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Sample GSM687315 Query DataSets for GSM687315
Status Public on Apr 28, 2011
Title 28bp_36hrs_10μmM_IPTG_5mM_3-AT_plates
Sample type SRA
 
Source name B1H selection
Organism synthetic construct
Characteristics iptg concentration (μm): 10
3-at concentration (mm): 5
duration of experiment (hours): 36
media: agarose gel
Extracted molecule other
Extraction protocol A prey library containing a 28bp long randomized region was used for this selection. A prey library containing a 6bp long randomized region immediately adjacent to the consensus site for finger 1 was used for most of the other selections. After 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 machine. See the supplemental material of Noyes et al. (2008). Cell. 133(7):1277-1289 for a more detailed description of the experimental protocol employed for each selection.
 
Library strategy OTHER
Library source other
Library selection other
Instrument model Illumina Genome Analyzer IIx
 
Description This selection was performed by the Woolf lab
Data processing The sequences from each B1H experiment were labeled using a barcode. The raw reads were parsed and assigned to the appropriate data set, based on the barcode sequence. Only reads that matched the expected constant region, or 'barcode' exactly were considered. N's correspond to randomized positions. In the case of samples bp_48hrs_10μM_IPTG_0mM_3-AT_plates and 28bp_48hrs_10μM_IPTG_5mM_3-AT_plates, mismatches were allowed at the second position only, which was expected to be a ligated 'T'. In the case of the N28_initial_library, the last two positions of the expected sequence ('GC'), or 'barcode,' were allowed allowed to be mismatches.
 
Submission date Mar 08, 2011
Last update date May 15, 2019
Contact name Scot Wolfe
E-mail(s) scot.wolfe@umassmed.edu
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 GPL11631
Series (1)
GSE26767 A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
Relations
SRA SRX047386
BioSample SAMN00217329

Data table header descriptions
SEQUENCE
COUNT

Data table
SEQUENCE COUNT
CGCGTGGGCGGCTGGGCGGGGACGGG 929
AACGTGGGCGTGCATCTACGCGCGGC 549
TACGTGGGCGTATTACTGCGTTGCCG 419
GCCCTCCCACGCGGTAAGACGGTCTC 403
CGCGTGGGCGGTTGAGGTAGTTTCCT 400
AGCGTGGGCGGTGATGGGTGTCCCTT 382
TGCGTGGGTGTGCGTGGTTTAGCTGC 350
TCCGCCCACGCCTTTCTTGAGGGGTC 344
CGCGTGGGTGGGTGTGGGAGAGGTAT 340
GTCGCGCCCACGGGTTGTTTATGAAT 331
CGCCGCCCACGTGCTCTCTGATATGA 316
GTTCGCCCACGCGATGTGCTGTTCGT 313
TGCGTGGGTGGGTTGTACACCAGGTA 291
TGTGTGGGCGTTGTCGGACTTGATGC 287
CGGCCAATGCCAGCACGCCCACGCGG 278
GCGCGTGGGCGTTGATGTGTTCCTGC 262
TCCTGTGTGGGCGTTGTGGTTGCCCC 254
CTATGCGTGGGCGGTTATGGGAGGCA 254
CTACCGCCCACGGTCCATAGAGGTTA 254
CGTGTGGGCGTGTCAGACGATTGGTC 254

Total number of rows: 26431

Table truncated, full table size 751 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Processed data included within Sample table
Raw data are available in SRA

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