|
| Status |
Public on May 08, 2020 |
| Title |
Arthritic mouse 4 [methylation] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
methylated DNA fraction by MIRA
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
gender: female
cell type: arthritic B cell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from naive and arthritic B cells by standard procedures by using proteinase K digestion, phenol chloroform extraction, and ethanol precipitation. Genomic DNA was fragmented by sonication and enrichment of methylated DNA fractions was conducted by MIRA method
|
| Label |
Cy5
|
| Label protocol |
According to the standard NimbleGen protocol
|
| |
|
| Channel 2 |
| Source name |
Input
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
sample type: input
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from naive and arthritic B cells by standard procedures by using proteinase K digestion, phenol chloroform extraction, and ethanol precipitation. Genomic DNA was fragmented by sonication and enrichment of methylated DNA fractions was conducted by MIRA method
|
| Label |
Cy3
|
| Label protocol |
According to the standard NimbleGen protocol
|
| |
|
| |
| Hybridization protocol |
According to NimbleGen kit
|
| Scan protocol |
Following NimbleScan's default using Agilent Scanner
|
| Description |
PGIA 4
The processed data is also provided as native .gff files
|
| Data processing |
Loes normalisation was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio
|
| |
|
| Submission date |
May 15, 2017 |
| Last update date |
May 08, 2020 |
| Contact name |
Tibor T Glant |
| E-mail(s) |
Tibor_Glant@rush.edu
|
| Organization name |
Rush University Medical Center
|
| Department |
Orthopedic Surgery
|
| Lab |
Molecular Medicine
|
| Street address |
1735 West Harrison
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL18360 |
| Series (1) |
| GSE98939 |
Autoimunne arthritis-associated B cell methylome in mice with proteoglycan (PG)-induced arthritis (PGIA) [methylation] |
|
