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Sample GSM2827710 Query DataSets for GSM2827710
Status Public on Feb 07, 2018
Title Hoxb5_Pro/pre-B_rep7
Sample type SRA
 
Source name Hoxb5_Pro/pre-B
Organism Mus musculus
Characteristics strain background: C57BL/6
tissue: Bone marrow
cell type: B220+ enriched cells
transduced with: Hoxb5 virus
transduced with: Pro/pre-B cells
Treatment protocol 1000 Hoxb5 or control transduced Pro-/pre-B cells were sorted for RNAseq analysis.
Growth protocol All mice in this study were kept in C57BL/6J backgroud. B220+ enriched cells from bone marrow, and then transduced with Hoxb5 virus or GFP control virus in vitro.
Extracted molecule polyA RNA
Extraction protocol The procedure of RNA extraction and reverse transcription into double-stranded DNA is based on published methods(PMID:20203668).
Libraries were prepared according to Illumina's instructions accompanying the illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.bt2 files to generate accepted_hits.bam file by tophat, and the used cuffquant scripts (cufflinks-2.2.1) to calculated genes expression level.
Gene expression levels of different samples were normalized by cuffnorm scripts (cufflinks-2.2.1), and finally generated genes.fpkm_table
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_table was generated by cuffnorm; gene expression value
 
Submission date Oct 22, 2017
Last update date May 15, 2019
Contact name Yong Dong
E-mail(s) dongyong@cmc.edu.cn
Organization name Chengdu medical college
Department Immunology
Street address Xindu road 783, Xindu district
City chengdu
State/province sichuan
ZIP/Postal code 610500
Country China
 
Platform ID GPL19057
Series (2)
GSE105057 Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes
GSE105768 Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes [RNA-seq2]
Relations
BioSample SAMN07821401
SRA SRX3311879

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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