|
| Status |
Public on Dec 06, 2012 |
| Title |
Br-PAPE_SOLEXA_2.5 |
| Sample type |
SRA |
| |
|
| Source name |
synthetic library
|
| Organism |
synthetic construct |
| Characteristics |
library: ZFP library
library selection: bacterial one-hybrid (B1H) selected
|
| Treatment protocol |
refer to Enuameh MS et al. 2012 [PMID 22689783]
|
| Growth protocol |
refer to Enuameh MS et al. 2012 [PMID 22689783]
|
| Extracted molecule |
other |
| Extraction protocol |
Following each selection, all of the cells were scraped off the plate. The randomized portion of the prey vector containing the selected transcription factor binding sites were extracted and amplified using PCR.
The PCR products from different experiments were digested with different restriction enzymes in the first step of uniquely encoding sequences from different experiments. The restriction enzyme fragments were then barcoded, pooled and sequenced using a Illumina Genome Analyzer IIx or Illumina HiSeq 2000 machine as indicated in Gupta et al. (2011). Nucleic Acids Res. 39(1): 381–392. A more detailed description of the selection conditions employed for each zinc finger cluster is given in the methods section of this publication as well as the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
molecule: plasmid DNA
Sample 95
|
| Data processing |
The extracted sequences from the Illumina data were submitted to MEME for analysis. The parameters used as follows: Motif width was set at 5 to 15, the distribution of motif set as zoops, while allowing sites on + or - DNA strands. All other parameters were at the default settings. Aligned sequences were subsequently extracted from the MEME results and output in fasta format.
Supplementary_files_format_and_content: fasta and contains aligned extracted binding site sequences along with 'sequence rank.number' For example, '457.1' represent the corresponding unique sequence is ranked 457th and is 1 in number.
Supplementary_files_format_and_content: In the file name, e.g. CG3407_SOLEXA_2.5.fa, CG3407 refers to Gene name, SOLEXA denotes the sequencing method and 2.5 is the inhibitor (3-AT) concentration used in the Bacterial One-Hybrid selection.
|
| |
|
| Submission date |
Dec 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Scot Wolfe |
| E-mail(s) |
[email protected]
|
| Organization name |
UMass Medical School
|
| Department |
MCCB
|
| Street address |
364 Plantation Street, LRB 619
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL15228 |
| Series (1) |
| GSE42709 |
Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. |
|
| Relations |
| SRA |
SRX208317 |
| BioSample |
SAMN01822915 |
