|
| Status |
Public on May 30, 2018 |
| Title |
T143-B |
| Sample type |
SRA |
| |
|
| Source name |
Foxp3-positive CD4-positive T cells isolated from T143 mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain/genotype: NOD-Foxp3GFP-Rag1-/-
cell type: T-cell
cd4 status: positive
foxp3 status: positive
model: T143
derivation: nuclear transfer
|
| Treatment protocol |
no treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Foxp3-positive and CD4-positive T cells were FACS-sorted and RNA was isolated using RNA Nucleospin XS kit, treated with Dnase (Machery-Nagel)
RNA was processed into RNA-Seq libraries using Truseq Stranded mRNA-Seq sample prep kit(Illumina) following manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
supplementary file column: T14312_Fplus
Replicate 2 of T143 T cell
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were quality filtered and adapter trimmed using bbmap v36.27 with the following options: ktrim=r k=28 mink=13 hdist=1, minlen=25.
Filtered reads were aligned to the moue genome using RNA-STAR v2.5.2b with the following options: --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1
Reads were quanitifed using Homer v4.8 using the analyzeRepeats.pl script with the following options: -count exons -strand - -condenseGenes
Normalized abundance calculated from EdgeR called by Homer v4.8 using the script getDiffExpression.pl
Genome_build: mm10
Supplementary_files_format_and_content: Tab deliminated text file of the matrix table encompassing normalized abundance measurements from EdgeR for each sample (column) of each gene (row)
|
| |
|
| Submission date |
Apr 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Manching Ku |
| Organization name |
Medical Center - University of Freiburg
|
| Department |
Hematology and Oncology
|
| Street address |
Mathildenstrasse 1
|
| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE97848 |
Deconstructive SCNT reveals heterogeneity within Treg population [bulk] |
| GSE97850 |
Deconstructive SCNT reveals heterogeneity within Treg population |
|
| Relations |
| BioSample |
SAMN06758735 |
| SRA |
SRX2741444 |
