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Sample GSM3476857 Query DataSets for GSM3476857
Status Public on Dec 31, 2018
Title Lrp5/6 dKO rep2
Sample type SRA
 
Source name CD34-Flt3- Lin-ScaI+C-Kithigh cells
Organism Mus musculus
Characteristics tissue: Bone marrow
age: 8 weeks
genotype: Vav-cre;Lrp5 fl/fl Lrp6 fl/fl
Treatment protocol CD34-Flt3- LSK cells were sorted with a BD AriaII directly into Trizol reagent
Growth protocol CD34-Flt3- LSK were isolated by cell sorting from WT or Lrp5/6 double deficient mice
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 6K CD34-Flt3- Lin-ScaI+C-Kithigh cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
Libraries are constructed according to the standard protocol for Smart-seq2 
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing FastQC version 0.11.5 was used to identify features of the raw data that may indicate quality problems
Low quality bases were removed using Trimmomatic
Reads were mapped to the mouse reference genome (mm9) with Tophat2 version 2.1.1. and post-processed with RSEM version 1.2.31. Default parameter settings were used for alignment
The uniquely mapped reads were assigned to genes using Htseq
The fold change and p-value of all the detected genes were estimated by DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: txt format. Read counts for each gene and TPM for each gene
 
Submission date Nov 16, 2018
Last update date Jan 01, 2019
Contact name Shuyang Yu
E-mail(s) ysy@cau.edu.cn
Organization name China Agricultural University
Department College of Biological Sciences
Street address 2 Yuanmingyuan West Road
City Beijing
ZIP/Postal code 100193
Country China
 
Platform ID GPL21273
Series (1)
GSE122635 LRP5 and LRP6 are required for maintaining self-renewal and differentiation of hematopoietic stem cells
Relations
BioSample SAMN10437005
SRA SRX5020225

Supplementary file Size Download File type/resource
GSM3476857_dKO2_TPM.txt.gz 312.3 Kb (ftp)(http) TXT
GSM3476857_dKO2_raw_counts.txt.gz 269.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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