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Sample GSM2443944 Query DataSets for GSM2443944
Status Public on Feb 07, 2018
Title DN3 rep2
Sample type SRA
 
Source name Double negative cells_phase3
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Thymus
Treatment protocol Target cells were sorted from the bone marrow or the thymus of recipients.
Growth protocol All mice in this study were kept in C57BL/6J backgroud. Pro-/pre B cells were sorted from bone marrow, and then infected with Hoxb5 virus in vitro. After the infection, Hoxb5 transduced Pro-/pre-B cells were sorted and transplanted into sublethal irradiation recipients.
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
 
Description DN3 rep2
Data processing Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to NCBIM37 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: NCBIM37
Supplementary_files_format_and_content: fpkm_table was generated by cuffnorm
 
Submission date Jan 04, 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)
GSE93107 Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes [RNA-Seq]
GSE105057 Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes
Relations
BioSample SAMN06200089
SRA SRX2459943

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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