title: Blood_Platelets_Vumc-MS-027 [Vumc-MS-Presto-027-TR1468]


title: Blood_Platelets_Vumc-MS-023 [Vumc-MS-Presto-023-TR1431]

status: Public on Oct 22 2020

type: SRA

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

library_source: transcriptomic

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

molecule: total RNA

organism: Homo sapiens

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations (12-19 samples per Hiseq lane) and submitted for 100 bp Single Read sequencing on the Hiseq 2500 platform (Illumina).

tag: group

value: multipleSclerose


title: Blood_Platelets_Vumc-MS-025 [Vumc-MS-Presto-025-TR1433]


title: VZA01701R.P06

city: Solna

first: Vasilios

last: Zachariadis

address: Visionsgatan 4

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
https://github.com/EngeLab/DNTRseq
Genome_build: hg38
Supplementary_files_format_and_content: mRNA read counts summarized over genes; DNA read counts summarized over genomic bins

source_name: DNTR-seq mRNA

growth_protocol: HCT116 and A375 cells were cultured in DMEM medium supplemented with 10% FBS and 1% Penicillin/strepotomycin at 37°C, 5% CO2 and humidified atmosphere.

extract_protocol:
Individual live cells were FACS-sorted into 384-well plates with lysis buffer, snap-frozen and stored at -80 degrees C.
After splitting each cell, separate mRNA- (*R suffix) and DNA-libraries (*D suffix) were constructed. As comparison, a set of cells had mRNA libraries prepared with Smart-Seq2 (no suffix).
Barcoded libraries were sequenced paired-end (37bp x 2) on an Illumina NextSeq.

treatment_protocol: Cells were untreated, treated with etoposide (ETO) or X-ray at increasing concentrations and harvested at different timepoints.

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: treatment

value: X-ray 5Gy

tag: time point

tag: cell count


title: VZA01701R.P07


title: VZA01701R.P08


title: VZA01701R.P04


title: Blood_Platelets_Vumc-MS-042 [Vumc-MS-Presto-042-TR1443]


title: VZA01701R.P03


title: VZA01701R.P05


title: VZA01701R.P01


title: Blood_Platelets_Vumc-MS-016 [Vumc-MS-016-TR852]


title: Blood_Platelets_Vumc-MS-018 [Vumc-MS-018-TR854]


title: Blood_Platelets_Vumc-MS-017 [Vumc-MS-017-TR853]


title: VZA01701R.O24

value: X-ray 3Gy


title: VZA01701R.O23


title: Blood_Platelets_Vumc-MS-012 [Vumc-MS-012-TR850]


title: Blood_Platelets_Vumc-MS-030 [Vumc-MS-Presto-030-TR1471]


title: Blood_Platelets_Vumc-MS-015 [Vumc-MS-015-TR696]


title: VZA01701R.O22


title: Blood_Platelets_Vumc-MS-014 [Vumc-MS-014-TR673]


title: Blood_Platelets_Vumc-MS-011 [Vumc-MS-011-TR645]


title: Blood_Platelets_Vumc-MS-013 [Vumc-MS-013-TR672]


title: VZA01701R.O19


title: Blood_Platelets_Vumc-MS-010 [Vumc-MS-010-TR644]


title: Blood_Platelets_Vumc-MS-019 [Vumc-MS-019-TR855]


title: VZA01701R.P02


title: Blood_Platelets_Vumc-MS-009 [Vumc-MS-009-TR643]


title: VZA01701R.O18


title: VZA01701R.O17


title: VZA01701R.O20


title: Blood_Platelets_Vumc-MS-008 [Vumc-MS-008-TR642]


title: VZA01701R.O15


title: Blood_Platelets_Vumc-MS-004 [Vumc-MS-004-TR639]


title: Blood_Platelets_Vumc-MS-007 [Vumc-MS-007-TR641]


