This README_FU.txt file was generated on 2022-08-09 by Xiaoqin Fu GENERAL INFORMATION 1. Titles of Dataset: 1) PULL-DOWN_RESULTS_FOR_DATABASE_UPLOAD.xlsx; 2) all_protein_list.xlsx 2. Author Information Corresponding Investigators: Dr. Xiaoqin Fu fuxq@wzhealth.com Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University Dr. Judy Shih-Hwa Liu judy_liu@brown.edu Brown University Dr. Arne Gennerich arne.gennerich@einsteinmed.edu Albert Einstein College of Medicine Co-investigator 1 Name: Lu Rao lu.rao@einsteinmed.edu Albert Einstein College of Medicine Co-investigator 2 Name: Peijun Li 218004@wzhealth.com Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University Co-investigator 3 Name: Xinglei Liu xinglei.liu@einsteinmed.edu Albert Einstein College of Medicine Co-investigator 4 Name: Qi Wang 1214436363@qq.com Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University Co-investigator 5 Name: Alexander I. Son sonai0130@gmail.com Children's National Research Institute 3. Date of data collection: 2021-2022 4. Geographic location of data collection: Wenzhou, China 5. Funding sources that supported the collection of the data: the National Natural Science Foundation of China 6. Recommended citation for this dataset: DATA & FILE OVERVIEW 1. Description of dataset These data were generated to investigate mouse proteins directly associated with purified DCX protein. Pull-down Assay and Mass Spectrometry procedure were used to achieve this porpose. In the excel file: For Proteins groups: Protein IDs:uniprot IDs Fasta headers:descriptions for proteins Number of proteins:The number of proteins corresponding to the identified peptides; Sequence coverage [%]:The percentage of identified peptide in full length protein; Peptides:The number of peptides identified for this protein; Unique Peptides:Number of unique peptides identified for the corresponding protein; Sequence length:The number of amino acids identified in the corresponding protein; Score:the higher the score, the higher the reliability for the protein; Intensity:relative abundance of proteins。 2. File list File 1 Name: PULL-DOWN_RESULTS_FOR_DATABASE_UPLOAD.xlsx; File 1 Description: identified proteins/peptides from HA-DCX pull down assays which have >10 fold higher intensity than those from HA pull down assays File 2 Name: all_protein_list.xlsx File 2 Description: all identified proteins METHODOLOGICAL INFORMATION HA or HA-tagged DCX proteins were immobilized on Anti-HA agarose beads and subsequently mixed with protein lysates from embryonic day-18 mouse brains and incubated with rotation for 16 h at 4 °C to pull down associating proteins. The beads were washed four times. The beads were then incubated with DTT solution (final concentration of 10 mmol/L) and reduced in a 56 ° C water bath for 1 h. IAA solution was added (final concentration of 50 mmol/L) and protected from light for 40 min. The proteins were digested with trypsin overnight at 37°C. After digestion, the peptides were desalted using a desalting column, and the solvent was evaporated in a vacuum centrifuge at 45 ° C. The peptides were dissolved in sample solution (0.1% formic acid in water) and ready for mass spectrometry analysis. Samples were loaded onto Nanocolumn (100 μm×10 cm) packed with a reversed-phase ReproSil-Pur C18-AQ resin (3 μm, 120 Å, Dr. Maisch GmbH, Germany). The mobile phases consisted of A (0.1% formic acid in water) and B (acetonitrile). Total flow rate is 600 nL/min using a nanoflow liquid chromatograph (Easy-nLC1000, ThermoFisher Scientific, USA). LC linear gradient: from 4% to 8% B for 2 min, from 8% to 28 % B for 43 min, from 28 % to 40% B for 10 min, from 40% to 95% B for 1 min and from 95% to 95% B for 10 min. Eluted peptides were introduced into the mass spectrometer (Q Exactive™ Hybrid Quadrupole-Orbitrap™ Mass Spectrometer, Thermo Fisher Scientific, USA). The spray voltage was set at 2.2 kV and the heated capillary at 270°C. The machine was operated with MS resolution at 70000 (400 m/z survey scan), MS precursor m/z range: 300.0-1800.0. The raw MS files were analyzed and searched against protein database based on the species of the samples using MaxQuant (1.6.2.10). The parameters were set as follows: the protein modifications were carbamidomethylation (C) (fixed), oxidation (M) (variable), Acetyl (Protein N-term) (variable); the enzyme specificity was set to trypsin; the maximum missed cleavages were set to 2; the precursor ion mass tolerance was set to 20 ppm, and MS/MS tolerance was 20 ppm. Only high confident identified peptides were chosen for downstream protein identification analysis. RIPA Lysis and Extraction Buffer, Pierce™ BCA Protein Assay Kit were purchased from Thermo Fisher Science. DL-dithiothreitol (DTT), iodoacetamide (IAA), formic acid (FA), acetonitrile (ACN), were purchased from Sigma (St. Louis, MO, USA), trypsin from bovine pancreas was purchased from Promega (Madison, WI, USA). Ultrapure water was prepared from a Millipore purification system (Billerica, MA, USA). An Ultimate 3000 system coupled with a Q Exactive™ Hybrid Quadrupole-Orbitrap™ Mass Spectrometer (Thermo Fisher Scientific, USA) with an ESI nanospray source. DATA-SPECIFIC INFORMATION FOR: PULL-DOWN_RESULTS_FOR_DATABASE_UPLOAD.xlsx 1. Number of variables: 4 3. Variable List: Two HA pull down assays and two HA-DCX pull down assays 4. Missing data codes: None 5. Abbreviations used: N/A; not applicable