 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 07, 2013 |
| Title |
COUP-TFII ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
atria
|
| Organism |
Mus musculus |
| Characteristics |
age: E13.5
chip antibody: NR2F2
chip antibody manufacturer: Active Motif
chip antibody catalog #: 61213
strain: C57BL/6
tissue: atria
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Flash frozen tissues were sent to Active Motif for chromatin extraction
Libraries were prepared by Active Motif
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Sequence Analysis: The 50-nt sequence reads identified by the Sequencing Service (using Illumina’s Hi-Seq) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Determination of Fragment Density: Since the 5 ́-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3 ́- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 150 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a Wig file.
Genome_build: mm9
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Apr 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
San-pin Wu |
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL15103 |
| Series (2) |
| GSE46497 |
Atrial Identity Is Determined by A COUP-TFII Regulatory Network (ChIP-Seq) |
| GSE46498 |
Atrial Identity Is Determined by A COUP-TFII Regulatory Network |
|
| Relations |
| BioSample |
SAMN02087274 |
| SRA |
SRX272830 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1131317_1_NR2F2_embryo_atrial_i34_uniqnorm_signal.wig.gz |
152.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
