Freely-diffusing smFRET example datasets in Photon-HDF5 format

This fileset contains freely-diffusing single-molecule FRET datasets on the Photon-HDF5 file format (http://photon-hdf5.readthedocs.org/). These files are also used as demo datasets for the FRETBursts burst analysis software (https://github.com/tritemio/FRETBursts). These datasets come from smFRET experiments on a us-ALEX, ns-ALEX and 8-spot smFRET setups. <strong>File format</strong> The file format is Photon-HDF5, an open binary format for single-molecule data: http://photon-hdf5.readthedocs.org/ <strong>Dataset description</strong> Currently, two datasets are published: the first is a single-spot usALEX dataset and the second one is an 8-spot smFRET with single laser excitation. <strong>usALEX: '0023uLRpitc_NTP_20dT_0.5GndCl.hdf5'</strong> This dataset is a usALEX measurement of 20dt ssDNA oligos doubly labeled with Cy3B and Atto647N. The excitation laser frequencies are 523nm and 635nm. The objective lens is a 1.2NA Olympus water immersion lens. The 2 detectors are both Perkin Elmer (now Excelitas) single-pixel SPADs. <strong>8-spot smFRET: '12d_New_30p_320mW_steer_3.hdf5'</strong> This dataset is a smFRET measurement performed on a 8-spot smFRET system employing a single laser excitation (8ps pulsed, 532nm). The setup is an 8 excitation spots smFRET setup employing 2 8-pixel SPAD arrays fabricated in custom technology by the SPADLab group at Politecnico di Milano (Italy). The 8 excitation spots are generated by an LCOS-SLM and focused in the sample with an water immersion NA 1.2 Olympus lens. The sample is 40 base-pairs dsDNA oligo doubly labeled with ATTO550 and ATTO647N. The base-pair separation between the dyes is 12 base-pairs.

本数据集集合包含采用Photon-HDF5文件格式的自由扩散单分子荧光共振能量转移（single-molecule fluorescence resonance energy transfer, smFRET）数据集，格式规范可参考：http://photon-hdf5.readthedocs.org/。这些文件同时作为FRETBursts光子爆发分析软件的演示数据集使用，该软件的开源地址为：https://github.com/tritemio/FRETBursts。本数据集源自us-ALEX、ns-ALEX及8-spot smFRET三种实验平台的smFRET实验。

<strong>文件格式</strong>
本数据集采用Photon-HDF5格式，这是一种面向单分子数据的开源二进制文件格式，详情可访问：http://photon-hdf5.readthedocs.org/

<strong>数据集说明</strong>
目前已公开两个数据集：其一为单通道usALEX数据集，其二为单激光激发的8-spot smFRET数据集。

<strong>usALEX数据集：0023uLRpitc_NTP_20dT_0.5GndCl.hdf5</strong>
该数据集为usALEX实验的测量数据，样品为20dt单链脱氧核糖核酸（single-stranded DNA, ssDNA）寡核苷酸链，其两端分别标记有Cy3B与Atto647N染料。激发激光波长为523nm与635nm，物镜采用奥林巴斯1.2NA水浸物镜，探测器为珀金埃尔默（现为Excelitas）生产的2路单像素单光子雪崩二极管（Single-Photon Avalanche Diode, SPAD）。

<strong>8-spot smFRET数据集：12d_New_30p_320mW_steer_3.hdf5</strong>
该数据集基于搭载8ps脉冲、532nm单激光激发系统的8-spot smFRET平台采集得到。该平台包含8个激发光斑，采用意大利米兰理工大学SPADLab团队定制工艺制备的2路8像素SPAD阵列；8个激发光斑由液晶硅基空间光调制器（Liquid Crystal on Silicon-Spatial Light Modulator, LCOS-SLM）生成，并通过奥林巴斯1.2NA水浸物镜聚焦至样品区域。实验样品为40碱基对的双链脱氧核糖核酸（double-stranded DNA, dsDNA）寡核苷酸链，其双标记染料为ATTO550与ATTO647N，两种染料之间的碱基间距为12个碱基对。