title: 11M-MP-P4-E3-C3_S2139

description: Biological replicate 1


title: 11M-MP-P4-E3-A4_S2116

status: Public on Oct 09 2022

type: SRA

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

country: USA

institute: The Rockefeller University

description: Biological replicate 1

library_source: transcriptomic single cell

data_processing:
Sequence reads from each lane were obtained and mapped together to the mouse genome (GENCODE release M23 (GRCm38.p6)) using STAR (version 2.5.2a). ERCC spike-ins were added to the mouse genome as artificial chromosomes.
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts, using Salmon (version 0.14.1) and Tximport (version 1.12.3).
Assembly: GENCODE release M23 (GRCm38.p6)
Supplementary files format and content: comma separated value text files contain either TPMs or raw counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: mouse back skin

extract_protocol:
Single squamous cell cancer cells were FACS purified, and collected into 96-well plates containing lysis buffer and snap frozen in liquid nitrogen. Plates were stored at -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Reverse transcription reaction and whole transcriptome amplification were performed according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and the tagmentation reaction was performed by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequenced on an Illumina NovaSeq SP with 50 cycles paired-end mode (2 lanes).

tag: tumor stage

value: SCC

tag: strain

value: FVB/N

tag: mouse age

tag: genotype

tag: mouse sex

value: Male

tag: lentivirus injected at e9.5

value: SBE-mCherry PGK-rtTA3

tag: sorting scheme

tag: read alignment program

tag: read quantification program

value: Tximport (v 1.12.3)