title: VZA01701R.O16


title: VZA01701R.O11


title: VZA01701R.O12


title: Blood_Platelets_Vumc-MS-001 [Vumc-MS-001-TR636]


title: VZA01701R.O13


title: VZA01701R.O14


title: Blood_Platelets_Vumc-MS-003 [Vumc-MS-003-TR638]


title: Blood_Platelets_Vumc-MS-002 [Vumc-MS-002-TR637]


title: Blood_Platelets_Vumc-MS-005 [Vumc-MS-005-TR640]


title: VZA01701R.O09


title: Blood_Platelets_Maas-GBM-NICT-035G-TR2170 [Maas-GBM-NICT-035G-TR2170]

description: Please note that this sample was included twice in the validation series

value: GBM


title: VZA01701R.O21


title: VZA01701R.O08


title: Blood_Platelets_Maas-GBM-M00012-TR2120 [Maas-GBM-M00012-TR2120]


title: Blood_Platelets_Maas-GBM-M00015-TR2121 [Maas-GBM-M00015-TR2121]


title: Blood_Platelets_Maas-GBM-M00009-TR2117 [Maas-GBM-M00009-TR2117]


title: VZA01701R.O07


title: Blood_Platelets_Maas-GBM-M00002-TR2114 [Maas-GBM-M00002-TR2114]


title: VZA01701R.O05


title: Blood_Platelets_Maas-GBM-M00007-TR2116 [Maas-GBM-M00007-TR2116]


title: Blood_Platelets_Maas-GBM-M00001-TR2112 [Maas-GBM-M00001-TR2112]


title: VZA01701R.O04


title: VZA01701R.O03


title: VZA01701R.O02


title: VZA01701R.O10


title: Blood_Platelets_Maas-GBM-M00003-TR2115 [Maas-GBM-M00003-TR2115]


title: VZA01701R.O01


title: VZA01701R.N24


title: Blood_Platelets_Maas-GBM-M00004-TR2113 [Maas-GBM-M00004-TR2113]


title: Blood_Platelets_Maas-GBM-NICT-040G-TR2172 [Maas-GBM-NICT-040G-TR2172]


title: Blood_Platelets_Maas-GBM-NICT-027G-TR2169 [Maas-GBM-NICT-027G-TR2169]


title: Blood_Platelets_Maas-GBM-NICT-037G-TR2171 [Maas-GBM-NICT-037G-TR2171]


title: Blood_Platelets_Maas-GBM-NICT-004G-TR2168 [Maas-GBM-NICT-004G-TR2168]


title: VZA01701R.N22


title: VZA01701R.N20


title: VZA01701R.N23


title: Blood_Platelets_Radb-GBM-N14-03-TR2142 [Radb-GBM-N14-03-TR2142]


title: VZA01701R.N19


title: Blood_Platelets_Radb-GBM-N14-10-TR2146 [Radb-GBM-N14-10-TR2146]


title: Blood_Platelets_Radb-GBM-N14-01-TR2140 [Radb-GBM-N14-01-TR2140]


title: Blood_Platelets_Radb-GBM-N15-02-TR2149 [Radb-GBM-N15-02-TR2149]


title: Blood_Platelets_Maas-GBM-M00010-TR2118 [Maas-GBM-M00010-TR2118]


title: Blood_Platelets_Vumc-GBM-follow-up-VU554t1-TR1908 [Vumc-GBM-follow-up-VU554t1-TR1908]


title: Blood_Platelets_Vumc-GBM-follow-up-VU554t2-TR1826 [Vumc-GBM-follow-up-VU554t2-TR1826]


title: Blood_Platelets_Vumc-GBM-follow-up-VU559t1-TR1827 [Vumc-GBM-follow-up-VU559t1-TR1827]


title: Blood_Platelets_Vumc-GBM-follow-up-VU551t2-TR1825 [Vumc-GBM-follow-up-VU551t2-TR1825]


