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Sample GSM2588486 Query DataSets for GSM2588486
Status Public on Jun 20, 2017
Title Total_brain_MG_LPS_WT_33
Sample type SRA
 
Source name Freshly isolated brain microglia
Organism Mus musculus
Characteristics strain: Cx3cr1CreER:Dicer+/-
tissue: brain
age (weeks): 10-12 weeks
transfer: CD45intCD11b+F4/80+Ly6C-Ly6G-
Extracted molecule total RNA
Extraction protocol oligo dT dynabeads
http://www.sciencemag.org/content/343/6172/776.abstract?ijkey=6c89f9e625c6efc35902e948462a6d1dad095f64&keytype2=tf_ipsecsha
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 6hr post LPS 1mg/Kg i.p
Figure 4 WT LPS 6hr
Data processing Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7
FastQ files were indexed and mapped for Mm9 genome assembly using HISAT 0.1.5
SAM files were converted to BAM using SAMtools
Gene count and normalization was done using Homer for Fig3 (analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7 ) and DESEQ2 (single factor) for all other tables
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
 
Submission date Apr 25, 2017
Last update date May 15, 2019
Contact name Steffen Jung
E-mail(s) s.jung@weizmann.ac.il
Phone 0097289342787
Organization name The Weizmann Institute of Science
Department Immunology and Regenerative Biology
Lab Steffen Jung
Street address Herzl
City REHOVOT
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL19057
Series (2)
GSE98142 Differential impact of Dicer deficiency on microglia of the developing and adult brain (Bulk RNA-Seq)
GSE98144 Differential impact of Dicer deficiency on microglia of the developing and adult brain
Relations
BioSample SAMN06828957
SRA SRX2762947

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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