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Status |
Public on Feb 17, 2015 |
Title |
B1H assay using AAGC as bait, replicate 1 |
Sample type |
SRA |
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Source name |
B1H assay using AAGC as bait
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Organism |
synthetic construct |
Characteristics |
bait: AAGC ols: OLS_B molecule type: Plasmid extracted from bacteria after selection in B1H assay
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Growth protocol |
We performed B1H screens essentially as described before (PMID 17406209), with the modification that we first transformed the bacterial selection strain with the bait plasmid, then made electrocompetent cells, then transformed these with the prey library of C2H2 variants. We plated ~10^7 transformants on three μM medium plates (150 mm) containing 1 mM 3-Amino-1,2,4-triazole (3-AT), 100 μg/ml ampicillin, 25 μg/ml kanamycin, 10 μM IPTG, no histidine, and 0.2 mM uracil. We incubated the plates at 37C for 2 days, or more if needed to obtain colonies (typically hundreds to thousands of visible colonies of varying size).
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Extracted molecule |
genomic DNA |
Extraction protocol |
We scraped the colonies from the plates, and prepared plasmid DNA. We PCR-amplified F3 from the plasmid DNA using Illumina barcoded primers.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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Description |
AAGC_1
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Data processing |
Reads were trimmed at the 3’ end, so that for each read the minimum Phred quality score of any base of the remaining part was 12, there were no more than 10 bases with Phred quality scores <20, and the reads, after removing the constant vector region and amplification adapters, were not longer than 80 bases. The trimmed reads were further filtered to remove those shorter than 50 bases. Reads were mapped to the library using Bowtie, allowing a maximum of 2 mismatches at the first 28 bases and a maximum of 70 for the sum of quality values at all mismatched read positions, retaining only reads that were uniquely mapped. The number of reads that mapped to each Egr1 variant was recorded. *count.txt contains unique ID given to each sequence in the library and its abundance count. The 'OLS.info.xlsx' file contains the mapping of these IDs to different sequences. Genome_build: Custom library Supplementary_files_format_and_content: Text files containing the number of reads that were uniquely mapped to each Egr1 variant
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Submission date |
Nov 19, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Hamed S Najafabadi |
Organization name |
McGill University
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Department |
Human Genetics
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Lab |
Computational and Statistical Genomics Lab
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Street address |
740 Dr. Penfield Avenue, Room 7202
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City |
Montreal |
State/province |
QC |
ZIP/Postal code |
H3A 0G1 |
Country |
Canada |
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Platform ID |
GPL15228 |
Series (2) |
GSE52521 |
Highly parallel identification of sequence preferences for eukaryotic C2H2 zinc finger domains using a bacterial 1-hybrid assay |
GSE52523 |
Large-scale characterization of DNA binding landscape of eukaryotic C2H2 zinc fingers |
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Relations |
BioSample |
SAMN02412603 |
SRA |
SRX379307 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1268447_AAGC_1.1.count.txt.gz |
76.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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