title: VZA01701R.N15


title: VZA01701R.N13


title: VZA01701R.N12


title: VZA01701R.N14


title: Blood_Platelets_Vumc-GBM-follow-up-VU551t1-TR1824 [Vumc-GBM-follow-up-VU551t1-TR1824]


title: VZA01701R.N21


title: Blood_Platelets_Vumc-GBM-follow-up-VU550t3-TR1823 [Vumc-GBM-follow-up-VU550t3-TR1823]


title: Blood_Platelets_Vumc-GBM-follow-up-VU550t2-TR1772 [Vumc-GBM-follow-up-VU550t2-TR1772]


title: Blood_Platelets_Vumc-GBM-follow-up-VU550t1-TR1771 [Vumc-GBM-follow-up-VU550t1-TR1771]


title: VZA01701R.N17


title: VZA01701R.N09


title: VZA01701R.N18


title: Blood_Platelets_Vumc-GBM-follow-up-VU548t3-TR1822 [Vumc-GBM-follow-up-VU548t3-TR1822]


title: VZA01701R.N06


title: VZA01701R.N07


title: VZA01701R.N16


title: Blood_Platelets_Vumc-GBM-follow-up-VU542t4-TR1748 [Vumc-GBM-follow-up-VU542t4-TR1748]


title: VZA01701R.N08


title: VZA01701R.N04


title: VZA01701R.N05


title: Blood_Platelets_Vumc-GBM-follow-up-VU542t1-TR1565 [Vumc-GBM-follow-up-VU542t1-TR1565]


title: VZA01701R.N03


title: Blood_Platelets_Vumc-GBM-follow-up-VU540t1-TR1770 [Vumc-GBM-follow-up-VU540t1-TR1770]


title: VZA01701R.N11


title: VZA01701R.O06


title: VZA01701R.N02


title: VZA01701R.N10


title: Blood_Platelets_Vumc-GBM-follow-up-VU535t4-TR1769 [Vumc-GBM-follow-up-VU535t4-TR1769]


title: VZA01701R.M24


title: VZA01701R.N01


title: Blood_Platelets_Vumc-GBM-follow-up-VU535t2-TR1768 [Vumc-GBM-follow-up-VU535t2-TR1768]


title: VZA01701R.M23


title: VZA01701R.M22


title: Blood_Platelets_Vumc-GBM-follow-up-VU527t2-TR1819 [Vumc-GBM-follow-up-VU527t2-TR1819]


title: VZA01701R.M21


title: Blood_Platelets_Vumc-GBM-follow-up-VU548t1-TR1821 [Vumc-GBM-follow-up-VU548t1-TR1821]


title: VZA01701R.M20


title: Blood_Platelets_Vumc-GBM-follow-up-VU523t5-TR1817 [Vumc-GBM-follow-up-VU523t5-TR1817]


title: VZA01701R.M18


title: Blood_Platelets_Vumc-GBM-follow-up-VU523t2-TR1747 [Vumc-GBM-follow-up-VU523t2-TR1747]


title: Blood_Platelets_Vumc-GBM-follow-up-VU535t1-TR1767 [Vumc-GBM-follow-up-VU535t1-TR1767]


title: Blood_Platelets_Vumc-GBM-follow-up-VU542t2-TR1564 [Vumc-GBM-follow-up-VU542t2-TR1564]


title: Blood_Platelets_Vumc-GBM-follow-up-VU527t1-TR1818 [Vumc-GBM-follow-up-VU527t1-TR1818]


title: VZA01701R.M19


title: VZA01701R.M17


title: Blood_Platelets_Vumc-GBM-follow-up-VU518t4-TR1766 [Vumc-GBM-follow-up-VU518t4-TR1766]


title: Blood_Platelets_Vumc-GBM-follow-up-VU523t1-TR1746 [Vumc-GBM-follow-up-VU523t1-TR1746]