title: 11M-MP-P4-E3-B7_S2131

description: Biological replicate 1


title: 11M-MP-P4-E3-A5_S2117

description: Biological replicate 1


title: 11M-MP-P4-E3-A3_S2115

description: Biological replicate 1


title: 11M-MP-P4-E3-A10_S2122

description: Biological replicate 1


title: 11M-MP-P4-E3-A11_S2123

description: Biological replicate 1


title: 11M-MP-P4-E3-A12_S2124

description: Biological replicate 1


title: 11M-MP-P4-E3-A1_S2113

description: Biological replicate 1


title: 11M-MP-P3-E2-H6_S2106

description: Biological replicate 1


title: 11M-MP-P3-E2-H9_S2109

description: Biological replicate 1


title: 11M-MP-P3-E2-H8_S2108

description: Biological replicate 1


title: 11M-MP-P3-E2-H4_S2104

description: Biological replicate 1


title: 11M-MP-P3-E2-H1_S2101

description: Biological replicate 1


title: 11M-MP-P3-E2-H2_S2102

description: Biological replicate 1


title: 11M-MP-P3-E2-H5_S2105

description: Biological replicate 1


title: 11M-MP-P4-E3-A8_S2120

description: Biological replicate 1


title: 11M-MP-P3-E2-H12_S2112

description: Biological replicate 1


title: 11M-MP-P3-E2-H11_S2111

description: Biological replicate 1


title: 11M-MP-P3-E2-G6_S2094

description: Biological replicate 1


title: 11M-MP-P3-E2-H10_S2110

description: Biological replicate 1


title: 11M-MP-P3-E2-G8_S2096

description: Biological replicate 1


title: 11M-MP-P3-E2-G7_S2095

description: Biological replicate 1


title: 11M-MP-P3-E2-G9_S2097

description: Biological replicate 1


title: 11M-MP-P3-E2-G5_S2093

description: Biological replicate 1


title: 11M-MP-P3-E2-G3_S2091

description: Biological replicate 1


title: 11M-MP-P3-E2-G4_S2092

description: Biological replicate 1


title: 11M-MP-P3-E2-G2_S2090

description: Biological replicate 1


title: 11M-MP-P3-E2-G10_S2098

description: Biological replicate 1


title: 11M-MP-P3-E2-G1_S2089

description: Biological replicate 1


title: 11M-MP-P3-E2-F8_S2084

description: Biological replicate 1


title: 11M-MP-P3-E2-F6_S2082

description: Biological replicate 1


title: 11M-MP-P3-E2-F7_S2083

description: Biological replicate 1


title: 11M-MP-P3-E2-F9_S2085

description: Biological replicate 1


title: 11M-MP-P3-E2-H7_S2107

description: Biological replicate 1


title: 11M-MP-P3-E2-G11_S2099

description: Biological replicate 1


title: 11M-MP-P3-E2-F5_S2081

description: Biological replicate 1


title: 11M-MP-P3-E2-H3_S2103

description: Biological replicate 1


title: 11M-MP-P3-E2-F4_S2080

description: Biological replicate 1


title: 11M-MP-P3-E2-F3_S2079

description: Biological replicate 1


title: 11M-MP-P3-E2-F2_S2078

description: Biological replicate 1


title: 11M-MP-P3-E2-F1_S2077

description: Biological replicate 1


title: 11M-MP-P3-E2-F11_S2087

description: Biological replicate 1


title: 11M-MP-P3-E2-F10_S2086

description: Biological replicate 1


title: 11M-MP-P3-E2-F12_S2088

description: Biological replicate 1


title: 11M-MP-P3-E2-E8_S2072

description: Biological replicate 1


title: 11M-MP-P3-E2-E5_S2069

description: Biological replicate 1


title: 11M-MP-P3-E2-E6_S2070

description: Biological replicate 1


title: 11M-MP-P3-E2-E9_S2073

description: Biological replicate 1


title: 11M-MP-P3-E2-G12_S2100

description: Biological replicate 1


title: 11M-MP-P3-E2-E4_S2068

description: Biological replicate 1


title: 11M-MP-P3-E2-E3_S2067

description: Biological replicate 1


title: 11M-MP-P3-E2-E1_S2065

description: Biological replicate 1


title: 11M-MP-P3-E2-E12_S2076

description: Biological replicate 1


title: 11M-MP-P3-E2-E11_S2075

description: Biological replicate 1


title: 11M-MP-P3-E2-E10_S2074

description: Biological replicate 1


title: 11M-MP-P3-E2-E2_S2066

description: Biological replicate 1


title: 11M-MP-P3-E2-D8_S2060

description: Biological replicate 1


title: 11M-MP-P3-E2-D7_S2059

description: Biological replicate 1


title: 11M-MP-P3-E2-D3_S2055

description: Biological replicate 1


title: 11M-MP-P3-E2-D2_S2054

description: Biological replicate 1


title: 11M-MP-P3-E2-D5_S2057

description: Biological replicate 1


title: 11M-MP-P3-E2-D6_S2058

description: Biological replicate 1


title: 11M-MP-P3-E2-D11_S2063

description: Biological replicate 1


title: 11M-MP-P3-E2-D12_S2064

description: Biological replicate 1


title: 11M-MP-P3-E2-C9_S2049

description: Biological replicate 1


title: 11M-MP-P3-E2-C8_S2048

description: Biological replicate 1


title: 11M-MP-P3-E2-C6_S2046

description: Biological replicate 1


title: 11M-MP-P3-E2-C5_S2045

description: Biological replicate 1


title: 11M-MP-P3-E2-E7_S2071

description: Biological replicate 1


title: 11M-MP-P3-E2-C4_S2044

description: Biological replicate 1


title: 11M-MP-P3-E2-C2_S2042

description: Biological replicate 1


title: 11M-MP-P3-E2-C3_S2043

description: Biological replicate 1


title: 11M-MP-P3-E2-C1_S2041

description: Biological replicate 1


title: 11M-MP-P3-E2-C11_S2051

description: Biological replicate 1


title: 11M-MP-P3-E2-C12_S2052

description: Biological replicate 1


title: 11M-MP-P3-E2-C10_S2050

description: Biological replicate 1


title: 11M-MP-P3-E2-B9_S2037

description: Biological replicate 1


title: 11M-MP-P3-E2-B8_S2036

description: Biological replicate 1


title: 11M-MP-P3-E2-D9_S2061

description: Biological replicate 1


title: 11M-MP-P3-E2-D1_S2053

description: Biological replicate 1


title: 11M-MP-P3-E2-B7_S2035

description: Biological replicate 1


title: 11M-MP-P3-E2-B5_S2033

description: Biological replicate 1


title: 11M-MP-P3-E2-B2_S2030

description: Biological replicate 1


title: 11M-MP-P3-E2-B6_S2034

description: Biological replicate 1


title: 11M-MP-P3-E2-B3_S2031

description: Biological replicate 1


title: 11M-MP-P3-E2-B1_S2029

description: Biological replicate 1


title: 11M-MP-P3-E2-D10_S2062

description: Biological replicate 1


title: 11M-MP-P3-E2-C7_S2047

description: Biological replicate 1


title: 11M-MP-P3-E2-D4_S2056

description: Biological replicate 1


title: 11M-MP-P3-E2-B11_S2039

description: Biological replicate 1


title: 11M-MP-P3-E2-B12_S2040

description: Biological replicate 1


title: 11M-MP-P3-E2-B4_S2032

description: Biological replicate 1


title: 11M-MP-P3-E2-A9_S2025

description: Biological replicate 1


title: 11M-MP-P3-E2-A6_S2022

description: Biological replicate 1


title: 11M-MP-P3-E2-A5_S2021

description: Biological replicate 1


title: 11M-MP-P3-E2-A7_S2023

description: Biological replicate 1


title: 11M-MP-P3-E2-A4_S2020

description: Biological replicate 1


title: 11M-MP-P3-E2-B10_S2038

description: Biological replicate 1


title: 11M-MP-P3-E2-A1_S2017

description: Biological replicate 1


title: 11M-MP-P3-E2-A10_S2026

description: Biological replicate 1


title: 11M-MP-P3-E2-A12_S2028

description: Biological replicate 1


title: 11M-MP-P2-D4-H9_S1821

description: Biological replicate 1


title: 11M-MP-P2-D4-H8_S1820

description: Biological replicate 1


title: 11M-MP-P3-E2-A11_S2027

description: Biological replicate 1


title: 11M-MP-P2-D4-H7_S1819

description: Biological replicate 1


title: 11M-MP-P2-D4-H5_S1817

description: Biological replicate 1


title: 11M-MP-P2-D4-H4_S1816

description: Biological replicate 1


title: 11M-MP-P2-D4-H1_S1813

description: Biological replicate 1


title: 11M-MP-P2-D4-H3_S1815

description: Biological replicate 1


title: 11M-MP-P2-D4-H2_S1814

description: Biological replicate 1


title: 11M-MP-P2-D4-H12_S1824

description: Biological replicate 1


title: 11M-MP-P3-E2-A2_S2018

description: Biological replicate 1


title: 11M-MP-P2-D4-H10_S1822

description: Biological replicate 1


title: 11M-MP-P2-D4-H6_S1818

description: Biological replicate 1


title: 11M-MP-P3-E2-A8_S2024

description: Biological replicate 1


title: 11M-MP-P2-D4-G8_S1808

description: Biological replicate 1


title: 11M-MP-P2-D4-H11_S1823

description: Biological replicate 1


title: 11M-MP-P2-D4-G7_S1807

description: Biological replicate 1


title: 11M-MP-P2-D4-G9_S1809

description: Biological replicate 1


title: 11M-MP-P2-D4-G4_S1804

description: Biological replicate 1


title: 11M-MP-P2-D4-G3_S1803

description: Biological replicate 1


title: 11M-MP-P2-D4-G2_S1802

description: Biological replicate 1


title: 11M-MP-P2-D4-G1_S1801

description: Biological replicate 1


title: 11M-MP-P2-D4-G5_S1805

description: Biological replicate 1


title: 11M-MP-P3-E2-A3_S2019

description: Biological replicate 1


title: 11M-MP-P2-D4-G12_S1812

description: Biological replicate 1


title: 11M-MP-P2-D4-G11_S1811

description: Biological replicate 1


title: 11M-MP-P2-D4-G10_S1810

description: Biological replicate 1


title: 11M-MP-P2-D4-F8_S1796

description: Biological replicate 1


title: 11M-MP-P2-D4-F9_S1797

description: Biological replicate 1


title: 11M-MP-P2-D4-F6_S1794

description: Biological replicate 1


title: 11M-MP-P2-D4-F4_S1792

description: Biological replicate 1


title: 11M-MP-P2-D4-F3_S1791

description: Biological replicate 1


title: 11M-MP-P2-D4-F2_S1790

description: Biological replicate 1


title: 11M-MP-P2-D4-F12_S1800

description: Biological replicate 1


title: 11M-MP-P2-D4-F1_S1789

description: Biological replicate 1


title: 11M-MP-P2-D4-F11_S1799

description: Biological replicate 1


title: 11M-MP-P2-D4-E8_S1784

description: Biological replicate 1


title: 11M-MP-P2-D4-F10_S1798

description: Biological replicate 1


title: 11M-MP-P2-D4-E7_S1783

description: Biological replicate 1


title: 11M-MP-P2-D4-G6_S1806

description: Biological replicate 1


title: 11M-MP-P2-D4-E4_S1780

description: Biological replicate 1


title: 11M-MP-P2-D4-E1_S1777

description: Biological replicate 1


title: 11M-MP-P2-D4-E3_S1779

description: Biological replicate 1


title: 11M-MP-P2-D4-E6_S1782

description: Biological replicate 1


title: 11M-MP-P2-D4-E5_S1781

description: Biological replicate 1


title: 11M-MP-P2-D4-E11_S1787

description: Biological replicate 1


title: 11M-MP-P2-D4-E2_S1778

description: Biological replicate 1


title: 11M-MP-P2-D4-F5_S1793

description: Biological replicate 1


title: 11M-MP-P2-D4-D8_S1772

description: Biological replicate 1


title: 11M-MP-P2-D4-D7_S1771

description: Biological replicate 1


title: 11M-MP-P2-D4-D9_S1773

description: Biological replicate 1


title: 11M-MP-P2-D4-E12_S1788

description: Biological replicate 1


title: 11M-MP-P2-D4-D6_S1770

description: Biological replicate 1


title: 11M-MP-P2-D4-D5_S1769

description: Biological replicate 1


title: 11M-MP-P2-D4-D2_S1766

description: Biological replicate 1


title: 11M-MP-P2-D4-D3_S1767

description: Biological replicate 1


title: 11M-MP-P2-D4-F7_S1795

description: Biological replicate 1


title: 11M-MP-P2-D4-E9_S1785

description: Biological replicate 1


title: 11M-MP-P2-D4-D4_S1768

description: Biological replicate 1


title: 11M-MP-P2-D4-D12_S1776

description: Biological replicate 1


title: 11M-MP-P2-D4-C8_S1760

description: Biological replicate 1


title: 11M-MP-P2-D4-D10_S1774

description: Biological replicate 1


title: 11M-MP-P2-D4-C7_S1759

description: Biological replicate 1


title: 11M-MP-P2-D4-C6_S1758

description: Biological replicate 1


title: 11M-MP-P2-D4-C5_S1757

description: Biological replicate 1


title: 11M-MP-P2-D4-E10_S1786

description: Biological replicate 1


title: 11M-MP-P2-D4-C4_S1756

description: Biological replicate 1


title: 11M-MP-P2-D4-C3_S1755

description: Biological replicate 1


title: 11M-MP-P2-D4-C12_S1764

description: Biological replicate 1


title: 11M-MP-P2-D4-C1_S1753

description: Biological replicate 1


title: 11M-MP-P2-D4-C11_S1763

description: Biological replicate 1


title: 11M-MP-P2-D4-C2_S1754

description: Biological replicate 1


title: 11M-MP-P2-D4-C10_S1762

description: Biological replicate 1


title: 11M-MP-P2-D4-B8_S1748

description: Biological replicate 1


title: 11M-MP-P2-D4-B9_S1749

description: Biological replicate 1


title: 11M-MP-P2-D4-B7_S1747

description: Biological replicate 1


title: 11M-MP-P2-D4-B6_S1746

description: Biological replicate 1


title: 11M-MP-P2-D4-B5_S1745

description: Biological replicate 1


title: 11M-MP-P2-D4-D1_S1765

description: Biological replicate 1


title: 11M-MP-P2-D4-B4_S1744

description: Biological replicate 1


title: 11M-MP-P2-D4-C9_S1761

description: Biological replicate 1


title: 11M-MP-P2-D4-D11_S1775

description: Biological replicate 1


title: 11M-MP-P2-D4-B1_S1741

description: Biological replicate 1


title: 11M-MP-P2-D4-B2_S1742

description: Biological replicate 1


title: 11M-MP-P2-D4-A9_S1737

description: Biological replicate 1


title: 11M-MP-P2-D4-B12_S1752

description: Biological replicate 1


title: 11M-MP-P2-D4-B11_S1751

description: Biological replicate 1


title: 11M-MP-P2-D4-A5_S1733

description: Biological replicate 1


title: 11M-MP-P2-D4-B10_S1750

description: Biological replicate 1


title: 11M-MP-P2-D4-A6_S1734

description: Biological replicate 1


title: 11M-MP-P2-D4-A7_S1735

description: Biological replicate 1


title: 11M-MP-P2-D4-A8_S1736

description: Biological replicate 1


title: 11M-MP-P2-D4-A2_S1730

description: Biological replicate 1


title: 11M-MP-P2-D4-A11_S1739

description: Biological replicate 1


title: 11M-MP-P2-D4-A1_S1729

description: Biological replicate 1


title: 11M-MP-P2-D4-A4_S1732

description: Biological replicate 1


title: 11M-MP-P2-D4-A3_S1731

description: Biological replicate 1


title: 11M-MP-P2-D4-A12_S1740

description: Biological replicate 1


title: 11M-MP-P2-D4-A10_S1738

description: Biological replicate 1


title: 11M-MP-P1-D3-H6_S1722

description: Biological replicate 1


title: 11M-MP-P1-D3-H8_S1724

description: Biological replicate 1


title: 11M-MP-P2-D4-B3_S1743

description: Biological replicate 1


title: 11M-MP-P1-D3-H5_S1721

description: Biological replicate 1


title: 11M-MP-P1-D3-H9_S1725

description: Biological replicate 1


title: 11M-MP-P1-D3-H7_S1723

description: Biological replicate 1


title: 11M-MP-P1-D3-H4_S1720

description: Biological replicate 1


title: 11M-MP-P1-D3-H1_S1717

description: Biological replicate 1


title: 11M-MP-P1-D3-H3_S1719

description: Biological replicate 1


title: 11M-MP-P1-D3-H2_S1718

description: Biological replicate 1


title: 11M-MP-P1-D3-H10_S1726

description: Biological replicate 1


title: 11M-MP-P1-D3-G12_S1716

description: Biological replicate 1


title: 11M-MP-P1-D3-G8_S1712

description: Biological replicate 1


title: 11M-MP-P1-D3-G1_S1705

description: Biological replicate 1


title: 11M-MP-P1-D3-H11_S1727

description: Biological replicate 1


title: 11M-MP-P1-D3-G4_S1708

description: Biological replicate 1


title: 11M-MP-P1-D3-G7_S1711

description: Biological replicate 1


title: 11M-MP-P1-D3-G9_S1713

description: Biological replicate 1


title: 11M-MP-P1-D3-G3_S1707

description: Biological replicate 1


title: 11M-MP-P1-D3-G5_S1709

description: Biological replicate 1


title: 11M-MP-P1-D3-G6_S1710

description: Biological replicate 1


title: 11M-MP-P1-D3-F9_S1701

description: Biological replicate 1


title: 11M-MP-P1-D3-G10_S1714

