|
| Status |
Public on Oct 18, 2019 |
| Title |
WT19 |
| Sample type |
SRA |
| |
|
| Source name |
Lymph node
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Lymph node
cell type: CD4+ T cell
Sex: Female
genotype: WT
floxed allele: floxed/floxed Kdm6a
cre: CD4-Cre (-/-)
|
| Growth protocol |
Animals were maintained under standard conditions in a 12 h dark/12 h light cycle with access to food and water ad libitum.
CD4-specific Kdm6a-/- or Kdm6a-/y mice (cKO) were generated by crossing Kdm6af/f-CD4-Cre females with Kdm6af/y males.
Lymph node cell suspensions were cultured at a concetnration of in complete RPMI medium with MOG 35-55 (25 ug/mL) for 18 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification was performed using the Direct-zol™ RNA MicroPrep Plus kit following manufacturer’s instructions (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
RNA from auto antigen specific CD4+ T cells
Kdm6a.CD4_rawcounts.xlsx
|
| Data processing |
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "Kdm6a.CD4_rawcounts.xlsx" has count values for each Sample
|
| |
|
| Submission date |
Oct 23, 2018 |
| Last update date |
Oct 18, 2019 |
| Contact name |
Yuichiro Itoh |
| E-mail(s) |
yitoh@ucla.edu
|
| Phone |
3102068999
|
| Organization name |
UCLA
|
| Department |
Neurology
|
| Street address |
635 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE121703 |
The X chromosome gene Kdm6a modulates multiple immune response genes in CD4+ T cells and is disease promoting in autoimmune disease |
|
| Relations |
| BioSample |
SAMN10283391 |
| SRA |
SRX4925979 |