title: Blood_Platelets_Vumc-GBM-follow-up-VU540t2-TR1820 [Vumc-GBM-follow-up-VU540t2-TR1820]


title: Blood_Platelets_Vumc-GBM-follow-up-VU518t2-TR1765 [Vumc-GBM-follow-up-VU518t2-TR1765]


title: VZA01701R.M16


title: VZA01701R.M15


title: Blood_Platelets_Vumc-GBM-follow-up-VU518t1-TR1764 [Vumc-GBM-follow-up-VU518t1-TR1764]


title: VZA01701R.M11


title: VZA01701R.M12


title: VZA01701R.M14


title: VZA01701R.M13


title: Blood_Platelets_Vumc-GBM-follow-up-VU517t4-TR1763 [Vumc-GBM-follow-up-VU517t4-TR1763]


title: Blood_Platelets_Vumc-GBM-follow-up-VU517t5-TR1816 [Vumc-GBM-follow-up-VU517t5-TR1816]


title: Blood_Platelets_Vumc-GBM-follow-up-VU517t2-TR1745 [Vumc-GBM-follow-up-VU517t2-TR1745]


title: Blood_Platelets_Vumc-GBM-follow-up-VU508t1-TR1737 [Vumc-GBM-follow-up-VU508t1-TR1737]


title: VZA01701R.M10


title: VZA01701R.M09


title: Blood_Platelets_Vumc-GBM-follow-up-VU517t3-TR1762 [Vumc-GBM-follow-up-VU517t3-TR1762]


title: Blood_Platelets_Vumc-GBM-follow-up-VU506t3-TR1736 [Vumc-GBM-follow-up-VU506t3-TR1736]


title: VZA01701R.M08


title: Blood_Platelets_Vumc-GBM-follow-up-VU508t6-TR1743 [Vumc-GBM-follow-up-VU508t6-TR1743]


title: VZA01701R.M06


title: Blood_Platelets_Vumc-GBM-follow-up-VU517t1-TR1744 [Vumc-GBM-follow-up-VU517t1-TR1744]


title: Blood_Platelets_Vumc-GBM-follow-up-VU504t2-TR1733 [Vumc-GBM-follow-up-VU504t2-TR1733]


title: Blood_Platelets_Vumc-GBM-follow-up-VU506t1-TR1734 [Vumc-GBM-follow-up-VU506t1-TR1734]


title: Blood_Platelets_Vumc-GBM-follow-up-VU506t2-TR1735 [Vumc-GBM-follow-up-VU506t2-TR1735]


title: VZA01701R.M03


title: VZA01701R.M05


title: VZA01701R.M02


title: VZA01701R.M04


title: Blood_Platelets_Vumc-GBM-follow-up-VU504t1-TR1732 [Vumc-GBM-follow-up-VU504t1-TR1732]


title: VZA01701R.M01


title: VZA01701R.L24


title: Blood_Platelets_Vumc-GBM-follow-up-VU501t4-TR1731 [Vumc-GBM-follow-up-VU501t4-TR1731]


title: Blood_Platelets_Vumc-GBM-follow-up-VU502t2-TR1815 [Vumc-GBM-follow-up-VU502t2-TR1815]


title: VZA01701R.L23


title: Blood_Platelets_Vumc-GBM-follow-up-VU501t3-TR1730 [Vumc-GBM-follow-up-VU501t3-TR1730]


title: Blood_Platelets_Vumc-GBM-follow-up-VU501t1-TR1813 [Vumc-GBM-follow-up-VU501t1-TR1813]


title: VZA01701R.L22


title: Blood_Platelets_Vumc-GBM-follow-up-VU502t1-TR1814 [Vumc-GBM-follow-up-VU502t1-TR1814]


title: VZA01701R.M07


title: VZA01701R.L21


title: VZA01701R.L20


title: Blood_Platelets_Vumc-GBM-follow-up-VU500t1-TR1729 [Vumc-GBM-follow-up-VU500t1-TR1729]