description: Biological replicate 1


title: 11M-MP-P1-D3-F6_S1698

description: Biological replicate 1


title: 11M-MP-P1-D3-F7_S1699

description: Biological replicate 1


title: 11M-MP-P1-D3-F3_S1695

description: Biological replicate 1


title: 11M-MP-P1-D3-G11_S1715

description: Biological replicate 1


title: 11M-MP-P1-D3-F2_S1694

description: Biological replicate 1


title: 11M-MP-P1-D3-H12_S1728

description: Biological replicate 1


title: 11M-MP-P1-D3-F8_S1700

description: Biological replicate 1


title: 11M-MP-P1-D3-F5_S1697

description: Biological replicate 1


title: 11M-MP-P1-D3-F1_S1693

description: Biological replicate 1


title: 11M-MP-P1-D3-F4_S1696

description: Biological replicate 1


title: 11M-MP-P1-D3-F11_S1703

description: Biological replicate 1


title: 11M-MP-P1-D3-F12_S1704

description: Biological replicate 1


title: 11M-MP-P1-D3-E8_S1688

description: Biological replicate 1


title: 11M-MP-P1-D3-E9_S1689

description: Biological replicate 1


title: 11M-MP-P1-D3-F10_S1702

description: Biological replicate 1


title: 11M-MP-P1-D3-G2_S1706

description: Biological replicate 1


title: 11M-MP-P1-D3-E7_S1687

description: Biological replicate 1


title: 11M-MP-P1-D3-E5_S1685

description: Biological replicate 1


title: 11M-MP-P1-D3-E6_S1686

description: Biological replicate 1


title: 11M-MP-P1-D3-E4_S1684

description: Biological replicate 1


title: 11M-MP-P1-D3-E1_S1681

description: Biological replicate 1


title: 11M-MP-P1-D3-E3_S1683

description: Biological replicate 1


title: 11M-MP-P1-D3-E12_S1692

description: Biological replicate 1


title: 11M-MP-P1-D3-E2_S1682

description: Biological replicate 1


title: 11M-MP-P1-D3-E10_S1690

description: Biological replicate 1


title: 11M-MP-P1-D3-D9_S1677

description: Biological replicate 1


title: 11M-MP-P1-D3-D7_S1675

description: Biological replicate 1


title: 11M-MP-P1-D3-D8_S1676

description: Biological replicate 1


title: 11M-MP-P1-D3-D4_S1672

description: Biological replicate 1


title: 11M-MP-P1-D3-D5_S1673

description: Biological replicate 1


title: 11M-MP-P1-D3-D6_S1674

description: Biological replicate 1


title: 11M-MP-P1-D3-D11_S1679

description: Biological replicate 1


title: 11M-MP-P1-D3-D2_S1670

description: Biological replicate 1


title: 11M-MP-P1-D3-C8_S1664

description: Biological replicate 1


title: 11M-MP-P1-D3-D1_S1669

description: Biological replicate 1


title: 11M-MP-P1-D3-D3_S1671

description: Biological replicate 1


title: 11M-MP-P1-D3-D12_S1680

description: Biological replicate 1


title: 11M-MP-P1-D3-C4_S1660

description: Biological replicate 1


title: 11M-MP-P1-D3-C9_S1665

description: Biological replicate 1


title: 11M-MP-P1-D3-C5_S1661

description: Biological replicate 1


title: 11M-MP-P1-D3-C2_S1658

description: Biological replicate 1


title: 11M-MP-P1-D3-C3_S1659

description: Biological replicate 1


title: 11M-MP-P1-D3-D10_S1678

description: Biological replicate 1


title: 11M-MP-P1-D3-C6_S1662

description: Biological replicate 1


title: 11M-MP-P1-D3-C12_S1668

description: Biological replicate 1


title: 11M-MP-P1-D3-C1_S1657

description: Biological replicate 1


title: 11M-MP-P1-D3-E11_S1691

description: Biological replicate 1


title: 11M-MP-P1-D3-B6_S1650

description: Biological replicate 1


title: 11M-MP-P1-D3-B7_S1651

description: Biological replicate 1


title: 11M-MP-P1-D3-B9_S1653

description: Biological replicate 1


title: 11M-MP-P1-D3-B8_S1652

description: Biological replicate 1


title: 11M-MP-P1-D3-C11_S1667

description: Biological replicate 1


title: 11M-MP-P1-D3-B5_S1649

description: Biological replicate 1


title: 11M-MP-P1-D3-B4_S1648

description: Biological replicate 1


title: 11M-MP-P1-D3-B3_S1647

description: Biological replicate 1


title: 11M-MP-P1-D3-B2_S1646

description: Biological replicate 1


title: 11M-MP-P1-D3-C7_S1663

description: Biological replicate 1


title: 11M-MP-P1-D3-B12_S1656

description: Biological replicate 1


title: 11M-MP-P1-D3-B11_S1655

description: Biological replicate 1


title: 11M-MP-P1-D3-B1_S1645

description: Biological replicate 1


title: 11M-MP-P1-D3-A7_S1639

description: Biological replicate 1


title: 11M-MP-P1-D3-A8_S1640

description: Biological replicate 1


title: 11M-MP-P1-D3-A9_S1641

description: Biological replicate 1


title: 11M-MP-P1-D3-A1_S1633

description: Biological replicate 1


title: 11M-MP-P1-D3-A3_S1635

description: Biological replicate 1


title: 11M-MP-P1-D3-A10_S1642

description: Biological replicate 1


title: 11M-MP-P1-D3-A6_S1638

description: Biological replicate 1


title: 11M-MP-P1-D3-A2_S1634

description: Biological replicate 1


title: 11M-MP-P1-D3-A4_S1636

description: Biological replicate 1


title: 11M-MP-P1-D3-C10_S1666

description: Biological replicate 1


title: 11M-MP-P1-D3-A5_S1637

description: Biological replicate 1


title: 11M-MP-P1-D3-A12_S1644

description: Biological replicate 1


title: 11M-MN-P2-B2-H7_S667

description: Biological replicate 1


title: 11M-MN-P2-B2-H6_S666

description: Biological replicate 1


title: 11M-MN-P2-B2-H5_S665

description: Biological replicate 1


title: 11M-MN-P2-B2-H4_S664

description: Biological replicate 1


title: 11M-MN-P2-B2-H8_S668

description: Biological replicate 1


title: 11M-MN-P2-B2-H3_S663

description: Biological replicate 1


title: 11M-MN-P2-B2-H9_S669

description: Biological replicate 1


title: 11M-MN-P2-B2-H2_S662

description: Biological replicate 1


title: 11M-MP-P1-D3-B10_S1654

description: Biological replicate 1


title: 11M-MN-P2-B2-H1_S661

description: Biological replicate 1


title: 11M-MN-P2-B2-H11_S671

description: Biological replicate 1


title: 11M-MN-P2-B2-H12_S672

description: Biological replicate 1


title: 11M-MN-P2-B2-H10_S670

description: Biological replicate 1


title: 11M-MN-P2-B2-G7_S655

description: Biological replicate 1


title: 11M-MN-P2-B2-G9_S657

description: Biological replicate 1


title: 11M-MN-P2-B2-G6_S654

description: Biological replicate 1


title: 11M-MN-P2-B2-G5_S653

description: Biological replicate 1


title: 11M-MP-P1-D3-A11_S1643

description: Biological replicate 1


title: 11M-MN-P2-B2-G4_S652

description: Biological replicate 1


title: 11M-MN-P2-B2-G3_S651

description: Biological replicate 1


title: 11M-MN-P2-B2-G12_S660

description: Biological replicate 1


title: 11M-MN-P2-B2-F9_S645

description: Biological replicate 1


title: 11M-MN-P2-B2-G10_S658

description: Biological replicate 1


title: 11M-MN-P2-B2-G11_S659

description: Biological replicate 1


title: 11M-MN-P2-B2-G1_S649

description: Biological replicate 1


title: 11M-MN-P2-B2-G2_S650

description: Biological replicate 1


title: 11M-MN-P2-B2-F8_S644

description: Biological replicate 1


title: 11M-MN-P2-B2-F7_S643

description: Biological replicate 1


title: 11M-MN-P2-B2-F6_S642

description: Biological replicate 1


title: 11M-MN-P2-B2-F2_S638

description: Biological replicate 1


title: 11M-MN-P2-B2-F4_S640

description: Biological replicate 1


title: 11M-MN-P2-B2-F11_S647

description: Biological replicate 1


title: 11M-MN-P2-B2-F5_S641

description: Biological replicate 1


title: 11M-MN-P2-B2-G8_S656

description: Biological replicate 1


title: 11M-MN-P2-B2-E9_S633

description: Biological replicate 1


title: 11M-MN-P2-B2-E6_S630

description: Biological replicate 1


title: 11M-MN-P2-B2-F10_S646

description: Biological replicate 1


title: 11M-MN-P2-B2-E3_S627

description: Biological replicate 1


title: 11M-MN-P2-B2-E4_S628

description: Biological replicate 1


title: 11M-MN-P2-B2-E2_S626

description: Biological replicate 1


title: 11M-MN-P2-B2-E5_S629

description: Biological replicate 1


title: 11M-MN-P2-B2-E1_S625

description: Biological replicate 1


title: 11M-MN-P2-B2-E12_S636

description: Biological replicate 1


title: 11M-MN-P2-B2-E8_S632

description: Biological replicate 1


title: 11M-MN-P2-B2-E7_S631

description: Biological replicate 1


title: 11M-MN-P2-B2-E11_S635

description: Biological replicate 1


title: 11M-MN-P2-B2-E10_S634

description: Biological replicate 1


title: 11M-MN-P2-B2-D8_S620

description: Biological replicate 1


title: 11M-MN-P2-B2-F1_S637

description: Biological replicate 1


title: 11M-MN-P2-B2-D7_S619

description: Biological replicate 1


title: 11M-MN-P2-B2-F3_S639

description: Biological replicate 1


title: 11M-MN-P2-B2-D5_S617

description: Biological replicate 1


title: 11M-MN-P2-B2-D9_S621

description: Biological replicate 1


title: 11M-MN-P2-B2-D4_S616

description: Biological replicate 1


title: 11M-MN-P2-B2-D2_S614

description: Biological replicate 1


title: 11M-MN-P2-B2-D12_S624

description: Biological replicate 1


title: 11M-MN-P2-B2-D10_S622

description: Biological replicate 1


title: 11M-MN-P2-B2-F12_S648

description: Biological replicate 1


title: 11M-MN-P2-B2-D1_S613

description: Biological replicate 1


title: 11M-MN-P2-B2-D11_S623

description: Biological replicate 1


title: 11M-MN-P2-B2-D3_S615

description: Biological replicate 1


title: 11M-MN-P2-B2-C6_S606

description: Biological replicate 1


title: 11M-MN-P2-B2-C8_S608

description: Biological replicate 1


title: 11M-MN-P2-B2-C3_S603

description: Biological replicate 1


title: 11M-MN-P2-B2-C5_S605

description: Biological replicate 1


title: 11M-MN-P2-B2-C4_S604

description: Biological replicate 1


title: 11M-MN-P2-B2-C9_S609

description: Biological replicate 1


title: 11M-MN-P2-B2-C2_S602

description: Biological replicate 1


title: 11M-MN-P2-B2-C7_S607

description: Biological replicate 1


title: 11M-MN-P2-B2-C12_S612

description: Biological replicate 1


title: 11M-MN-P2-B2-C11_S611

description: Biological replicate 1


title: 11M-MN-P2-B2-C10_S610

description: Biological replicate 1


title: 11M-MN-P2-B2-D6_S618

description: Biological replicate 1


title: 11M-MN-P2-B2-B9_S597

description: Biological replicate 1


title: 11M-MN-P2-B2-B8_S596

description: Biological replicate 1


title: 11M-MN-P2-B2-B7_S595

description: Biological replicate 1


title: 11M-MN-P2-B2-B5_S593

description: Biological replicate 1


title: 11M-MN-P2-B2-B6_S594

description: Biological replicate 1


title: 11M-MN-P2-B2-B3_S591

description: Biological replicate 1


title: 11M-MN-P2-B2-B12_S600

description: Biological replicate 1


title: 11M-MN-P2-B2-B2_S590

description: Biological replicate 1


title: 11M-MN-P2-B2-B1_S589

description: Biological replicate 1


title: 11M-MN-P2-B2-B11_S599

description: Biological replicate 1


title: 11M-MN-P2-B2-A8_S584

description: Biological replicate 1


title: 11M-MN-P2-B2-A6_S582

description: Biological replicate 1


title: 11M-MN-P2-B2-A7_S583

description: Biological replicate 1


title: 11M-MN-P2-B2-C1_S601

description: Biological replicate 1


title: 11M-MN-P2-B2-A5_S581

description: Biological replicate 1


title: 11M-MN-P2-B2-A2_S578

description: Biological replicate 1


title: 11M-MN-P2-B2-A3_S579

description: Biological replicate 1


title: 11M-MN-P2-B2-A4_S580

description: Biological replicate 1


title: 11M-MN-P2-B2-A12_S588

description: Biological replicate 1


title: 11M-MN-P2-B2-A1_S577

description: Biological replicate 1


title: 11M-MN-P2-B2-A11_S587

description: Biological replicate 1


title: 11M-MN-P1-C1-H8_S1052

description: Biological replicate 1


title: 11M-MN-P1-C1-H6_S1050

description: Biological replicate 1


title: 11M-MN-P1-C1-H7_S1051

description: Biological replicate 1


title: 11M-MN-P1-C1-H9_S1053

description: Biological replicate 1


title: 11M-MN-P1-C1-H5_S1049

description: Biological replicate 1


title: 11M-MN-P1-C1-H4_S1048

description: Biological replicate 1


title: 11M-MN-P1-C1-H3_S1047

description: Biological replicate 1


title: 11M-MN-P2-B2-B4_S592

description: Biological replicate 1


title: 11M-MN-P1-C1-H1_S1045

description: Biological replicate 1


title: 11M-MN-P1-C1-H12_S1056

description: Biological replicate 1


title: 11M-MN-P2-B2-B10_S598

description: Biological replicate 1


title: 11M-MN-P1-C1-H11_S1055

description: Biological replicate 1


title: 11M-MN-P1-C1-H10_S1054

description: Biological replicate 1


title: 11M-MN-P2-B2-A9_S585

description: Biological replicate 1


title: 11M-MN-P1-C1-H2_S1046

description: Biological replicate 1


title: 11M-MN-P1-C1-G7_S1039

description: Biological replicate 1


title: 11M-MN-P1-C1-G6_S1038

description: Biological replicate 1


title: 11M-MN-P2-B2-A10_S586

description: Biological replicate 1


title: 11M-MN-P1-C1-G2_S1034

description: Biological replicate 1


title: 11M-MN-P1-C1-G4_S1036

description: Biological replicate 1


title: 11M-MN-P1-C1-G5_S1037

description: Biological replicate 1


title: 11M-MN-P1-C1-G3_S1035

description: Biological replicate 1


title: 11M-MN-P1-C1-F9_S1029

description: Biological replicate 1


title: 11M-MN-P1-C1-G10_S1042

description: Biological replicate 1


title: 11M-MN-P1-C1-F7_S1027

description: Biological replicate 1


title: 11M-MN-P1-C1-F8_S1028

description: Biological replicate 1


title: 11M-MN-P1-C1-G12_S1044

description: Biological replicate 1


title: 11M-MN-P1-C1-F6_S1026

description: Biological replicate 1


title: 11M-MN-P1-C1-G11_S1043

description: Biological replicate 1


title: 11M-MN-P1-C1-F5_S1025

description: Biological replicate 1


title: 11M-MN-P1-C1-F2_S1022

description: Biological replicate 1


title: 11M-MN-P1-C1-G8_S1040

description: Biological replicate 1


title: 11M-MN-P1-C1-F1_S1021

description: Biological replicate 1


title: 11M-MN-P1-C1-F12_S1032

description: Biological replicate 1


title: 11M-MN-P1-C1-F3_S1023

description: Biological replicate 1


title: 11M-MN-P1-C1-F4_S1024

description: Biological replicate 1


title: 11M-MN-P1-C1-G9_S1041

description: Biological replicate 1


title: 11M-MN-P1-C1-F10_S1030

description: Biological replicate 1


title: 11M-MN-P1-C1-E7_S1015

description: Biological replicate 1


title: 11M-MN-P1-C1-E8_S1016

description: Biological replicate 1


title: 11M-MN-P1-C1-F11_S1031

description: Biological replicate 1


title: 11M-MN-P1-C1-E6_S1014

description: Biological replicate 1


title: 11M-MN-P1-C1-E4_S1012

description: Biological replicate 1


title: 11M-MN-P1-C1-E5_S1013

description: Biological replicate 1


title: 11M-MN-P1-C1-E9_S1017

description: Biological replicate 1


title: 11M-MN-P1-C1-E1_S1009

description: Biological replicate 1


title: 11M-MN-P1-C1-G1_S1033

description: Biological replicate 1


title: 11M-MN-P1-C1-E2_S1010

description: Biological replicate 1


title: 11M-MN-P1-C1-E10_S1018

description: Biological replicate 1


title: 11M-MN-P1-C1-D9_S1005

description: Biological replicate 1


title: 11M-MN-P1-C1-E3_S1011

description: Biological replicate 1


title: 11M-MN-P1-C1-E11_S1019

description: Biological replicate 1


title: 11M-MN-P1-C1-D8_S1004

description: Biological replicate 1


title: 11M-MN-P1-C1-D7_S1003

description: Biological replicate 1


title: 11M-MN-P1-C1-D6_S1002

description: Biological replicate 1


title: 11M-MN-P1-C1-D3_S999

description: Biological replicate 1


title: 11M-MN-P1-C1-D5_S1001

