|
| Status |
Public on Aug 21, 2019 |
| Title |
XX5 |
| Sample type |
SRA |
| |
|
| Source name |
Lymph node
|
| Organism |
Mus musculus |
| Characteristics |
strain: SJL
tissue: Lymph node
cell type: CD4+ T cell
Sex: Female
genotype: XX
|
| Treatment protocol |
Young mice (age 4-6 weeks) were gonadectomized (females: ovariectomy, males: castration). Prior to surgery and 24 hours after, the mice received 1.2 mg/mL Carprofen (Zoetis). The mice were given Amoxicillin (50 mg/mL, Virbac) as antibiodic in the water source for 7 days following surgery.
At 8 weeks of age, the mice were immunized with PLP 139-151 peptide (Mimotopes) emulsified in Complete Freund's adjuvant supplemented with mycobacterium tubercusosis H37Ra (Difco Laboratories) for 10 days.
|
| 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.
Lymph node cell suspensions were cultured at a concentration of 4x10^6 cells/mL in 24 well plates in complete RPMI medium with PLP 139-151 (25 ug/mL) for 36 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Auxillary, brahcial, and inguinal draning lymph nodes were collected and processed into single cell suspensions. The cells were cultured in the presence of autoantigen (PLP 139-151) for 36 hours. Cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
RNA from auto antigen specific CD4+ T cells
SJL.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: "SJL.CD4_rawcounts.xlsx" has count values for each Sample
|
| |
|
| Submission date |
Oct 23, 2018 |
| Last update date |
Aug 21, 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) |
| GSE121705 |
Sex chromsomes affect gene expression of autoantigen specific CD4+ T cells. |
|
| Relations |
| BioSample |
SAMN10283413 |
| SRA |
SRX4925983 |