title: VZA01701R.L19


title: VZA01701R.L18


title: VZA01701R.L17


title: Blood_Platelets_Vumc-GBM-follow-up-VU493t5-TR1727 [Vumc-GBM-follow-up-VU493t5-TR1727]


title: Blood_Platelets_Vumc-GBM-follow-up-VU493t3-TR1812 [Vumc-GBM-follow-up-VU493t3-TR1812]


title: VZA01701R.L16


title: Blood_Platelets_Vumc-GBM-follow-up-VU493t1-TR1563 [Vumc-GBM-follow-up-VU493t1-TR1563]


title: Blood_Platelets_Vumc-GBM-follow-up-VU493t7-TR1728 [Vumc-GBM-follow-up-VU493t7-TR1728]


title: Blood_Platelets_Vumc-GBM-follow-up-VU488t5-TR1725 [Vumc-GBM-follow-up-VU488t5-TR1725]


title: VZA01701R.L13


title: Blood_Platelets_VUmc-GBM-follow-up-VU489t4-TR1726 [VUmc-GBM-follow-up-VU489t4-TR1726]


title: Blood_Platelets_Vumc-GBM-follow-up-VU488t4-TR1724 [Vumc-GBM-follow-up-VU488t4-TR1724]


title: VZA01701R.L12


title: VZA01701R.L15


title: VZA01701R.L11


title: VZA01701R.L14


title: Blood_Platelets_Vumc-GBM-follow-up-VU488t1-TR1886 [Vumc-GBM-follow-up-VU488t1-TR1886]


title: Blood_Platelets_Vumc-GBM-follow-up-VU484t6-TR1811 [Vumc-GBM-follow-up-VU484t6-TR1811]


title: VZA01701R.L10


title: VZA01701R.L09


title: Blood_Platelets_Vumc-GBM-follow-up-VU484t4-TR1810 [Vumc-GBM-follow-up-VU484t4-TR1810]


title: VZA01701R.L08


title: Blood_Platelets_Vumc-GBM-follow-up-VU484t2-TR1742 [Vumc-GBM-follow-up-VU484t2-TR1742]


title: VZA01701R.L07


title: Blood_Platelets_Vumc-GBM-follow-up-VU480t2-TR1562 [Vumc-GBM-follow-up-VU480t2-TR1562]


title: VZA01701R.L06


title: VZA01701R.L05


title: Blood_Platelets_Vumc-GBM-follow-up-VU477t1-TR1740 [Vumc-GBM-follow-up-VU477t1-TR1740]


title: Blood_Platelets_Vumc-GBM-follow-up-VU480t1-TR1831 [Vumc-GBM-follow-up-VU480t1-TR1831]


title: Blood_Platelets_Vumc-GBM-follow-up-VU491t1-TR1887 [Vumc-GBM-follow-up-VU491t1-TR1887]


title: VZA01701R.L04


title: Blood_Platelets_Vumc-GBM-follow-up-VU476t1-TR1566 [Vumc-GBM-follow-up-VU476t1-TR1566]


title: VZA01701R.L03


title: Blood_Platelets_Vumc-GBM-follow-up-VU474t6-TR1561 [Vumc-GBM-follow-up-VU474t6-TR1561]


title: VZA01701R.L02


title: VZA01701R.L01


title: Blood_Platelets_Vumc-GBM-follow-up-VU474t4-TR1809 [Vumc-GBM-follow-up-VU474t4-TR1809]


title: Blood_Platelets_Vumc-GBM-follow-up-VU474t3-TR1568 [Vumc-GBM-follow-up-VU474t3-TR1568]


title: VZA01701R.K24


title: Blood_Platelets_Vumc-GBM-follow-up-VU472t4-TR1559 [Vumc-GBM-follow-up-VU472t4-TR1559]


title: Blood_Platelets_Vumc-GBM-follow-up-VU474t1-TR1560 [Vumc-GBM-follow-up-VU474t1-TR1560]