description: Biological replicate 1


title: 11M-MN-P1-C1-D4_S1000

description: Biological replicate 1


title: 11M-MN-P1-C1-D2_S998

description: Biological replicate 1


title: 11M-MN-P1-C1-D12_S1008

description: Biological replicate 1


title: 11M-MN-P1-C1-D10_S1006

description: Biological replicate 1


title: 11M-MN-P1-C1-C9_S993

description: Biological replicate 1


title: 11M-MN-P1-C1-C7_S991

description: Biological replicate 1


title: 11M-MN-P1-C1-C8_S992

description: Biological replicate 1


title: 11M-MN-P1-C1-C6_S990

description: Biological replicate 1


title: 11M-MN-P1-C1-C4_S988

description: Biological replicate 1


title: 11M-MN-P1-C1-C5_S989

description: Biological replicate 1


title: 11M-MN-P1-C1-C3_S987

description: Biological replicate 1


title: 11M-MN-P1-C1-C1_S985

description: Biological replicate 1


title: 11M-MN-P1-C1-E12_S1020

description: Biological replicate 1


title: 11M-MN-P1-C1-C2_S986

description: Biological replicate 1


title: 11M-MN-P1-C1-C11_S995

description: Biological replicate 1


title: 11M-MN-P1-C1-C12_S996

description: Biological replicate 1


title: 11M-MN-P1-C1-B8_S980

description: Biological replicate 1


title: 11M-MN-P1-C1-C10_S994

description: Biological replicate 1


title: 11M-MN-P1-C1-B9_S981

description: Biological replicate 1


title: 11M-MN-P1-C1-B5_S977

description: Biological replicate 1


title: 11M-MN-P1-C1-B7_S979

description: Biological replicate 1


title: 11M-MN-P1-C1-B2_S974

description: Biological replicate 1


title: 11M-MN-P1-C1-B4_S976

description: Biological replicate 1


title: 11M-MN-P1-C1-B11_S983

description: Biological replicate 1


title: 11M-MN-P1-C1-B3_S975

description: Biological replicate 1


title: 11M-MN-P1-C1-B1_S973

description: Biological replicate 1


title: 11M-MN-P1-C1-A9_S969

description: Biological replicate 1


title: 11M-MN-P1-C1-B6_S978

description: Biological replicate 1


title: 11M-MN-P1-C1-A8_S968

description: Biological replicate 1


title: 11M-MN-P1-C1-A7_S967

description: Biological replicate 1


title: 11M-MN-P1-C1-D1_S997

description: Biological replicate 1


title: 11M-MN-P1-C1-A6_S966

description: Biological replicate 1


title: 11M-MN-P1-C1-D11_S1007

description: Biological replicate 1


title: 11M-MN-P1-C1-A5_S965

description: Biological replicate 1


title: 11M-MN-P1-C1-A11_S971

description: Biological replicate 1


title: 11M-MN-P1-C1-A12_S972

description: Biological replicate 1


title: 11M-MN-P1-C1-A2_S962

description: Biological replicate 1


title: 11M-MN-P1-C1-A1_S961

description: Biological replicate 1


title: 11M-MN-P1-C1-A10_S970

description: Biological replicate 1


title: 33

city: Genova

first: Lorenzo

last: Ferrando

address: Viale Benedetto XV

department: Department of Internal Medicine

country: Italy

institute: University of Genoa

library_source: transcriptomic

data_processing:
basecaller
tmap
Assembly: AmpliSeq Mouse Transcriptome V1 Reference
Supplementary files format and content: normalized counts (DESeq2)

source_name: primary bone marrow

growth_protocol: Lineage-/Sca1+/cKit+ cells isolated from the bone marrow of  3 naive C57BL/6 mice; 3 C57BL/6 mice 3 days after immunization for EAE; 3 C57BL/6 mice immunized for EAE and treated for 3  days with SR59230A, an antagonist of beta 3 adrenergic receptors.

extract_protocol: RNeasy micro kit

treatment_protocol: Lineage-/Sca1+/cKit+ cells isolated by cell sorting from the bone marrow of: 3 naive C57BL/6 mice; 3 C57BL/6 mice 3 days after immunization with complete Freund’s adjuvant and the encephalitogenic peptide of myelin oligodendrocyte glicoprotein (MOG35-55, EAE model); 3 C57BL/6 mice treated for 3  days after immunization with SR59230A, an antagonist of beta 3 adrenergic receptors.

tag: cell type

value: primary bone marrow

tag: treatment

value: EAE

tag: time

value: 3 days after immunization


title: 11M-DP-P1-A2-H9_S189

description: Biological replicate 1


title: 11M-MN-P1-C1-A4_S964

description: Biological replicate 1


title: 11M-DP-P1-A2-H8_S188

description: Biological replicate 1


title: S3

value: treated for 3 days


title: 11M-DP-P1-A2-H7_S187

description: Biological replicate 1


title: 11M-MN-P1-C1-B12_S984

description: Biological replicate 1


title: 11M-MN-P1-C1-B10_S982

description: Biological replicate 1


title: S2


title: 11M-DP-P1-A2-H6_S186

description: Biological replicate 1


title: N5

value: naive


title: N4


title: 11M-DP-P1-A2-H4_S184

description: Biological replicate 1


title: 11M-MN-P1-C1-A3_S963

description: Biological replicate 1


title: 11M-DP-P1-A2-H3_S183

description: Biological replicate 1


title: 11M-DP-P1-A2-H2_S182

description: Biological replicate 1


title: 34


title: 11M-DP-P1-A2-H1_S181

description: Biological replicate 1


title: 11M-DP-P1-A2-H12_S192

description: Biological replicate 1


title: 32


title: 11M-DP-P1-A2-H11_S191

description: Biological replicate 1


title: LGG_MYB X888

type: genomic

city: BETHESDA

first: Zhichao

last: Wu

state: MD

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

description:
LGG_MYB
Tumor

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
R package minfi v1.40.0
Normalized (preprocessFunnorm) Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

tag: gender

value: Female

tag: age

tag: material

value: FFPE


title: LGG_MYB Y630

description:
LGG_MYB
Tumor


title: LGG_MYB Z951

description:
LGG_MYB
Tumor


title: LGG_MYB Z111

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-G9_S177

description: Biological replicate 1


title: 11M-DP-P1-A2-G8_S176

description: Biological replicate 1


title: 11M-DP-P1-A2-H10_S190

description: Biological replicate 1


title: 11M-DP-P1-A2-G6_S174

description: Biological replicate 1


title: LGG_MYB X834

description:
LGG_MYB
Tumor


title: LGG_MYB V559

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-G7_S175

description: Biological replicate 1


title: LGG_MYB W446

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-H5_S185

description: Biological replicate 1


title: LGG_MYB Y323

description:
LGG_MYB
Tumor


title: S1


title: 11M-DP-P1-A2-G5_S173

description: Biological replicate 1


title: N3


title: LGG_MYB BG83

description:
LGG_MYB
Tumor


title: LGG_MYB BI28

description:
LGG_MYB
Tumor


title: LGG_MYB BD97

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-G3_S171

description: Biological replicate 1


title: 11M-DP-P1-A2-G4_S172

description: Biological replicate 1


title: LGG_MYB BB69

description:
LGG_MYB
Tumor


title: LGG_MYB BD71

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-G1_S169

description: Biological replicate 1


title: 11M-DP-P1-A2-G2_S170

description: Biological replicate 1


title: 11M-DP-P1-A2-G12_S180

description: Biological replicate 1


title: LGG_MYB AZ04

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-G11_S179

description: Biological replicate 1


title: LGG_MYB AW01

description:
LGG_MYB
Tumor


title: LGG_MYB AV30

description:
LGG_MYB
Tumor


title: LGG_MYB AT95

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-G10_S178

description: Biological replicate 1


title: 11M-DP-P1-A2-F8_S164

description: Biological replicate 1


title: 11M-DP-P1-A2-F9_S165

description: Biological replicate 1


title: 11M-DP-P1-A2-F7_S163

description: Biological replicate 1


title: LGG_MYB AM91

description:
LGG_MYB
Tumor


title: LGG_MYB AN05

description:
LGG_MYB
Tumor


title: LGG_MYB AK61

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-F5_S161

description: Biological replicate 1


title: 11M-DP-P1-A2-F4_S160

description: Biological replicate 1


title: 11M-DP-P1-A2-F3_S159

description: Biological replicate 1


title: HGNET_MN1 NL-AR-14

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-F6_S162

description: Biological replicate 1


title: HGNET_MN1 MR0124

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-F2_S158

description: Biological replicate 1


title: 11M-DP-P1-A2-F1_S157

description: Biological replicate 1


title: HGNET_MN1 Z655

description:
HGNET_MN1
Tumor


title: HGNET_MN1 Y873

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-F12_S168

description: Biological replicate 1


title: 11M-DP-P1-A2-F11_S167

description: Biological replicate 1


title: HGNET_MN1 Y599

description:
HGNET_MN1
Tumor


title: HGNET_MN1 X887

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-F10_S166

description: Biological replicate 1


title: 11M-DP-P1-A2-E9_S153

description: Biological replicate 1


title: HGNET_MN1 X859

description:
HGNET_MN1
Tumor


title: LGG_MYB AY33

description:
LGG_MYB
Tumor


title: HGNET_MN1 T456

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-E8_S152

description: Biological replicate 1


title: HGNET_MN1 T647

description:
HGNET_MN1
Tumor


title: HGNET_MN1 W267

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-E7_S151

description: Biological replicate 1


title: 11M-DP-P1-A2-E5_S149

description: Biological replicate 1


title: HGNET_MN1 BF46

description:
HGNET_MN1
Tumor


title: LGG_MYB AA31

description:
LGG_MYB
Tumor


title: 11M-DP-P1-A2-E6_S150

description: Biological replicate 1


title: 11M-DP-P1-A2-E3_S147

description: Biological replicate 1


title: HGNET_MN1 AZ72

description:
HGNET_MN1
Tumor


title: HGNET_MN1 AM97

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-E4_S148

description: Biological replicate 1


title: 11M-DP-P1-A2-E2_S146

description: Biological replicate 1


title: HGNET_MN1 AN03

description:
HGNET_MN1
Tumor


title: HGNET_MN1 AD67

description:
HGNET_MN1
Tumor


title: 11M-DP-P1-A2-E1_S145

description: Biological replicate 1


title: 11M-DP-P1-A2-E12_S156

description: Biological replicate 1


title: BCOR-ITD Y504

description:
BCOR-ITD
Tumor

source_name: BCOR-ITD


title: 11M-DP-P1-A2-E11_S155

description: Biological replicate 1


title: 11M-DP-P1-A2-E10_S154

description: Biological replicate 1


title: BCOR-ITD X232

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-D9_S141

description: Biological replicate 1


title: BCOR-ITD DKFZ00533

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-D8_S140

description: Biological replicate 1


title: BCOR-ITD CBTN-7316-740

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-D7_S139

description: Biological replicate 1


title: 11M-DP-P1-A2-D6_S138

description: Biological replicate 1


title: BCOR-ITD CBTN-7316-3897

description:
BCOR-ITD
Tumor


title: BCOR-ITD CBTN-7316-3775

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-D5_S137

description: Biological replicate 1


title: 11M-DP-P1-A2-D4_S136

description: Biological replicate 1


title: BCOR-ITD CBTN-7316-2857

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-D3_S135

description: Biological replicate 1


title: BCOR-ITD CBTN-7316-185

description:
BCOR-ITD
Tumor


title: BCOR-ITD CBTN-7316-1797

description:
BCOR-ITD
Tumor


title: BCOR-ITD AZ23

description:
BCOR-ITD
Tumor


title: BCOR-ITD BM64

description:
BCOR-ITD
Tumor


title: BCOR-ITD Y326

description:
BCOR-ITD
Tumor


title: BCOR-ITD AW19

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-D10_S142

description: Biological replicate 1


title: 11M-DP-P1-A2-D11_S143

description: Biological replicate 1


title: BCOR-ITD AW84

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-D12_S144

description: Biological replicate 1


title: 11M-DP-P1-A2-D2_S134

description: Biological replicate 1


title: BCOR-fusion AX30

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-C8_S128

description: Biological replicate 1


title: BCOR-fusion Y691

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-C9_S129

description: Biological replicate 1


title: BCOR-fusion Y844

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-C6_S126

description: Biological replicate 1


title: 11M-DP-P1-A2-C5_S125

description: Biological replicate 1


title: BCOR-fusion Y290

description:
BCOR-fusion
Tumor

source_name: BCOR-Stop


title: BCOR-fusion Y624

description:
BCOR-fusion
Tumor


title: BCOR-ITD Y272

description:
BCOR-ITD
Tumor


title: 11M-DP-P1-A2-C4_S124

description: Biological replicate 1


title: BCOR-fusion X535

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-C3_S123

description: Biological replicate 1


title: BCOR-fusion S454

description:
BCOR-fusion
Tumor


title: BCOR-fusion DKFZ08224

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-C2_S122

description: Biological replicate 1


title: 11M-DP-P1-A2-C1_S121

description: Biological replicate 1


title: BCOR-fusion DKFZ07409

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-D1_S133

description: Biological replicate 1


title: 11M-DP-P1-A2-C12_S132

description: Biological replicate 1


title: 11M-DP-P1-A2-C11_S131

description: Biological replicate 1


title: BCOR-fusion CH20

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-B9_S117

description: Biological replicate 1


title: BCOR-fusion DKFZ02322

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-C10_S130

description: Biological replicate 1


title: 11M-DP-P1-A2-C7_S127

description: Biological replicate 1


title: BCOR-fusion CBTN-7316-4274

description:
BCOR-fusion
Tumor


title: BCOR-fusion CBTN-7316-4035

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-B7_S115

description: Biological replicate 1


title: 11M-DP-P1-A2-B8_S116

description: Biological replicate 1


title: 11M-DP-P1-A2-B6_S114

description: Biological replicate 1


title: Nef 4

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I street NW, Ross Hall, Suite 731

institute: George Washington University

library_source: genomic

data_processing:
Illumina’s RTA and CASAVA pipeline
Sequencing datasets were quality assessed using fastqc (v. 0.11.9).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.38
High quality sequencing reads were aligned with bowtie2 (Langmead and Salzberg, 2012) using ‘—very-sensitive’ as an option
The alignments were subsequently sorted using samtools v. 1.16.1. (Li et al., 2009).
Differential analyses between exNef-treated cells and controls for the 1092 genes from the cholesterol metabolism, inflammation response and aerobic glycolysis pathways were performed using Hurdle model (Cragg, 1971), and a threshold of 10% False Discovery Rate (FDR<0.1) were considered significant.
Assembly: GRCh38
Supplementary files format and content: Least square (LS) means of reads obtained from open chromatin regions, together with fold-change and significance value (p and FDR) for differential chromatin accessibility between Nef and Control; aggregated file

source_name: monocyte-derived macrophages

growth_protocol: Buffy coats from donors were obtained from Gulf Coast Blood Center. PBMCs were isolated by density centrifugation using Ficoll-Paque (GE Healthcare) and, after washing 3 times with PBS, cells (9 x 106/ml) were plated in Primaria T-75 flasks or Primaria plates in Dutch modified RPMI (Gibco) supplemented with 1% Pen/Strep (Corning), 10 mM L-Glutamine (Corning) and 10 mM sodium pyruvate (Corning) and incubated in a humidified 37oC incubator with 5% CO2 for 2 hours to adhere to plastic.

