|
| Status |
Public on May 28, 2009 |
| Title |
CdLS patient PT3 |
| Sample type |
RNA |
| |
|
| Source name |
Lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
Gender: Female
Age, year: 0
Genotype: c.1444_1447delAGAG / Frameshift
disease_severity = Severe
Picture_availability = No
Chart_Ref.: CDL-198-04P
|
| Treatment protocol |
Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction
|
| Growth protocol |
Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction
|
| Label |
biotin
|
| Label protocol |
Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.
|
| |
|
| Hybridization protocol |
Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
|
| Description |
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian
|
| Data processing |
CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization
|
| |
|
| Submission date |
Aug 11, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
IAN D. KRANTZ |
| E-mail(s) |
ian2@mail.med.upenn.edu
|
| Phone |
215-590-2828
|
| Organization name |
The Children's Hospital of Philadelphia
|
| Department |
Division of Human and Molecular Genetics
|
| Lab |
1012G, ARC
|
| Street address |
34th and Civic Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE12408 |
Defective Cohesin in CdLS Mediates Gene Expression with Characteristics of Transcription Factor and Insulator Activity |
|
| Relations |
| Reanalyzed by |
GSE119087 |