title: VZA01701R.K21


title: VZA01701R.K23


title: Blood_Platelets_Vumc-GBM-follow-up-VU484t1-TR1741 [Vumc-GBM-follow-up-VU484t1-TR1741]


title: VZA01701R.K20


title: Blood_Platelets_Vumc-GBM-follow-up-VU472t1-TR1557 [Vumc-GBM-follow-up-VU472t1-TR1557]


title: Blood_Platelets_Vumc-GBM-follow-up-VU445t2-TR1555 [Vumc-GBM-follow-up-VU445t2-TR1555]


title: VZA01701R.K19


title: VZA01701R.K18


title: Blood_Platelets_Vumc-GBM-follow-up-VU440t3-TR1498 [Vumc-GBM-follow-up-VU440t3-TR1498]


title: VZA01701R.K17


title: Blood_Platelets_Vumc-GBM-follow-up-VU429t7-TR1739 [Vumc-GBM-follow-up-VU429t7-TR1739]


title: VZA01701R.K15


title: Blood_Platelets_Vumc-GBM-follow-up-VU429t4-TR1496 [Vumc-GBM-follow-up-VU429t4-TR1496]


title: Blood_Platelets_Vumc-GBM-follow-up-VU423t9-VU561t0-TR1551 [Vumc-GBM-follow-up-VU423t9-VU561t0-TR1551]


title: VZA01701R.K14


title: VZA01701R.K16


title: VZA01701R.K13


title: Blood_Platelets_Vumc-GBM-follow-up-VU423t5-TR1549 [Vumc-GBM-follow-up-VU423t5-TR1549]


title: Blood_Platelets_Vumc-GBM-follow-up-VU423t10-TR1552 [Vumc-GBM-follow-up-VU423t10-TR1552]


title: VZA01701R.K12


title: VZA01701R.K22


title: Blood_Platelets_Vumc-GBM-follow-up-VU472t2-TR1558 [Vumc-GBM-follow-up-VU472t2-TR1558]


title: VZA01701R.K11


title: Blood_Platelets_Vumc-GBM-follow-up-VU508t4 [Vumc-GBM-follow-up-VU508t4-TR1738]


title: VZA01701R.K09


title: Blood_Platelets_Vumc-GBM-follow-up-VU438t1 [Vumc-GBM-follow-up-VU438t1-TR1553]


title: VZA01701R.K08


title: VZA01701R.K07


title: Blood_Platelets_Vumc-GBM-follow-up-VU438t5-TR1554 [Vumc-GBM-follow-up-VU438t5-TR1554]


title: VZA01701R.K10


title: VZA01701R.K05


title: Blood_Platelets_Vumc-GBM-follow-up-VU548t0 [Vumc-GBM-follow-up-VU548t0-TR1652]


title: VZA01701R.K06


title: Blood_Platelets_Vumc-GBM-follow-up-VU535t0 [Vumc-GBM-follow-up-VU535t0-TR1660]


title: Blood_Platelets_Vumc-GBM-follow-up-VU423t6-TR1550 [Vumc-GBM-follow-up-VU423t6-TR1550]


title: Blood_Platelets_Vumc-GBM-follow-up-VU559t0 [Vumc-GBM-follow-up-VU559t0-TR1659]


title: VZA01701R.K04


title: VZA01701R.K03


title: Blood_Platelets_Vumc-GBM-follow-up-VU551t0 [Vumc-GBM-follow-up-VU551t0-TR1653]


title: Blood_Platelets_Vumc-GBM-follow-up-VU523t0 [Vumc-GBM-follow-up-VU523t0-TR1650]


title: Blood_Platelets_Vumc-GBM-follow-up-VU527t0 [Vumc-GBM-follow-up-VU527t0-TR1651]


