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To investigate whether Esrrb-specific occupancy translates into Esrrb-specific candidate target genes, we mapped binding peaks to genes (see Table S1 and Experimental Procedures section) and intersected the resulting gene lists.
A number of other suggestions have been suggested by the reviewers to improve the manuscript, including adding more detail to the Experimental Procedures section and clarifying the data provided in the Table.
We constructed three more trees by applying BIONJ (Gascuel 1997) to distance matrices of whole genomes generated by alignment-free approaches the FFP method with K = 11, Repeating Pattern Distance (RPD) (described in Experimental Procedures section) and Normalized Compression Distance (NCD) (Rosa et al. 2008; Ito, Zeugmann and Zhan 2010).
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Experiments were performed as described in the experimental procedure section and each comparison was performed 3 times.
The experimental setups consisted of 10 urinary BC samples of different histology (see Tissue Sampling and Surgical Procedure section) and 5 control samples.
Of these, 44 participants read the alcohol booklets (see the Procedure section) and 49 participants read the smoking booklets.
Details about the initial sequences used for the search, corresponding to proteins of known 3D structures, are given in the Experimental procedure section and the complete list of detected proteins can be found in Additional file 2: Table S1.
Imagery in PTSD has largely been assessed using techniques such as script-driven imagery procedures (Section 5.6.1), and intrusion diaries and interviews (Sections 5.6.4 and 5.6.5), in which the objective is to explore the content and frequency of image-based intrusions.
Cryosections (150 μm thick) of tumors and lungs were prepared and imaged as described in the Extended Experimental Procedures section "Immunostainings and Confocal Microscopy of Tissue Sections".
For the purpose of this analysis, knowledge was categorized and compared based upon the criteria described in the statistical procedures (section Materials and Methods).
Script-driven imagery procedures (Section 5.6.1) and intrusion triggering tasks (Section 5.6.3) confer the advantage of assessing intrusions "as they happen", but could be regarded as being less naturalistic than intrusion diaries or interviews that focus on re-experiencing phenomena occurring outside of clinical or experimental sessions.
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