|
| Status |
Public on May 05, 2010 |
| Title |
Tumor WT1_K4 |
| Sample type |
SRA |
| |
|
| Source name |
WT1-mutated Wilms tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: primary Wilms tumor
tumor region: blastemal compartments of Wilms tumor
mutation: WT1
chip antibody: H3K4me3
|
| Treatment protocol |
Frozen tissues corresponding to either sections of mature or fetal kidney, or to blastemal compartments of Wilms tumor were thawed and chopped into small fragments. Tissue fragments were crosslinked in 1% formaldehyde, quenched with glycine, washed and disaggregated into single cells using the 50mm medicones on the Medimachine (Beckon Dickinson) according to manufacturer’s protocol. Cells were then lysed and sonicated with a Branson 250 Sonifier to achieve a chromatin fragment size range from 200 to 700bp. Cell lysate was diluted 1:10 in ChIP dilution buffer and subjected to immunoprecipitation with respective antibodies against K4me3 (Abcam 8580), K27me3 (Upstate 07-449) or K36me3 (Abcam 9050). Whole cell lysate was retained for input control. All buffers were supplemented with protease inhibitor cocktail (Roche 14696200).
|
| Growth protocol |
Surgical samples of primary Wilms tumors, normal kidney, and fetal kidney were obtained from Boston Children’s Hospital. All samples were collected with institutional review board approval.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA samples were quantified using PicoGreen (Invitrogen), and three to ten nanograms were used to prepare sequencing libraries, as described (Mikkelsen et al., 2007). Libraries were loaded onto flow cells and sequenced on the Illumina Genome Analyzer using standard operating procedures.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
wig files (signal tracks): Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the human (March, 2006) genomes using MAQ. All reads mapping with two or fewer mismatches were retained. Reads with multiple best matches on the genome were discarded. Each read was extended in the direction of its strand out to 200bp, and with a fractional value of 0.25 between 200 and 300bps. Every 25pbs along the genome the number of overlapping tags was calculated. A value of -1 indicates locations for which signal cannot be obtained due to low complexity and the consequential multiple alignment hits for reads from that region.
|
| |
|
| Submission date |
Feb 25, 2010 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Noam Shoresh |
| E-mail(s) |
[email protected]
|
| Phone |
617-714-7907
|
| Organization name |
Broad Institute
|
| Department |
Epigenomics
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE20512 |
Chromatin Analysis of Wilms Tumor Highlights Stem Cell Properties and a Renal Developmental Network |
|
| Relations |
| BioSample |
SAMN02196199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM515645_Broad_WT1_K4_chr1.wig.gz |
1.1 Mb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr10.wig.gz |
650.3 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr11.wig.gz |
647.3 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr12.wig.gz |
656.6 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr13.wig.gz |
440.9 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr14.wig.gz |
432.6 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr15.wig.gz |
410.3 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr16.wig.gz |
409.2 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr17.wig.gz |
433.8 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr18.wig.gz |
354.3 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr19.wig.gz |
341.2 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr2.wig.gz |
1.1 Mb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr20.wig.gz |
318.4 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr21.wig.gz |
176.3 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr22.wig.gz |
193.6 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr3.wig.gz |
919.5 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr4.wig.gz |
823.9 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr5.wig.gz |
819.0 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr6.wig.gz |
804.7 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr7.wig.gz |
704.8 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr8.wig.gz |
668.1 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chr9.wig.gz |
544.2 Kb |
(ftp)(http) |
WIG |
| GSM515645_Broad_WT1_K4_chrX.wig.gz |
594.0 Kb |
(ftp)(http) |
WIG |
| Processed data provided as supplementary file |