extract_protocol:
Nuclei were suspended in transposition reaction mix (25 μl 2 x TD buffer, 2.5 μl Transposome and 22.5 μl nuclease free H20), incubated at 37oC for 60 min and purified using Qiagen MinElute kit (Quigen, cat# 28004).
ATAC-seq was performed using ATAC-seq Kit (Cell Biologics, cat# CB6936) according to the instruction manual.

treatment_protocol: Monocytes were treated with control or Nef EVs for 48 h and then differentiated intom monocyte-derived macrophages (MDM) for 7 days, and then analyzed by ATAC-seq.

value: monocyte-derived macrophages

tag: group

value: HIV-1 Nef


title: Nef 3


title: BCOR-fusion BM60

description:
BCOR-fusion
Tumor


title: Cont 4

value: control


title: 11M-DP-P1-A2-B5_S113

description: Biological replicate 1


title: Nef 2


title: Nef 1


title: BCOR-fusion BL89

description:
BCOR-fusion
Tumor

source_name: CREBBP-BCOR


title: Cont 3


title: Cont 1

source_name: monocytederived macrophages

value: monocytederived macrophages


title: Cont 2


title: 11M-DP-P1-A2-B4_S112

description: Biological replicate 1


title: BCOR-fusion CC93

description:
BCOR-fusion
Tumor


title: BCOR-fusion BJ64

description:
BCOR-fusion
Tumor


title: Cont8

data_processing:
Illumina’s RTA and CASAVA pipeline
Sequencing datasets were quality assessed using fastqc (v. 0.11.9).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.38
High quality RNA-sequencing reads were aligned to the latest version of the human genome reference (GRCh38, Dec 2013) using STAR v.2.7.3.c in 2-pass mode with transcript annotations from the assembly GRCh38.79 (Dobin et al., 2013).
Gene counts were estimated using the featureCounts utility of SubRead (Liao et al., 2013)
The normalized gene counts were used for differential expression analysis by DeSeq2 (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts for each sample

growth_protocol: Monocytes were treated with control or Nef EVs for 48 h and then differentiated intom monocyte-derived macrophages (MDM) for 7 days.

extract_protocol:
Total RNA was isolated and cleaned using RNeasy Plus Mini kit (Qiagen)
paired-end 2 x 150 bp configuration, single index, 50 million reads per sample

treatment_protocol: MDM were stimulated with 2 ng/ml LPS for 3h, washed and subjected to RNA-extraction.

value: control EV 48h, differentiation for 6 days followed by LPS (2ng/ml) for 24h


title: Nef8

value: NEF EV 48h, differentiation for 6 days followed by LPS (2ng/ml) for 24h


title: Nef7


title: 11M-DP-P1-A2-B2_S110

description: Biological replicate 1

value: SCC

value: FVB/N


title: Cont7


title: BCOR-fusion BE54

description:
BCOR-fusion
Tumor


title: Co_Lcasei_3

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

description: repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: FastQC
Step 4: Map with Bowtie2
Step 5: sort
Step 6: featurecounts (see our publication for details)
Assembly: Streptococcus mutans: NC_004350.2
Supplementary files format and content: Counts obtained from step 6: featurecounts, listed along side each open reading frame
Supplementary files format and content: Read counts for monoculture, coculture with NIDR 6715, 4646 and 14266, and quadculture conditions, in triplicate.

molecule: polyA RNA

organism:
Lacticaseibacillus casei
Streptococcus mutans UA159

source_name: Whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TYG medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen).
cDNA libraries were constructed by MiGS
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: grown in coculture (TYG) to OD600 nm = 0.5

tag: molecule subtype

value: enriched mRNA


title: BCOR-fusion CB22

description:
BCOR-fusion
Tumor


title: 11M-DP-P1-A2-B1_S109

description: Biological replicate 1

tag: tumor stage

value: Male

value: SBE-mCherry PGK-rtTA3

value: Tximport (v 1.12.3)


title: BCOR-fusion AY30

description:
BCOR-fusion
Tumor


title: Nef6


title: BCOR-fusion AN98

description:
BCOR-fusion
Tumor


title: Cont6


title: Co_Lcasei_1

description: repeat 1 of 3

tag: strain


title: Nef5


title: 11M-DP-P1-A2-B11_S119

description: Biological replicate 1

tag: mouse age


title: 11M-DP-P1-A2-B12_S120

description: Biological replicate 1

tag: genotype


title: Co_6715_3

description: repeat 3 of 3

organism:
Streptococcus sobrinus
Streptococcus mutans UA159


title: 11M-DP-P1-A2-B10_S118

description: Biological replicate 1

tag: mouse sex


title: BCOR-fusion BK22

description:
BCOR-fusion
Tumor


title: Cont5


title: Co_6715_2

description: repeat 2 of 3


title: 11M-DP-P1-A2-B3_S111

description: Biological replicate 1

tag: lentivirus injected at e9.5


title: Nef4


title: 11M-DP-P1-A2-A9_S105

description: Biological replicate 1

tag: sorting scheme


title: Co_6715_1

description: repeat 1 of 3


title: 11M-DP-P1-A2-A8_S104

description: Biological replicate 1

tag: read alignment program


title: 11M-DP-P1-A2-A7_S103

description: Biological replicate 1

tag: read quantification program


title: Co_Lcasei_2

description: repeat 2 of 3


title: Nef3

tag: cell type


title: Cont3

tag: treatment


title: 11M-DP-P1-A2-A6_S102

description: Biological replicate 1


title: CAR-T cells given on day 0 and collected 8 days later (second experiment)

city: Bethesda

first: Margaret

last: Cam

address: 9000 Rockville Pike

institute: NCI

description: Second experiment - sorted viable CAR T cells - transplanted on day 0 and retrieved for sorting on day +8

data_processing:
Basecalling by RTA 1.12.4.2, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 2.17, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq reads were aligned to mouse genome (mm10) using STAR (STAR_2.5.1b)
10x genomics data analysis was performed with the Cellranger v6.0.0 software using the default parameters. Cells with extremely low number of UMI counts were filtered out.
Assembly: refdata-gex-mm10-2020-A

source_name: CAR T-Cells

extract_protocol:
samples were isolated by cell sorting from spleen single cell suspensions (copy out more information from the paper methods)
10x Genomics Single Cell Chromium v2 mRNA libraries were made and sequenced on the NextSeq with v2 chemistry

value: H2kb+ / H2kk+ / H2kd-

tag: tissue

value: Spleen

tag: sorting profile

tag: batch


title: Primary YPAC-05

city: Incheon

first: ENZHI

last: LUO

department: Pharmacy

country: South Korea

institute: yonsei university

description:
Primary tissue
Primary YPAC-05

data_processing:
Raw data quality control through FastQC
Read mapping through STAR package.
Reads were counted through HTSeq with the following parameters:  htseq-count -s no -m intersection-nonempty -f bam
Differential gene expression analysis by using Deseq2 package.
Assembly: hg38
Supplementary files format and content: Matrix table for every samples and genes (Ensembl ID) with a sum of Deseq count value greater than 10 for each sample, txt file

source_name: Patient drived pancreatic cancer cells

growth_protocol: PFour-week-old male athymic nu/nu mice were used for the stereotactic injection of pancreatic cancer cells. Pancreatic cancer cells were treated with trypsin/EDTA (Sigma) and washed twice with FBS-supplemented serum-free medium. The mice were anesthetized using isoflurane, and a small incision was made in the left abdomen. A cell (5 × 105 cells) suspension was injected into the tail of the mouse pancreas under isoflurane (Pfizer). After 5 week, the mice were sacrificed by carbon dioxide asphyxiation and pancreatic tumor tissue was taken out and obtained.

extract_protocol:
RNA was isolated using the MiniBEST Universal RNA Extraction kit (TAKARA, 9767A) according to the manufacturer’s instructions. RNA Extraction kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nontreatment

tag: disease

value: Pancreatic cancer

value: Primary tissue


title: CAR-T cells given on day 5 and collected 16 days later (second experiment)

description: Second experiment - sorted viable CAR T cells - transplanted on day +5 and retrieved for sorting on day +21


title: 11M-DP-P1-A2-A5_S101

description: Biological replicate 1


title: 11M-DP-P1-A2-A4_S100

description: Biological replicate 1


title: CAR-T cells given on day 0 and collected 16 days later (second experiment)

description: Second experiment - sorted viable CAR T cells - transplanted on day 0 and retrieved for sorting on day +16


title: Cont2

value: monocyte-derived macrophages

tag: time


title: Primary YPAC-25

description:
Primary tissue
Primary YPAC-25


title: 11M-DP-P1-A2-A3_S99

description: Biological replicate 1


title: CAR-T cells given on day 0 and collected 3 days later (second experiment)

description: Second experiment - sorted viable CAR T cells - transplanted on day 0 and retrieved for sorting on day +3


title: CAR-T cells given on day 5 and collected 3 days later (second experiment)

description: Second experiment - sorted viable CAR T cells - transplanted on day +5 and retrieved for sorting on day +8


title: Orthotopic YPAC-16

description:
Orthotopic injection
Orthotopic YPAC-16

value: Orthotopic tissue


title: Nef1


title: Cont4


title: CD34+ injected retina rep2

type: RNA

city: Davis

first: Zeljka

last: Smit-McBride

state: CA

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

description: gene expression data form retinal tissue

hyb_protocol: Hybridization was performed at the Genomics Shared Resource at UC Davis Medical Center using a standard manufacturer’s procedure (Affymetrix).

scan_protocol: GeneChips were scanned using Genomics Shared Resource at UC Davis Medical Center using a standard manufacturer’s procedure (Affymetrix).

data_processing: Microarray data were analyzed using Affymetrix Expression Console followed by Transcriptome Analysis Console 3.0.  One-way ANOVA was used in the Transcriptome Analysis Console to identify statistically significant genes at a significance level of P ≤ 0.05. We used the standard approach of using a dual criterium of P-value ≤ 0.05 and fold change (FC) -1.5 ≥ FC ≥ 1.5 to identify differentially expressed genes. This approach ensures control of false positive candidates and preserves the desired biological significance.

label: biotin

source_name: mouse eyes 1 week post intravitreal injection

label_protocol: Samples of RNA were labeled using 50 ng total RNA, following the manufacturer’s protocol for GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) combined with Ambion WT Expression Kit (Ambion, Inc., Foster City, CA, USA). ). After labeling, the probes were hybridized to the Affymetrix Mouse Transcriptome Array 1.0 (MTA1) GeneChip microarrays. This array analyzes the expression of >114,000 transcripts for protein coding genes and >101,000 transcripts for nonprotein coding content (noncoding RNA, such as microRNA, pseudogenes, and rRNA).

growth_protocol: Retinal tissue was collected based on a standard protocol after animal sacrifice at 1 week following intravitreal injection

extract_protocol: Qiagen protocol that accompanies microRNeasy kit was used. Isolated total RNAs, including microRNA, were labeled for microarray gene expression analysis following a published protocol with slight modifications (Smit-McBride et al, 2011). Isolated RNA samples were run on an Agilent BioAnalyzer microfluidics chip RNA Nano 6000 (Agilent Technologies, Santa Clara, CA, USA) to assess quality and quantity. Out of four samples, the three samples having the highest quality (RNA Integrity Number [RIN] > 7 value) were labeled as probes for the Affymetrix GeneChip microarrays (Affymetrix, Santa Clara, CA, USA).

