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Sample GSM2519933

Query DataSets for GSM2519933

Status

Public on Nov 02, 2018

Title

BM - WT - 1

Sample type

SRA

Source name

macrophages

Organism

Mus musculus

Characteristics

tissue: bone marrow
genotype: wild type
strain: fvb

Treatment protocol

Mice were injected with 2ml of Thoglycolalte i.p.. Bones and peritoneal levage was conduceted 6 hours after injection.

Extracted molecule

total RNA

Extraction protocol

Cells were extracted from the peritoneal cavity and bone marrow of each mouse in PBS and 5mM EDTA. These cells were FACS sorted directly into Trizol prior to total RNA extraction with chloroform and purification with the Qiagen RNEasy MinElute Cleanup Kit
For library preparation we used the NEBNext Ultra RNA Library Prep Kit for Illumina, using Illumina TruSeq Adapters for barcoding. Depending on the concentration of adaptor-ligated cDNA, as determined by Qubit quantitation, 6-15 PCR cycles were carried out to amplify the libraries.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

altanalyze version 2.0 was used to handle all processing of RNAseq samples
used standard program settings for RNASeq and Mus Musculus for Processing of RNA-Seq reads of the FASTA files
use multithreading for read genomic annotation, removed genes with RPKM less than 1, used Benjamini-Hochberg false discovery rate statistic.

Submission date

Mar 02, 2017

Last update date

May 15, 2019

Contact name

Kristopher David Marjon

E-mail(s)

[email protected]

Organization name

Stanford

Department

ISCBRM