS stimulation
Growth protocol Cells were cultured and stimulated as previously described (Amit et. al 2009)
Extracted molecule polyA RNA
Extraction protocol cDNA from each sample was prepared using the SMARTer cDNA synthesis (Clontech). RNA libraries were prepared for sequencing using Nextera XT (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Tnfr_KO_LPS_4h_S18
Data processing We created a Bowtie index based on the UCSC knownGene (8) transcriptome, and aligned paired-end reads directly to this index using Bowtie v 0.12.7 with command line options -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -a -m 200.
Next, we ran RSEM v1.11 with default parameters on these alignments to estimate expression levels. RSEM’s gene level expression estimates (tau) were multiplied by 1,000,000 to obtain transcript per million (TPM) estimates for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: matrix of gene expression estimates across all samples
 
Submission date Jul 17, 2013
Last update date May 15, 2019
Contact name Rahul Satija
E-mail(s) rsatija@nygenome.org
Phone 6177022468
Organization name New York Genome Center
Lab Satija Lab
Street address 101 Avenue of the Americas
City New York City
State/province NY
ZIP/Postal code 10013
Country USA
 
Platform ID GPL17021
Series (1)
GSE48968 Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
Relations
BioSample SAMN02258132
SRA SRX325588

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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