|
| Status |
Public on Feb 28, 2020 |
| Title |
NRN1 WT eTreg |
| Sample type |
SRA |
| |
|
| Source name |
Nrn1+/- CD4+CD25+Cd62LlowCD44highFoxp3gfp+
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Nrn1+/-
cell type: eTreg cells
|
| Treatment protocol |
Sorting with FACSAria Fusion.
|
| Growth protocol |
Nrn1-/- and Nrn1+/- CD4+CD25+Cd62LlowCD44highFoxp3gfp+ were sorted from Nrn1-/- and Nrn1+/- mice on Foxp3DTRgfp background and subjected to RNASeq analysis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells stored in RNA protect before subject to RNA extraction.
Samples were sent to Admera Health for RNA extraction (RNeasy Mini Kit (QIAGEN)) and to process library construction and data analysis. Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A
mRNA
|
| Data processing |
Sequencing was performed on Illumina NextSeq500 with the type of paired-end, 76bp.
The quality of sequencing data were assessed by the software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The mapping to mouse reference genome of mm10 was conducted by TopHat.
Differentially-Expressed genes were called by Cuffdiff, and the normalized FPKM values were called by Cuffnorm.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_eTreg.txt: Tab-delimited text files include FPKM values.
|
| |
|
| Submission date |
Apr 29, 2019 |
| Last update date |
Feb 28, 2020 |
| Contact name |
Jinsong Yan |
| E-mail(s) |
yanjsdmu@dmu.edu.cn
|
| Organization name |
Dalian Medical University
|
| Department |
Institute of Cancer Stem Cell
|
| Street address |
9 west section, Lvshun south road, Dalian, Liaoning Province, China
|
| City |
Dalian |
| ZIP/Postal code |
116044 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE130470 |
RNASeq analysis of gene expression in effector Treg cells from Nrn1+/- and Nrn1-/- mice |
|
| Relations |
| BioSample |
SAMN11533718 |
| SRA |
SRX5767020 |
