|
| Status |
Public on Mar 03, 2019 |
| Title |
WT_1_Non-TFH |
| Sample type |
SRA |
| |
|
| Source name |
WT SP-NonTFH
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Ets1 flox/flox
tissue: spleen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll, Korea)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
QC/adapter sequence trimming for raw FASTQ sequences: Raw read quality evaluation by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) with default options.
QC/adapter sequence trimming for raw FASTQ sequences: Adapter sequence trimming by CutAdapt (https://pypi.python.org/pypi/cutadapt)
Mapping on mouse reference genome: TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
Expression analysis by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options[4]
Expression and DEG analysis: DEG analysis by CuffDiff (http://cufflinks.cbcb.umd.edu) with significance thresholds as FDR<0.05, p<0.001, and p<0.01. Scatter plot and volcano plot by in-house R scripts. Unsupervised clustering by in-house R scripts
Genome_build: mm10
|
| |
|
| Submission date |
Feb 14, 2018 |
| Last update date |
Mar 03, 2019 |
| Contact name |
Chan Johng Kim |
| E-mail(s) |
cjkim@postech.ac.kr
|
| Organization name |
Institute for Basic Science / Pohang University of Science and Technology
|
| Street address |
Nam-Gu, Cheongam-Ro 77, POSTECH Biotech Center
|
| City |
Pohang |
| State/province |
Gyeongbuk |
| ZIP/Postal code |
37673 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE110595 |
Upregulation of TFH profile in absence of Ets1 expression |
| GSE110647 |
Ets1 suppresses the expression of key TFH genes to block TFH differentiation |
|
| Relations |
| BioSample |
SAMN08535934 |
| SRA |
SRX3699148 |
