|
| Status |
Public on Feb 07, 2018 |
| Title |
iDN3 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Induced 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 |
iDN3 rep3
|
| 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 |
SAMN06200124 |
| SRA |
SRX2459967 |