treatment_protocol: Mice were sacrificed, eyes were collected, disected and retina and RPE were placed in 300ul of RNALater, and kept at -20 till total RNA isolation

value: retina


title: PBS injected retina rep1


title: PBS injected retina rep2


title: PBS injected retina rep3


title: CD34+ injected retina rep3


title: CD34+ injected retina rep1


title: Orthotopic YPAC-05

description:
Orthotopic injection
Orthotopic YPAC-05


title: CAR-T cells prior to administration (second experiment)

description: Second experiment - sorted viable CAR T cells prior to transplant


title: 11M-DP-P1-A2-A1_S97

description: Biological replicate 1


title: CAR-T cells given on day 5 and collected 8 days later (second experiment)

description: Second experiment - sorted viable CAR T cells - transplanted on day +5 and retrieved for sorting on day +13


title: Nef2


title: Orthotopic YPAC-02

description:
Orthotopic injection
Orthotopic YPAC-02


title: CAR-T cells given on day 0 and collected 16 days later (first experiment)

description: First experiment - sorted viable CAR T cells - transplanted on day 0 and retrieved for sorting on day +16


title: CAR-T cells given on day 5 and collected 16 days later (first experiment)

description: First experiment - sorted viable CAR T cells - transplanted on day +5 and retrieved for sorting on day +21


title: Orthotopic YPAC-25

description:
Orthotopic injection
Orthotopic YPAC-25


title: CAR-T cells given on day 0 and collected 8 days later (first experiment)

description: First experiment - sorted viable CAR T cells - transplanted on day 0 and retrieved for sorting on day +8


title: SCC_Fig1_bulkRNA_rep1

description:
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_TPM.csv
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_counts.csv
processed data column: 46_M_Tumor

data_processing:
read alignment program:  Bowtie2 (version 2.2.9)
read quantification program:  RSEM (v1.2.30)
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm10) using either Salmon (v 1.4.0) or Bowtie2 (v 2.2.9)
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts with Tximport (v 1.12.3) in R (v 3.6.1)(Salmon aligned data) or by RSEM (v 1.2.30)(Bowtie2 aligned data).
Genome_build: mm10 (UCSC release)
Supplementary_files_format_and_content: tab-delineated text files or comma separated value files contain raw counts, and tab-delineated text files or comma separated value files contain calculated TPM

source_name: mouse back skin tumor

extract_protocol:
Cells were isolated by FACS, and collected into trizol. RNA was extracted using the Direct-zol RNA extraction kit (Zymo) following manufacturer's instructions.
RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit. Libraries were sequenced on an Illumina HiSeq 4000 or NovaSeq instrument as indicated.

value: mouse back skin tumor

tag: mouse strain

tag: treatment (lentivirus injected at e9.5)

tag: biological replicate


title: 11M-DP-P1-A2-A12_S108

description: Biological replicate 1

tag: tumor stage

tag: strain

tag: mouse age


title: Orthotopic YPAC-30

description:
Orthotopic injection
Orthotopic YPAC-30


title: 11M-DP-P1-A2-A2_S98

description: Biological replicate 1

tag: genotype

tag: mouse sex

tag: lentivirus injected at e9.5


title: CAL-62_si-LINC00886

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in NCBI were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: CAL-62 cells

extract_protocol:
We extracted total RNA samples for high-through RNA sequencing from CAL-62 cells transfected with LINC00886 smart silencer and negative control using Trizol reagent.
RNA libraries were prepared for sequencing using polyA selection RNA-seq protocols

value: Cell line

tag: transfection


title: CAR-T cells given on day 5 and collected 8 days later (first experiment)

description: First experiment - sorted viable CAR T cells - transplanted on day +5 and retrieved for sorting on day +13


title: KPOG organoid at 48hr treated with RT and FAKi [kpog_fak_8_48hr_#3]

city: St Louis

first: David

last: DeNardo

email: varintra@wustl.edu, ddenardo@wustl.edu

address: 425 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Pancreas

growth_protocol: 3D organoid cell lines (KPOG) were derived from tumor-bearing female KPC-OG mice. Cell suspension derived after tumor harvest (detailed below) was plated on Matrigel (Cultrex® Organoid Qualified BME, Type 2) dome under standard antibiotics for the generation of 3D organoid cell culture. Protocol for the generation of 3D organoid cell culture was adapted from Dr. Tuveson’s laboratory (Cold Spring Harbor Laboratory). GFP+ tumor cells were sorted on FACSAria-II (BD Biosciences), and re-plated in complete medium until stable cell lines were established. All 3D cell lines were cultured in complete medium (Advanced DMEM-F12 with 1% HEPES, 1% L-glutamine, and 1% PenStrep) at 37C and 5% CO2.

extract_protocol:
Total RNA was extracted from live cultured cells using an E.Z.N.A.® Total RNA kit (OMEGA) according to manufacturer’s instructions and banked in -80° C until use. cDNA for downstream applications were synthesized using qScript cDNA SuperMix kit (QuantaBio) according to manufacturer’s instructions.
Clontech SMARTer v1

treatment_protocol: One day post organoid culture preparation, organoid cultures were treated with 1uM of FAKi. Two hours post FAKi treatment, culture was treated with radiation (8Gy). Cells were isolated for RNA at 24hr or 48hr post RT.

value: Pancreas

tag: cell line

value: PDAC 3D organoid cell line

value: RT and FAKi


title: 11M-DP-P1-A2-A10_S106

description: Biological replicate 1

value: SCC

value: FVB/N

tag: sorting scheme

tag: read alignment program

tag: read quantification program


title: 11M-DP-P1-A2-A11_S107

description: Biological replicate 1

value: Male


title: Cont1

tag: cell type

tag: treatment

value: control EV 48h, differentiation for 6 days followed by LPS (2ng/ml) for 24h


title: SCC_Fig1_bulkRNA_rep2

description:
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_TPM.csv
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_counts.csv
processed data column: 83F_TGFbRIIfl_TetOHras

tag: tissue

value: Female


title: Orthotopic YPAC-26

description:
Orthotopic injection
Orthotopic YPAC-26

tag: disease


title: CAR-T cells given on day 5 and collected 3 days later (first experiment)

description: First experiment - sorted viable CAR T cells - transplanted on day +5 and retrieved for sorting on day +8

value: H2kb+ / H2kk+ / H2kd-

tag: sorting profile

tag: batch


title: CAL-62_Negative control

value: Negative control


title: CAR-T cells given on day 0 and collected 3 days later (first experiment)

description: First experiment - sorted viable CAR T cells - transplanted on day 0 and retrieved for sorting on day +3

value: Spleen


title: Patient 6 POST-treatment FNA PDAC tissue biopsy

data_processing:
The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50,000 mean reads per cell. FASTQ files from each sample were processed and aligned with BD Rhapsody WTA Analysis Pipeline (SevenBridges) using reference genome (GRCh38-PhiX-gencodev29.tar.gz) to generate feature barcode matrix.
Assembly: GRCh38-PhiX-gencodev29.tar.gz
Supplementary files format and content: CSV

extract_protocol:
PDAC tissue was then isolated, minced with scissors, and digested in ~15-25mL Dulbecco’s Modified Eagle Medium (DMEM) with 2mg/mL Collagenase A and 1x DNase I for 25 minutes at 37°C with constant stirring. Digestion buffer was quenched with 3mL fetal bovine serum (FBS) and filtered through 100uM Nylon mesh, pelleted by centrifugation (2000rmp for 5 min) and resuspended in FACS buffer (1% BSA in PBS).
Following tissue digestion, processed cells from each sample were encapsulated into droplets and libraries using BD Rhapsody Single-Cell Capture and cDNA Synthesis Analysis System (BD Biosciences) according to the manufacturer’s protocol.

treatment_protocol: PDAC tissues were taken from patients using ultrasound-guided biopsies and details of the trial design are available on clincaltrials.gov (NCT04331041) and briefly here. Patients received SBRT with a total of 50Gy given in 5 fractions. FAKi (VS-6063) was given at a dose of 400mg BID starting the end of day 2 post-SBRT and continued up to one year. Tissues were obtained pre-treatment and after 12-14 weeks post-SBRT.

value: Whole PDAC tissue biopsy

value: SBRT and FAKi (VS-6063)


title: Papilloma_Fig1_bulkRNA_rep2

description:
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_TPM.csv
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_counts.csv
processed data column: 85F_TGFbRIIflfl_TetOHras

tag: tumor stage

value: papilloma

tag: mouse strain

tag: treatment (lentivirus injected at e9.5)

tag: biological replicate


title: KPOG organoid at 48hr treated with RT and FAKi [kpog_fak_8_48hr_#2]

tag: genotype


title: KPOG organoid at 48hr treated with RT and FAKi [kpog_fak_8_48hr_#1]


title: KPOG organoid at 24hr treated with RT and FAKi [kpog_fak_8_24hr_#3]


title: Papilloma_Fig1_bulkRNA_rep1

description:
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_TPM.csv
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_counts.csv
processed data column: 47_M_Tumor

tag: mouse age

tag: mouse sex


title: Patient 6 PRE-treatment FNA PDAC tissue biopsy


title: KPOG organoid at 24hr treated with RT and FAKi [kpog_fak_8_24hr_#2]

tag: cell line


title: KPOG organoid at 24hr treated with RT and FAKi [kpog_fak_8_24hr_#1]


title: Patient 4 POST-treatment FNA PDAC tissue biopsy


title: Normal_skin_Fig1_bulkRNA_rep1

description:
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_TPM.csv
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_counts.csv
processed data column: 102F_TGFbRIIhet_TetOHras_normal

value: mouse back skin

value: normal skin

value: WT

tag: sorting scheme


title: Normal_skin_Fig1_bulkRNA_rep2

description:
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_TPM.csv
Yuan2021_Bl6_Norm_Pap_SCC_RNAseq_counts.csv
processed data column: 100F_TGFbRIIcKO_TetOHras_normal


title: Patient 4 PRE-treatment FNA PDAC tissue biopsy

value: Pancreas


title: Patient 3 PRE-treatment FNA PDAC tissue biopsy 2


title: KPOG organoid at 48hr treated with FAKi (1uM) [kpog_fak_0_48hr_#2]

value: PDAC 3D organoid cell line

value: FAKi (1uM)


title: KPOG organoid at 48hr treated with FAKi (1uM) [kpog_fak_0_48hr_#3]


title: SCC_mpos_bulkRNA_rep1

description:
Yuan2021_PAP_SCC_RNAseq_TPM.txt
Yuan2021_PAP_SCC_RNAseq_counts.txt

data_processing:
read alignment program:  Salmon (v 1.4.0)
read quantification program:  Tximport (v 1.12.3)
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm10) using either Salmon (v 1.4.0) or Bowtie2 (v 2.2.9)
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts with Tximport (v 1.12.3) in R (v 3.6.1)(Salmon aligned data) or by RSEM (v 1.2.30)(Bowtie2 aligned data).
Genome_build: mm10 (UCSC release)
Supplementary_files_format_and_content: tab-delineated text files or comma separated value files contain raw counts, and tab-delineated text files or comma separated value files contain calculated TPM

value: mouse back skin tumor

value: SCC

value: SBE-mCherry PGK-rtTA3


title: Patient 2 PRE-treatment FNA PDAC tissue biopsy 2


title: SCC_mpos_ATAC_rep1

data_processing:
The raw sequencing reads were aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome.
The aligned reads were deduplicated with Picard (v. 2.3.0) and shifted to correct for Tn5 insertion bias.
Bamfiles from biological replicates are combined with Samtools (1.9)
Peaks were called on replicate-pooled bamfiles with MACS2 (v. 2.1.1) with default settings.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bedfiles of narrowpeaks called from MACS2

extract_protocol:
Cells were isolated by FACS into FACS sorting buffer. Cells were pelleted and lysed using 0.01% IGEPAL CA-630. ATAC libraries were prepared on these solubilized nuclei, according to Buenrostro et al. 2015.
Illumina Nextera, Buenrostro et al., 2015

value: FVB/N

value: female

value: CD31/45/117/140a – CD49f/CD29 High CD44+ mCherry +

tag: molecule type

value: transposed DNA


title: SCC_mpos_ATAC_rep2


title: Patient 2 PRE-treatment FNA PDAC tissue biopsy 1


title: Patient 3 PRE-treatment FNA PDAC tissue biopsy 1


title: SCC_mpos_bulkRNA_rep2

value: Female


title: SCC_mneg_bulkRNA_rep1

value: Male


title: SCC_mneg_bulkRNA_rep2


title: KPOG organoid at 24hr treated with FAKi (1uM) [kpog_fak_0_24hr_#3]


title: CAR-T cells prior to administration (first experiment)

