|
Status |
Public on Feb 07, 2018 |
Title |
control_Pro/pre-B_rep3 |
Sample type |
SRA |
|
|
Source name |
control_Pro/pre-B
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 tissue: Bone marrow cell type: B220+ enriched cells transduced with: GFP control 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
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|
|
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 |
SAMN07821413 |
SRA |
SRX3311867 |