|
| Status |
Public on Oct 01, 2021 |
| Title |
Th1_KO_2_1 |
| Sample type |
SRA |
| |
|
| Source name |
Splenocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Junbfl/flCd4cre
polarizing condition: Th1
cell type: Naive CD4+ T cells
|
| Treatment protocol |
For RNA-Seq, polarized cells were first stained by Zombie-NIR and viable cells were sorted by FACS. Typically, 2e+5 cells were used for one RNA-seq. For ChIP-Seq, 1e+6 cells were directly collected.
|
| Growth protocol |
Naïve CD4+ T cells were isolaated from mice spleen and cultured under Th0, Th1 and Th2 conditions for 48h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq: QIAGEN RNAeasy. ChIP-Seq: Cell signaling SimpleChIP Plus Enzymatic Chromatin IP Kit (9005S; Cell Signaling)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
all raw reads were trimmed by Cutadapt 2.10.
RNA-Seq: trimmed reads were then directly mapped to the UCSC mouse genome mm10, and transcripts were quantified with Salmon 1.3.0 using default settings (k = 31).
RNA-Seq: After transcript quantification, raw feature counts of each transcript were first normalized within and between samples to obtain TPM (Transcripts Per kilobase Million). conducted with DeSeq2
RNA-SEQ: Differential gene expression analysis was analyzed by DESeq2
ChIP-Seq: Trimmed reads were then mapped to mouse genome mm10 by calling Bowtie2 2.3.4.3 in TopHat2 2.1.1
ChIP-Seq: Peaks were called for each sample replicate using Homer 4.11 with default parameters (FDR < 0.001)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq: csv files include log2FC, pvalue, qvalue for each T helper cell subset
Supplementary_files_format_and_content: ChIP-Seq: bed files include peak annotation for each antibody
|
| |
|
| Submission date |
Apr 21, 2021 |
| Last update date |
Oct 01, 2021 |
| Contact name |
Hiroki Ishikawa |
| E-mail(s) |
oist.ishikawa@gmail.com
|
| Organization name |
Okinawa Institute of Science and Technology Graduate University
|
| Street address |
1919-1 Tancha
|
| City |
Onna son |
| State/province |
Okinawa |
| ZIP/Postal code |
9040495 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE172490 |
JunB regulates the common and lineage-specific transcriptional programs of distinct CD4+ effector T cells |
|
| Relations |
| BioSample |
SAMN18821665 |
| SRA |
SRX10652544 |
