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Sample GSM1617048 Query DataSets for GSM1617048
Status Public on Mar 31, 2015
Title Mecp2-null Microglia #1
Sample type SRA
Source name Microglia
Organism Mus musculus
Characteristics age: 10-12wk
genotype: Mecp2-null
cell type: Acutely isolated microglia
Extracted molecule total RNA
Extraction protocol Cells were acutely isolated from mouse tissues and sorted via AutoMACS prior to RNA isolation. Qiagen Rneasy mini kit (Cat #74106) was used per manufacturer's protocol for RNA isolation.
RNA-Seq Poly A selection using NEBNext library prep modules
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Mecp2-null microglia, 3 pooled mice 10-12wks old
Data processing Basecalls performed using CASAVA
Data were aligned to the mm9 genome using STAR version 2.3.0
Aligned reads were counted against genes from the UCSC mm9 annotation using the htseq-count python library
Data were normalized for library size using the DESeq2 median ratio normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R.
Genome_build: mm9
Supplementary_files_format_and_content: Counts of reads aligning to genes from the mm9 annotation as output from htseq-count
Submission date Feb 23, 2015
Last update date May 15, 2019
Contact name Stephen Turner
Organization name Signature Science, LLC
Street address 1670 Discovery Drive
City Charlottesville
State/province VA
ZIP/Postal code 22911
Country USA
Platform ID GPL13112
Series (2)
GSE66211 Mecp2: an unexpected regulator of macrophage gene expression and function [RNA-Seq]
GSE66502 Mecp2: an unexpected regulator of macrophage gene expression and function
BioSample SAMN03366532
SRA SRX886154

Supplementary file Size Download File type/resource
GSM1617048_SL44398_KO_Mg_10wk_Mid_counts.txt.gz 97.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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