description: First experiment - sorted viable CAR T cells prior to transplant

tag: strain

value: H2kb+ / H2kk+ / H2kd-

value: Spleen


title: SCC_mneg_ATAC_rep2

value: CD31/45/117/140a – CD49f/CD29 High CD44+ mCherry -


title: KPOG organoid at 24hr treated with FAKi (1uM) [kpog_fak_0_24hr_#2]


title: KPOG organoid at 24hr treated with FAKi (1uM) [kpog_fak_0_24hr_#1]


title: SCC_mneg_ATAC_rep1


title: PAP_mpos_bulkRNA_rep1

value: papilloma


title: Patient 1 POST-treatment FNA PDAC tissue biopsy 2

tag: cell type

value: Whole PDAC tissue biopsy

value: SBRT and FAKi (VS-6063)


title: PAP_mpos_ATAC_rep2


title: Patient 1 POST-treatment FNA PDAC tissue biopsy 1

value: Pancreas

tag: treatment


title: PAP_mneg_bulkRNA_rep2

tag: tissue


title: KPOG organoid at 48hr treated with FAKi (1uM) [kpog_fak_0_48hr_#1]

value: PDAC 3D organoid cell line

value: FAKi (1uM)


title: KPOG organoid at 48hr treated with RT (8Gy) [kpog_dmso_8_48hr_#3]

value: RT (8Gy)


title: PAP_mpos_ATAC_rep1

value: mouse back skin tumor

value: SBE-mCherry PGK-rtTA3


title: KPOG organoid at 48hr treated with RT (8Gy) [kpog_dmso_8_48hr_#2]


title: PAP_mneg_bulkRNA_rep1

value: FVB/N


title: Patient 1 PRE-treatment FNA PDAC tissue biopsy 2


title: Patient 1 PRE-treatment FNA PDAC tissue biopsy 1


title: PAP_mneg_ATAC_rep1

value: female


title: S2_3-KO_TGF_24h_n2

city: LYON

first: Laurent

last: Bartholin

state: AUVERGNE-RHONE-ALPES

address: 28 RUE LAENNEC

country: France

institute: Centre de Recherche en Cancérologie de Lyon

data_processing:
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a), with the annotation of known genes from gencode v33.
Gene expression was quantified using Salmon (1.1.0) and the annotation of protein coding genes from gencode v33
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with raw counts from salmon for each sample

source_name: BxPC3 cells

growth_protocol: BxPC-3 cells were seeded in 10%-FBS RPMI in 6 wells plate

extract_protocol:
RNA was isolated, quantified and integrity was mesured using and RNA assay kit on a 2100 BioAnalyzer
TrueSeq poly-A+ kit from Illumina

treatment_protocol: After 3 hours of serum-starvation (0%-FBS RPMI), TGF-β was added at 10ng/mL for 1 or 24h.

value: pancreas

tag: crispr

value: SMAD2 and SMAD3 KO

value: TGFB


title: KPOG organoid at 24hr treated with RT (8Gy) [kpog_dmso_8_24hr_#3]


title: S2_3-KO_TGF_24h_n3


title: IFE_ATAC_rep1

value: mouse back skin

value: 8 wks

value: WT

value: transposed DNA


title: KPOG organoid at 24hr treated with RT (8Gy) [kpog_dmso_8_24hr_#2]


title: smRNA pol2a_1_sdlg_2

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

data_processing:
FASTQ reads were analyzed using the plant sequencing analysis pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools).
raw reads were treated using cutadapt v3.4 to remove the adapters and masked for rRNA, tRNA, and other noncoding RNAs.
The remaining reads were mapped to TAIR10 using ShortStack v3.8.5 with parameters “--align_only --bowtie_m 1000 --ranmax 50 --mismatches 0 --nohp”
For calculating and comparing sRNA abundance in the WT and mutant libraries, the Arabidopsis genome was tiled into 100-bp bins, and reads were assigned to bins based on their 5′ nucleotide
Normalization was conducted by calculating the RPM value (reads per million mapped reads) for each bin, and comparison was performed for each bin using DESeq2
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files containing raw read counts in length 18-26nt on 100bp bins

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: All the plants were grown in a greenhouse at 20°C under long-day cycle (16 h light/8 h dark, humidity 75%).

extract_protocol:
For meiocyte, 1 U/μL Recombinant RNase Inhibitor (Takara, 2313A) was added to the collection buffer. 300-400 meiocyte masses were used to extract ~400-1000 ng RNA for a biological replicate. The RNA was extracted using Trizol (ThermoFisher, 15596026). For seedling, 4-5 plants were ground in liquid nitrogen and the total RNA was also extracted using Trizol.
Small RNA libraries were constructed following the TruSeq small RNA library prep reference guide (Illumina)

value: 20-day-old seedlings


title: PAP_mpos_bulkRNA_rep2

value: papilloma

value: Female


title: smRNA suvh2suvh9_sdlg_2


title: smRNA suvh2suvh9_sdlg_1


title: KPOG organoid at 24hr treated with RT (8Gy) [kpog_dmso_8_24hr_#1]

value: Pancreas

value: PDAC 3D organoid cell line


title: HFSC_ATAC_rep1


title: S2_3-KO_TGF_24h_n1


title: S2_3-KO_TGF_1h_n3


title: S2_3-KO_TGF_1h_n2


title: smRNA pol2a_1_sdlg_1


title: smRNA WT_sdlg_2


title: PAP_mneg_ATAC_rep2

value: CD31/45/117/140a – CD49f/CD29 High CD44+ mCherry -


title: iDUX4 DMSO rep4 [RSA0000107826_RSA0000107706]

city: Cambridge

first: Abby

middle: Shuman

last: Hill

state: MA

address: 610 Main Street

department: Rare Disease Research Unit

institute: Pfizer

description:
orientation: inward
strandedness: reverse
75 bp paired end reads

data_processing:
Basecalls were performed with RTA v2.4.11
Bcl files were demultiplexed using bcl2fastq
Quality of fastq files was assessed using FastQC v0.11.8
Reads were aligned using STAR v2.7.3a to the hg38 genome modified to include the codon altered inducible DUX4 sequence
Estimated counts were obtained using Salmon v0.14.2 in alignment-based mode with the --gcBias flag
Assembly: hg38
Supplementary files format and content: comma separated text file of Salmon transcript counts
Supplementary files format and content: comma separated text file of Salmon TPM

source_name: MB135 iDUX4

growth_protocol: Cells were grown in Ham’s F10 Nutrient Mix (Gibco) containing 15% FBS (Gibco), 10 ng/mL rhFGF (Promega), and 1 µM dexamethasone (Sigma). 3µg/mL Puromycin (Gibco) was included in MB135 iDUX4 culture medium to ensure presence of the DUX4 inducible cassette.

extract_protocol:
RNA was isolated using an RNeasy mini kit (Qiagen)
mRNA-seq libraries were prepared from 200ng total RNA using the TruSeq Stranded mRNA Library Prep Kit (cat. 20020594, Illumina, San Diego, CA) on the Janus G3 Automated Liquid Handler System (PerkinElmer, Akron, OH).

treatment_protocol: Cells were allowed to attach overnight before the addition of either DMSO or 1 µg/mL doxycycline hydrochloride (Sigma) to induce DUX4 expression

value: MB135 iDUX4

value: myoblast

value: DMSO

tag: time

value: 14 hr


title: KPOG organoid at 48hr [kpog_dmso_0_48hr_#3]


title: iDUX4 DMSO rep3 [RSA0000107825_RSA0000107705]


title: KPOG organoid at 48hr treated with RT (8Gy) [kpog_dmso_8_48hr_#1]

value: RT (8Gy)


title: smRNA WT_sdlg_1


title: iDUX4 DMSO rep2 [RSA0000107824_RSA0000107704]


title: KPOG organoid at 48hr [kpog_dmso_0_48hr_#1]


title: smRNA suvh2suvh9_meiocyte_2

source_name: Meiocyte

value: Meiocytes isolated from stage 9-10 floral buds


title: iDUX4 DMSO rep1 [RSA0000107823_RSA0000107703]


title: S2_3-KO_TGF_1h_n1

value: pancreas

value: SMAD2 and SMAD3 KO

value: TGFB


title: smRNA suvh2suvh9_meiocyte_1


title: KPOG organoid at 24hr [kpog_dmso_0_24hr_#3]


title: S2_3-KO_NT_24h_n2


title: S2_3-KO_NT_24h_n1


title: WT t14 dox rep3 [RSA0000107821_RSA0000107701]

source_name: MB135 parental

value: MB135 parental

value: WT

value: doxycycline


title: WT t14 dox rep4 [RSA0000107822_RSA0000107702]


title: KPOG organoid at 24hr [kpog_dmso_0_24hr_#1]


title: smRNA pol2a_1_meiocyte_1


title: KPOG organoid at 24hr [kpog_dmso_0_24hr_#2]


title: smRNA pol2a_1_meiocyte_2


title: KPOG organoid at 48hr [kpog_dmso_0_48hr_#2]


title: smRNA WT_meiocyte_2


title: S2_3-KO_NT_1h_n2


title: WT t14 dox rep2 [RSA0000107820_RSA0000107700]


title: WT t14 dox rep1 [RSA0000107819_RSA0000107699]


title: S2_3-KO_NT_24h_n3


title: smRNA WT_meiocyte_1


title: iDUX4 t02 dox rep4 [RSA0000107818_RSA0000107698]

value: 2 hr


title: Ctl_KO_TGF_24h_n3

value: No


title: S2_3-KO_NT_1h_n1


title: iDUX4 t02 dox rep3 [RSA0000107817_RSA0000107697]


title: Immune cells from PDAC treated with RT and FAK inhibitor

description: KPPC, RTFAK, Immune

data_processing:
The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50,000 mean reads per cell. Cellranger mkfastq pipeline (10X Genomics) was used to demultiplex illumine base call files to FASTQ files. Afterward, fastq files from each sample were processed with Cellranger counts and aligned to the mouse mm10 reference genome (Cellranger v.4.0.0, 10X Genomics, mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) to generate feature barcode matrix.
Assembly: mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz
Supplementary files format and content: Cell barcodes: TSV, features: TSV, expression matrix: MTX

extract_protocol:
Mice were sacrificed by cardiac perfusion with ~10-15mL PBS-heparin under isofluorane anesthesia. PDAC tissue was then isolated, minced with scissors, and digested in ~15-25mL Dulbecco’s Modified Eagle Medium (DMEM) with 2mg/mL Collagenase A and 1x DNase I for 25 minutes at 37°C with constant stirring. Digestion buffer was quenched with 3mL fetal bovine serum (FBS) and filtered through 100uM Nylon mesh, pelleted by centrifugation (2000rmp for 5 min) and resuspended in FACS buffer (1% BSA in PBS). Cells were then resuspended in FACS Buffer containing CD16/CD32 antibodies to block for 10 minutes on ice, pelleted by centrifugation, then resuspended in fluorophore-conjugated antibodies, stained for 25 minutes on ice, then washed with FACS Buffer. Cells were then immediately sorted on Aria-II (BD Biosciences).  After cells were sorted into FACS Buffer, they were pelleted by centrifugation, resuspended in 0.04% BSA in PBS, and cell counts were obtained.
Single-cell RNA-sequencing library preparation was then conducted by the Genome Technology Access Center at Washington University. Briefly, cells from each sample were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’v3 Reagent kits according to the manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).

treatment_protocol: Mice received Radiation Therapy (RT) as five daily hypofractionated doses (6Gy x 5) using the Small Animal Radiation Research Platform (SARRP200, XStrahl Life Sciences). Mice were injected i.p. with an iodine contrast agent (2100mg/kg) before being placed on the irradiation platform one at a time under isoflurane anesthesia. Conebeam computed tomography (CT) imaging was performed for each individual mouse to pinpoint the pancreas, images were imported into Muriplan and used to select an isocenter. The tumor was then irradiated using anterior-posterior-opposed beams using either the 5mm x 5mm collimator at a dose rate of 3.9 Gy/min. Mice were monitored over 2 weeks for signs of radiation sickness or weight-loss. DietGel recovery gel was provided for 14-day window immediately following radiation therapy in survival studies. FAKi (VS-4718), provided by Verastem, Inc., is a selective bispecific inhibitor with activity against FAK1/PTK2 and Pyk2/PTK2b kinases. Cell-based assays have determined it has biochemical half-maximal inhibitory concentrations (IC50) of 6.0 nM and 20 nM for FAK and Pyk2. For animal experiments, 75mg/kg VS-4718 was formulated in vehicle (0.5% carboxymethyl cellulose and 0.1% Tween-80 (Sigma-Aldrich) in sterile water) and administered by oral gavage twice a day.