title: VZA01701R.K02


title: Blood_Platelets_Vumc-GBM-follow-up-VU423t1-TR1548 [Vumc-GBM-follow-up-VU423t1-TR1548]


title: VZA01701R.K01


title: Blood_Platelets_Vumc-GBM-follow-up-VU502t0 [Vumc-GBM-follow-up-VU502t0-TR1661]


title: VZA01701R.J22


title: VZA01701R.J23


title: Blood_Platelets_Vumc-GBM-follow-up-VU472t0 [Vumc-GBM-follow-up-VU472t0-TR1556]


title: Blood_Platelets_Vumc-GBM-follow-up-VU474t0 [Vumc-GBM-follow-up-VU474t0-TR1569]


title: VZA01701R.J20


title: Blood_Platelets_Vumc-GBM-follow-up-VU423t0 [Vumc-GBM-follow-up-VU423t0-TR1547]


title: VZA01701R.J21


title: Blood_Platelets_Vumc-GBM-follow-up-VU554t0 [Vumc-GBM-follow-up-VU554t0-TR1658]


title: Blood_Platelets_Vumc-GBM-445t4 [Vumc-GBM-445t4-TR1501]


title: VZA01701R.J19


title: Blood_Platelets_Vumc-GBM-429t8 [Vumc-GBM-429t8-TR1500]


title: VZA01701R.J18


title: VZA01701R.J17


title: Blood_Platelets_Vumc-GBM-429t1 [Vumc-GBM-429t1-TR1495]


title: VZA01701R.J24


title: Blood_Platelets_Vumc-GBM-follow-up-VU501t0-2 [Vumc-GBM-follow-up-VU501t0]


title: VZA01701R.J15


title: Blood_Platelets_Vumc-GBM-504t0 [Vumc-GBM-504t0-TR1516]


title: Blood_Platelets_Vumc-GBM-491t0-2 [Vumc-GBM-491t0]


title: Blood_Platelets_Vumc-GBM-497t2 [Vumc-GBM-497t2-TR1492]


title: Blood_Platelets_Vumc-GBM-488t0 [Vumc-GBM-488t0-TR1514]


title: VZA01701R.J12


title: VZA01701R.J13


title: VZA01701R.J14


title: VZA01701R.J11


title: Blood_Platelets_Vumc-GBM-517t0 [Vumc-GBM-517t0-TR1518]


title: VZA01701R.J10


title: Blood_Platelets_Vumc-GBM-477t0.2 [Vumc-GBM-477t0]


title: VZA01701R.J08


title: Blood_Platelets_Vumc-GBM-440t1 [Vumc-GBM-440t1-TR1499]


title: Blood_Platelets_Vumc-GBM-550t0 [Vumc-GBM-550t0-TR1519]


title: Blood_Platelets_Vumc-GBM-518t0 [Vumc-GBM-518t0-TR1584]


title: VZA01701R.J07


title: VZA01701R.J06


title: Blood_Platelets_Vumc-GBM-508t0 [Vumc-GBM-508t0-TR1517]


title: Blood_Platelets_Vumc-GBM-429t5 [Vumc-GBM-429t5-TR1497]


title: VZA01701R.J16


title: Blood_Platelets_Vumc-GBM-506t0 [Vumc-GBM-506t0-TR1483]


title: VZA01701R.J05


title: VZA01701R.J04


title: Blood_Platelets_Vumc-GBM-500t0 [Vumc-GBM-500tO-TR1582]


title: VZA01701R.J03


title: Blood_Platelets_Vumc-GBM-542t0 [Vumc-GBM-542t0-TR1486]


title: Blood_Platelets_Vumc-GBM-540t0 [Vumc-GBM-540t0-TR1485]

description: Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses (Seq 1 plus Seq 2 plus Seq 2 plus Seq 3).


