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Sample GSM1268442 Query DataSets for GSM1268442
Status Public on Feb 17, 2015
Title B1H assay using AACA as bait, replicate 2
Sample type SRA
 
Source name B1H assay using AACA as bait
Organism synthetic construct
Characteristics bait: AACA
ols: OLS_A
molecule type: Plasmid extracted from bacteria after selection in B1H assay
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).
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description AACA_2
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
 
Submission date Nov 19, 2013
Last update date May 15, 2019
Contact name Hamed S Najafabadi
Organization name McGill University
Department Human Genetics
Lab Computational and Statistical Genomics Lab
Street address 740 Dr. Penfield Avenue, Room 7202
City Montreal
State/province QC
ZIP/Postal code H3A 0G1
Country Canada
 
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
Relations
BioSample SAMN02412594
SRA SRX379302

Supplementary file Size Download File type/resource
GSM1268442_AACA_2.1.count.txt.gz 37.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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