value: Pancreas

value: CD45+ immune cells

value: p48-Cre/LSL-KrasG12D/p53Flox/Flox (KPC)

value: RT + VS-4718 (75mg/kg) BID


title: Ctl_KO_TGF_24h_n2


title: iDUX4 t02 dox rep2 [RSA0000107816_RSA0000107696]

value: MB135 iDUX4

value: myoblast


title: BiSulfite-seq pol2a-1suvh2suvh9_sdlg_2

description: Bisulfite treated

data_processing:
FASTQ reads were analyzed using the plant sequencing analysis pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools).
raw reads were treated using cutadapt v3.4 to remove the adapters
remaining reads were mapped to the genome, deduplicated, and quantified using bismark v0.22.3 with Arabidopsis genome assembly TAIR10 (http://www.arabidopsis.org) and the modified parameter “--cutoff 4”
CG, CHG, and CHH DMRs were called using an R package DMRcaller v1.22.0 with the “bins” mode and threshold 0.4/0.2/0.1 for CG/CHG/CHH respectively
Assembly: TAIR10
Supplementary files format and content: standard CX_report.txt files output by Bismark

extract_protocol:
For meiocytes, over 1500 meiocytes were used to extract ~30-100 ng DNA for each biological replicate using the ChargeSwitch gDNA Micro Tissue Kit (ThermoFisher, CS11203). For seedlings, 4-5 plants were ground in liquid nitrogen and the genomic DNA was extracted by the CTAB method.
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China).

value: 20-day-old seedlings


title: Immune cells from PDAC treated with FAK inhibitor

description: KPPC, FAK, Immune


title: BiSulfite-seq suvh2suvh9_sdlg_2

description: Bisulfite treated


title: S2_3-KO_NT_1h_n3


title: BiSulfite-seq suvh2suvh9_sdlg_1

description: Bisulfite treated


title: CAFs from PDAC treated with RT

description: KPPC, RT, CAF

value: CD45- CD31- Epcam- PDPN+ CAFs

value: RT (6Gy x 5)


title: Immune cells from PDAC treated with RT

description: KPPC, RT, Immune


title: iDUX4 t02 dox rep1 [RSA0000107815_RSA0000107695]


title: Ctl_KO_TGF_1h_n3

value: pancreas


title: WT DMSO rep4 [RSA0000107814_RSA0000107694]

value: DMSO

value: 14 hr


title: CAFs from PDAC treated with RT and FAK inhibitor

description: KPPC, RTFAK, CAF


title: WT DMSO rep3 [RSA0000107813_RSA0000107693]

value: MB135 parental


title: Ctl_KO_TGF_1h_n1

value: TGFB


title: CAFs from PDAC treated with FAK inhibitor

description: KPPC, FAK, CAF


title: Ctl_KO_TGF_1h_n2


title: Immune cells from PDAC, Vehicle B

description: KPPC, Vehicle, B, Immune


title: BiSulfite-seq pol2a-1_sdlg_2

description: Bisulfite treated


title: BiSulfite-seq WT_sdlg_2

description: Bisulfite treated

value: WT


title: CAFs from PDAC

description: KPPC, Vehicle, CAF


title: BiSulfite-seq pol2a-1suvh2suvh9_sdlg_1

description: Bisulfite treated


title: BiSulfite-seq pol2a-1_sdlg_1

description: Bisulfite treated


title: WT DMSO rep2 [RSA0000107812_RSA0000107692]


title: Immune cells from PDAC, Vehicle A

description: KPPC, Vehicle, A, Immune


title: Ctl_KO_NT_24h_n3


title: WT DMSO rep1 [RSA0000107811_RSA0000107691]


title: BiSulfite-seq WT_sdlg_1

description: Bisulfite treated


title: Immune cells from PDAC, Vehicle

description: KPPC, Vehicle, Immune


title: Ctl_KO_NT_24h_n2


title: iDUX4 t14 dox rep4 [RSA0000107810_RSA0000107690]

value: doxycycline


title: PDV_WT_bulkRNA_rep4

description:
Yuan2021_PDV_WT_leprKO_RNAseq_TPM.txt
Yuan2021_PDV_WT_leprKO_RNAseq_counts.txt

source_name: mouse back skin tumor from grafted PDV tumor cell line

value: SCC

value: Nude/Nude

value: 8 wks

value: Female


title: Ctl_KO_TGF_24h_n1

value: No


title: BiSulfite-seq suvh2suvh9_meiocyte_2

description: Bisulfite treated

value: Meiocytes isolated from stage 9-10 floral buds


title: Ctl_KO_NT_24h_n1


title: iDUX4 t14 dox rep3 [RSA0000107809_RSA0000107689]

value: MB135 iDUX4

value: myoblast


title: PDV_WT_bulkRNA_rep3

value: mouse back skin tumor from grafted PDV tumor cell line


title: BiSulfite-seq suvh2suvh9_meiocyte_1

description: Bisulfite treated


title: iDUX4 t14 dox rep2 [RSA0000107808_RSA0000107688]


title: Ctl_KO_NT_1h_n3


title: PDV_WT_bulkRNA_rep2


title: Ctl_KO_NT_1h_n2


title: BiSulfite-seq pol2a-1_meiocyte_2

description: Bisulfite treated


title: PDV_WT_bulkRNA_rep1


title: BiSulfite-seq pol2a-1_meiocyte_1

description: Bisulfite treated


title: Ctl_KO_NT_1h_n1


title: PDV_LeprKO_bulkRNA_rep4

value: LeprKO


title: iDUX4 t14 dox rep1 [RSA0000107807_RSA0000107687]


title: iDUX4 t06 dox rep4 [RSA0000107806_RSA0000107686]

value: 6 hr


title: BiSulfite-seq WT_meiocyte_2

description: Bisulfite treated


title: Co_Cmat_3

description: repeat 3 of 3

organism:
Corynebacterium matruchotii
Streptococcus mutans UA159

value: grown in coculture (TYG) to OD600 nm = 0.5

tag: molecule subtype

value: enriched mRNA


title: PDV_LeprKO_bulkRNA_rep3

tag: tumor stage


title: PDV_LeprKO_bulkRNA_rep2

tag: mouse strain


title: iDUX4 t06 dox rep3 [RSA0000107805_RSA0000107685]


title: iDUX4 t06 dox rep2 [RSA0000107804_RSA0000107684]


title: Co_Cmat_2

description: repeat 2 of 3


title: BiSulfite-seq WT_meiocyte_1

description: Bisulfite treated


title: Myb-68 GFP+ bone marrow cells

city: Singapore

first: Takayoshi

last: Matsumura

address: 14 Medical Drive #12-01

country: Singapore

institute: National University of Singapore

description: 10x Genomics

data_processing:
Raw reads were aligned to the pre-build mm10 reference genome using cellranger count (10X Genomics) with default settings.
Cells were removed if the number of genes detected was less than 500, or more than 20% of reads were mapped to mitochondrial genes.
The variation due to cell cycle phase scores was regressed out.
Marker genes for each cluster was identified using the Seurat FindAllMarkers function.
Clusters were annotated by comparing the marker genes to known cell type markers from literatures.
Assembly: mm10
Supplementary files format and content: HDF5 file continaing a feature barcode matrix. This file can be loaded into R using Seurat.

source_name: bone marrow

extract_protocol:
Cells were FACS-sorted, washed, and processed using the 10x Genomics Chromium controller and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following manufacturer's instructions.
The library was prepared using 10xGenomics's Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and dual index kit following manufacturer's instructions.  Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.  Sequencing was done by DNBseq platform at BGI Genomics.

value: bone marrow

value: bone marrow cells

value: Myb-68 GFP+


title: RS_rep2

status: Public on Oct 08 2022

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

data_processing:
Using FASTX-Toolkit, raw data derived from RNA-seq was filtered to a minimum phred quality score of 28.
The BWA-MEM algorithm was employed to align the filtered reads into the reference genome.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by featureCounts tool in the Subread package.
Counted values were normalised in the RPKM method.
Genome_build: Bifidobacterium adolescentis P2P3 GCF_003856735.1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Bifidobacterium adolescentis

source_name: Bacterial culture with resistant starch

growth_protocol: B. adolescentis P2P3 was anaerobically incubated in 50 mL of CM broth containing each carbon substrateds (0.5% GLC, SS, GRS, and RS) at 37'C with constant shaking. At the initial stationary phase, the cells were kept on ice to stop the growth.

extract_protocol:
1 ml of each culture centrifuged and total RNA was prepared using RNeasy Midi kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Austin, TX, USA) was used to remove bacterial rRNA from the total RNA samples.
Eight libraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq4000 instrument.

value: wild type

tag: conditions

value: 0.5% resistant starch


title: RS_rep1


title: Myb-68 GFP+ Ly6C- GMP cells cultured with IL3 for 3 days

description: 10x Genomics

data_processing:
Raw reads were aligned to the pre-build mm10 reference genome using cellranger count (10X Genomics) with default settings.
Cells were removed if the number of UMIs was less than 500, the number of genes detected was less than 250, or more than 40% of reads were mapped to mitochondrial genes.
The variation due to mitochondrial RNA ratio and cell cycle phase scores were regressed out.
Marker genes for each cluster was identified using the Seurat FindAllMarkers function.
Clusters were annotated by comparing the marker genes to known cell type markers from literatures.
Assembly: mm10
Supplementary files format and content: HDF5 file continaing a feature barcode matrix. This file can be loaded into R using Seurat.

growth_protocol: Cells were cultured with IL3 for 3 days

extract_protocol:
Cultured clls were harvested, washed, and processed using the 10x Genomics Chromium controller and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following manufacturer's instructions.
The library was prepared using 10xGenomics's Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and dual index kit following manufacturer's instructions.  Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.  Sequencing was done by DNBseq platform at BGI Genomics.

value: Ly6C- GMP cells

value: cultured with IL3 for 3 days


title: PDV_LeprKO_bulkRNA_rep1

value: SCC

value: Nude/Nude

value: 8 wks

value: Female

tag: treatment (lentivirus injected at e9.5)

tag: biological replicate


title: GRS_rep1

source_name: Bacterial culture with gelatinized resistant starch

tag: genotype

value: 0.5% gelatinized resistant starch


title: iDUX4 t06 dox rep1 [RSA0000107803_RSA0000107683]

value: MB135 iDUX4

value: myoblast

value: doxycycline


title: GLC_rep2

source_name: Bacterial culture with glucose

value: 0.5% glucose


title: GRS_rep2


title: SS_rep2

source_name: Bacterial culture with soluble starch

value: 0.5% soluble starch


title: GLC_rep1


title: SS_rep1


title: PyMT cell lines + Test CD4+ T cell Supernatant [Test2-2]

city: Charleston

first: Heehwa

last: Son

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
RNA sequencing data were analyzed using the pipeline Version 5.0.
Sequences were aligned to the mouse reference genome (mm10) using Bowtie
Differentially expressed genes were screened using the Poisson distribution method, the Noiseq, or EBSeq packages
Assembly: mm10
Supplementary files format and content: FPKM values

source_name: breast

growth_protocol: PyMt cell line were plated in low adherence 48-wells plate in RPMI medium 1640 (Gibco), supplemented with 10% fetal bovine serum (Corning), 1% penicillin/streptavidin/glutamine (Thermo Fisher Scientific), 22 mM 2-mercaptoethanol (Gibco), and 5ug/ml insulin (medium) or in CD4+ T cell supernatants derived from Tslp-PyMttg (test), Tslp-PyMttg TslprKO and PyMttg (control) also supplemented with 5 μg/ml insulin (Sigma-Aldrich).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sorted CD4+ T cells were stimulated and rested ex vivo, and supernatants derived from these cultures were used for PyMt culture experiments

value: breast

value: PyMt cancer cell line

value: cancer


title: PyMT cell lines + Test CD4+ T cell Supernatant [Test3-1]


title: PyMT cell lines + Test CD4+ T cell Supernatant [Test3-2]


title: PyMT cell lines + Control CD4+ T cell Supernatant [Control-2]


title: PyMT cell lines + Control CD4+ T cell Supernatant [Blank-2]


title: PyMT cell lines + Test CD4+ T cell Supernatant [Test1-2]


title: PyMT cell lines + Control CD4+ T cell Supernatant [Blank-1]


title: Co_Cmat_1

description: repeat 1 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: FastQC
Step 4: Map with Bowtie2
Step 5: sort
Step 6: featurecounts (see our publication for details)
Assembly: Streptococcus mutans: NC_004350.2
Supplementary files format and content: Counts obtained from step 6: featurecounts, listed along side each open reading frame
Supplementary files format and content: Read counts for monoculture, coculture with NIDR 6715, 4646 and 14266, and quadculture conditions, in triplicate.

source_name: Whole cell lysate

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen).
cDNA libraries were constructed by MiGS
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

value: grown in coculture (TYG) to OD600 nm = 0.5

value: enriched mRNA


title: PyMT cell lines + Test CD4+ T cell Supernatant [Test2-1]


title: PyMT cell lines + Test CD4+ T cell Supernatant [Test1-1]