|
| Status |
Public on Oct 30, 2012 |
| Title |
LaminA ChIP, HGPS, p16, INPUT, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
patient forearm skin biopsy, input
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: Hutchinson-Gilford progeria syndrome
tissue: forearm skin biopsy
cell type: fibroblasts
gender: male
cell line: HGADFN167
passage: 16
chip antibody: none
|
| Treatment protocol |
Cells were grown to confluency and then crosslinked in 1% formaldehyde.
|
| Growth protocol |
Primary human dermal fibroblasts were cultured in MEM (Invitrogen/GIBCO) supplemented with 15% fetal bovine serum (FBS) (Invitrogen) and 2 mM L-glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells and nuclei were lysed, and then chromatin was sonicated on ice for 12 times 20 seconds at 30% amplitude with a microtip attached to a Branson 450 sonifier. Immunoprecipitations were performed overnight with 15-25 μg of antibody (mouse anti-H3K27me3 [Abcam ab6002], mouse anti-lamin A/C [Millipore MAB3211], goat anti-lamin A/C N18) coupled to Dynal Protein G Magnetic Beads. Beads were washed 5 times in RIPA buffer and 1 time in ice-cold PBS. DNA was eluted in Elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1.0% SDS).
DNA was prepared for sequencing as recommended by Illumina/Solexa 1G.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
LaminA-HGPS-p16-R1-INPUT
HGPS patient.
|
| Data processing |
DNA fragments were sequenced by the Illumina Genome Analyzer 1G and aligned to the hg18 genome assembly using ELAND.
We removed reads that mapped to satellite repeat regions as defined in hg18. To avoid PCR amplification artifacts, we applied a stringent filter to remove duplicated reads by allowing only one mapped read at any position in the genome in one direction.
Genome_build: hg18
Supplementary_files_format_and_content: .bed files contain mapped sequence reads that are filtered as described above.
|
| |
|
| Submission date |
Oct 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Rachel Patton McCord |
| E-mail(s) |
[email protected]
|
| Phone |
508-856-4377
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Gene Function and Expression
|
| Lab |
Job Dekker Lab
|
| Street address |
364 Plantation St. LRB 570M
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE41757 |
Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome (ChIP-seq) |
| GSE41764 |
Correlated alterations in genome organization, histone methylation, and DNA-lamina interactions in Hutchinson-Gilford progeria syndrome |
|
| Relations |
| SRA |
SRX200051 |
| BioSample |
SAMN01774264 |
