UNIVERSITY OF WASHINGTON
In this Administrative Supplement request, we propose funding to expand the UW ENCODE Project in four key areas. First, we plan to perform deep sequencing / digital genomic footprinting for 15 additional cell types. Second, we plan to boost DHSs that have not achieved footprinting-level coverage at the target depth of resequencing (200M uniquely mapping reads) to dense coverage using targeted array capture of up to 100K elements per cell type. Third, we plan to supplement the current cross-cell-type profiling plan by studying cellular perturbations, including (i) response to glucocorticoids and (ii) response to histone deacetylase inhibitors. Finally, we plan to perform definitive in vivo validation of up to 100 DHSs through knock-out experiments.
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| AWARD OVERVIEW |
| Award Number |
3U54HG004592-03S1 |
Funding Agency |
Department of Health and Human Services |
| Total Award Amount |
$899,883 |
Project Location - City |
SEATTLE |
| Award Date |
09/30/2009 |
Project Location - State |
WA |
| Project Status |
Completed |
Project Location - Zip |
98195-0000
|
| Jobs Reported |
0.00 |
Congressional District |
07 |
| Project Location - Country |
US |
|
|
Recipient Information
(Grants)
| Recipient Information (Grants) |
|
Recipient Name
|
UNIVERSITY OF WASHINGTON |
| Recipient DUNS Number |
605799469
|
| Recipient Address |
4333 BROOKLYN AVE NE |
| Recipient City |
SEATTLE |
| Recipient State |
Washington |
| Recipient Zip |
98195-0001 |
| Recipient Congressional District |
07 |
| Recipient Country |
USA |
Required to Report Top 5
Highly Compensated Officials |
No |
Projects and Jobs Information
| Projects and Jobs Information |
| Project Title |
A Comprehensive catalog of human DNasel hypersensitive sites |
| Project Status |
Completed |
| Final Project Report Submitted |
Yes |
| Project Activities Description |
Medical Research, General/Other |
| Quarterly Activities/Project Description |
The major goal of UW ENCODE Project is to create comprehensive, high resolution maps of human regulatory DNA. The ARRA supplement to our ENCODE Project encompasses three major aims: 1) To increase the sensitivity and resolution of ENCODE data by performing deep sequencing of high-quality digital DNaseI libraries; 2) To perform high-resolution validation of DNaseI footprints using conventional assays; and 3) To pilot definitive in vivo validation of regulatory DNA elements demarcated by digital DNaseI profiling through the use of novel knockout technologies. For Aim 1, we have completed deep sequencing 30 unique cell types, and generated over 7.3 Billion uniquely mapping sequence tags from cell specific digital DNaseI libraries. The DGF data from19 unique cell types have been submitted to DCC. The data from 11 additional cell types will be submitted shortly. For Aim 2, we have developed 560 gels (70X 2-sidesX4 cell types) for conventional in vivo footprinting. 180 primers have been designed to investigate 30 additional sites We focused our efforts on footprints: (i) that coincide with motifs that have overlying compatible ChIP-Seq signals generated by the ENCODE TF groups; and (ii) footprints that suggest alternate binding modes of TFs, with an initial focus on CTCF. For Aim 3, we have generated the data from 5 pilot regulatory region knock-outs plus controls and these are currently being analyzed. 22 Zinc Finger (ZFN) design constructs worked successfully for creating K562 clones with targeted regulatory elements knockouts. The knock out regions was characterized at the nucleotide sequence level. The deleted clones are being studied to determine the effects of DHS deletions on chromatin accessibility profiles and their biological effects on gene expression. |
| Jobs Created |
0.00 |
| Description of Jobs Created |
No Jobs Were Created or Retained. |
Purchaser Information
(Grants)
| Purchaser Information |
| Contracting Office ID |
Not Reported |
| Contracting Office Name |
Not Available |
| Contracting Office Region |
Not Available |
| TAS Major Program |
75-0906 |
| Award Information |
| Award Date |
09/30/2009 |
| Award Number |
3U54HG004592-03S1 |
| Order Number |
|
| Award Type |
Grants |
| Funding Agency ID |
75 |
| Funding Agency Name |
Department of Health and Human Services |
| Funding Office Name |
Not Available |
| Awarding Agency ID |
75 |
| Awarding Agency Name |
Department of Health and Human Services |
| Amount of Award |
$899,883 |
| Funds Invoiced/Received |
$899,883 |
| Expenditure Amount |
$899,883 |
| Infrastructure Expenditure Amount |
$0 |
| Infrastructure Purpose and Rationale |
Not Reported |
| Infrastructure Point of Contact Name |
Not Reported |
| Infrastructure Point of Contact Email |
Not Reported |
| Infrastructure Point of Contact Phone |
Not Reported |
| Infrastructure Point of Contact Address |
Not Reported |
| Infrastructure Point of Contact City |
Not Reported |
| Infrastructure Point of Contact State |
Not Reported |
| Infrastructure Point of Contact Zip |
Not Reported |
Product or Service Information
(Grants)
| Product or Service Information |
| Primary Activity Code |
H01 |
| Activity Description |
Medical Research, General/Other |
| Sub-Awards Information |
| Sub-awards to Organizations |
0 |
| Sub-award Amounts to Organizations |
$0 |
| Sub-Awards to Individuals |
0 |
| Sub-Award Amounts to Individuals |
$0 |
| Number of Sub-awards less than $25,000/award |
0 |
| Amount of Sub-awards less than $25,000/award |
$0 |
| Number of payments to vendors greater than $25,000 |
1 |
| Total Amount of payments to vendors greater than $25,000/award |
$46,022 |
| Number of payments to vendors less than $25,000/award |
304 |
| Total Amount of payments to vendors less than $25,000/award |
$225,898 |
Supelco, Inc. - Award Number 3U54HG004592-03S1 - Supelco, Inc.
| Award Number |
3U54HG004592-03S1 |
| Sub-Award Number |
N/A |
| Vendor DUNS Number |
041422718 |
| Vendor HQ Zip Code + 4 |
16823-6217 |
| Vendor Name |
Supelco, Inc. |
| Product and Service Description |
#0010 CUSTOMIZED ZINC FINGER NUCLEASES (ZFN) PER |
| Payment Amount |
$46,022 |
| Location Information |
| Latitude, Longitude |
47º 39' 17",
-122º 18' 7" |
| Congressional District |
07 |
| Address 1 |
4333 Brooklyn Avenue NE |
| Address 2 |
Box 359472 |
| City |
SEATTLE |
| County |
King |
| State |
WA |
| Zip |
98195-0000 |
|
|