|
| Status |
Public on Jul 07, 2015 |
| Title |
damNKX2-5YRD^(Y-A) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
dam-NKX2-5YRD^(Y-A) DamID DNA from HL1 cells (experiment #3)
|
| Organism |
Mus musculus |
| Characteristics |
cell line: HL-1 cardiomyocyte
treatment: dam-NKX2-5YRD^(Y-A)
|
| Treatment protocol |
HL-1 cells were transduced for 18 hours with Dam fusions and then cultered for another 23 hours before extraction
|
| Growth protocol |
HL-1 cells were grown in Claycomb medium, 10% FBS, 0.1mM Norepinephrine and 2mM L-Glutamine at 37°C in an atmosphere of 5% CO2 at a relative humidity of ~95%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Gentra PureGene (Qiagen) following manufacturers instructions, digested by DpnI, LM-PCR amplified and fragemented with DNaseI
|
| Label |
biotin
|
| Label protocol |
Fragmented double-stranded DNA was end labelled with biotin according to manufacturers instructions.
|
| |
|
| Channel 2 |
| Source name |
dam-ONLY DamID DNA from HL1 cells (experiment #2)
|
| Organism |
Mus musculus |
| Characteristics |
cell line: HL-1 cardiomyocyte
treatment: control
|
| Treatment protocol |
HL-1 cells were transduced for 18 hours with Dam fusions and then cultered for another 23 hours before extraction
|
| Growth protocol |
HL-1 cells were grown in Claycomb medium, 10% FBS, 0.1mM Norepinephrine and 2mM L-Glutamine at 37°C in an atmosphere of 5% CO2 at a relative humidity of ~95%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Gentra PureGene (Qiagen) following manufacturers instructions, digested by DpnI, LM-PCR amplified and fragemented with DNaseI
|
| Label |
biotin
|
| Label protocol |
Fragmented double-stranded DNA was end labelled with biotin according to manufacturers instructions.
|
| |
|
| |
| Hybridization protocol |
7.5μg of fragmented, biotin labelled DNA was hybridized to each array. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The arrays were washed according to manufacturers instructions on an Affymetrix FS450 fluidics station.
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner GC3000 7G
|
| Description |
dam-NKX2-5YRD^(Y-A) DamID Biological Rep 1-4, promoter
|
| Data processing |
Probe remapping to NCBI Build 37 (mm9) was performed using the Starr R package. Data was quantile normalized and analyzed with TileMapv2 implemented in cisGenome. TileMapv2 moving average (ma) >3.5 and a minimum of 8 probes were used as thresholds for contrasting inputs versus controls. Statistics are reported in the COD files.
DamID.bed
.cod are generated by CisGenome software and summarises binding regions detected and summary statistics. File DamID.bed contains all binding regions (18,505 peaks) detected for each C/N-terminal fusion as reported in the paper; this file has been prepared for uploading into the UCSC genome browser.
|
| |
|
| Submission date |
Feb 14, 2014 |
| Last update date |
Jul 07, 2015 |
| Contact name |
Ashley Waardenberg |
| E-mail(s) |
a.waardenberg@gmail.com
|
| Organization name |
Children's Medical Research Institute
|
| Lab |
Waardenberg
|
| Street address |
214 Hawkesbury Road
|
| City |
Westmead |
| State/province |
NSW |
| ZIP/Postal code |
2145 |
| Country |
Australia |
| |
|
| Platform ID |
GPL5811 |
| Series (1) |
| GSE44902 |
NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1328467_RB_AW01_control.CEL.gz |
19.5 Mb |
(ftp)(http) |
CEL |
| GSM1328467_RB_AW02_control.CEL.gz |
19.6 Mb |
(ftp)(http) |
CEL |
| GSM1328467_RB_AW03_control.CEL.gz |
19.7 Mb |
(ftp)(http) |
CEL |
| GSM1328467_RB_AW04_control.CEL.gz |
19.6 Mb |
(ftp)(http) |
CEL |
| GSM1328467_RB_AW09.CEL.gz |
19.2 Mb |
(ftp)(http) |
CEL |
| GSM1328467_RB_AW10.CEL.gz |
19.3 Mb |
(ftp)(http) |
CEL |
| GSM1328467_RB_AW11.CEL.gz |
19.5 Mb |
(ftp)(http) |
CEL |
| GSM1328467_RB_AW12.CEL.gz |
20.1 Mb |
(ftp)(http) |
CEL |
| GSM1328467_damNKX2-5YRD.cod.gz |
41.0 Kb |
(ftp)(http) |
COD |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
