|
| Status |
Public on Mar 05, 2013 |
| Title |
Heart_Tbx3_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Myh6-MCM;CAG-CAT-TBX3_Tbx3_ChIP
|
| Organism |
Mus musculus |
| Characteristics |
strain background: FVB/N
genotype/variation: Myh6-MCM;CAG-CAT-TBX3
Stage: adult
tissue: heart
chip antibody: Tbx3 (A-20)
chip antibody vendor: Santa Cruz Biotechnology
chip antibody cat#: sc-17871
chip antibody lot#: J0306
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Material was used for library preparation with standard SOLiD library construction kit for SOLiD sequencing (Applied Biosystems, #4443713, #4400413).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
Sample run through SOLiD v3.0
|
| Data processing |
Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) as previously described, allowing a maximum of two mismatches. To generate a WIG file, all tags were extended to the calculated shear length as given by MACS (159bp). The WIG was then converted to a bigWig using the Galaxy Wig-to-bigWig conversion tool. To generate the bed file, peaks were called on the WIG file using the OccuPeak method (submitted for publication).
Genome_build: mm9
Supplementary_files_format_and_content: Tbx3_heart_adult_mouse.bigWig is a bigWig file visualizing the binding profile of Tbx3 in the mouse heart. Tbx3_heart_adult_mouse.bed is a bed file containing peaks called with the OccuPeak method (submitted for publication).
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Vincent M. Christoffels |
| E-mail(s) |
v.m.christoffels@amsterdamumc.nl
|
| Phone |
0205667821
|
| Organization name |
Amsterdam UMC
|
| Department |
Medical Biology
|
| Lab |
Vincent Christoffels
|
| Street address |
Meibergdreef 15 K2-159
|
| City |
Amsterdam |
| State/province |
N/A (NA) |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9318 |
| Series (1) |
| GSE44821 |
Genome-wide occupancy profile of Tbx3 in adult mouse whole heart |
|
| Relations |
| SRA |
SRX248439 |
| BioSample |
SAMN01974737 |
| Named Annotation |
GSM1092105_Tbx3_heart_adult_mouse.bigwig |