title: VZA01701R.J01


title: Blood_Platelets_Vumc-GBM-493t0-2 [Vumc-GBM-493t0]


title: VZA01701R.J02


title: Blood_Platelets_Vumc-GBM-497t0 [Vumc-GBM-497t0-TR1481]


title: VZA01701R.J09


title: VZA01701R.I24


title: Blood_Platelets_Vumc-GBM-489-t0 [Vumc-GBM-489-t0-TR1479]


title: VZA01701R.I22


title: VZA01701R.I21


title: VZA01701R.I20


title: Blood_Platelets_Vumc-GBM-486 [Vumc-GBM-486-TR1366]


title: Blood_Platelets_Vumc-GBM-499 [Vumc-GBM-499-TR1388]


title: Blood_Platelets_Vumc-GBM-485 [Vumc-GBM-485-TR1365]


title: Blood_Platelets_Vumc-GBM-484 [Vumc-GBM-484-TR1387]

description: Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses (Seq 1 plus Seq 2 plus Seq 2).


title: VZA01701R.I17


title: VZA01701R.I18


title: Blood_Platelets_Vumc-GBM-480 [Vumc-GBM-480-TR1364]


title: VZA01701R.I16


title: Blood_Platelets_Vumc-GBM-475 [Vumc-GBM-475-TR1362]


title: VZA01701R.I15


title: Blood_Platelets_Vumc-GBM-476 [Vumc-GBM-476-TR1363]


title: VZA01701R.I14


title: VZA01701R.I13


title: Blood_Platelets_Vumc-GBM-468 [Vumc-GBM-468-TR1360]


title: Blood_Platelets_Vumc-GBM-456 [Vumc-GBM-456-TR1386]


title: VZA01701R.I23


title: Blood_Platelets_Vumc-GBM-505 [Vumc-GBM-505-TR1389]


title: VZA01701R.I11


title: Blood_Platelets_Vumc-GBM-454 [Vumc-GBM-454-TR1359]


title: VZA01701R.I12


title: Blood_Platelets_Vumc-GBM-443 [Vumc-GBM-443-TR1357]


title: VZA01701R.I08


title: VZA01701R.I09


title: Blood_Platelets_Vumc-GBM-439 [Vumc-GBM-439-TR1355]


title: Blood_Platelets_Vumc-GBM-445 [Vumc-GBM-445-TR1358]


title: VZA01701R.I07


title: Blood_Platelets_Vumc-GBM-440 [Vumc-GBM-440-TR1356]


title: VZA01701R.I06


title: Blood_Platelets_Vumc-GBM-471 [Vumc-GBM-471-TR1361]

description: Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.


title: VZA01701R.I05


title: Blood_Platelets_Vumc-GBM-422 [Vumc-GBM-422-TR1352]


title: Blood_Platelets_Vumc-GBM-417 [Vumc-GBM-417-TR1351]


title: VZA01701R.I03


title: Blood_Platelets_Vumc-GBM-436 [Vumc-GBM-436-TR1353]


title: VZA01701R.I02


title: Blood_Platelets_Vumc-GBM-406 [Vumc-GBM-406-TR1349]


title: Blood_Platelets_Vumc-GBM-408 [Vumc-GBM-408-TR1350]


title: VZA01701R.I04


title: VZA01701R.I01


title: Blood_Platelets_Vumc-GBM-402 [Vumc-GBM-402-TR1348]


title: VZA01701R.I10


title: VZA01701R.I19


title: VZA01701R.H24


title: VZA01701R.H23


title: Blood_Platelets_Vumc-GBM-438 [Vumc-GBM-438-TR1354]


title: Blood_Platelets_Vumc-GBM-306 [Vumc-GBM-306-TR1346]


title: VZA01701R.H22


title: VZA01701R.H21


title: VZA01701R.H20


title: SF7761_BMI1_shRNA_3-9

city: Aurora

first: Etienne

last: Danis

state: CO

country: USA

institute: University of Colorado, Denver - Anschutz Medical Campus

description: DIPG4_SF7761_BMI1_knockdown_raw_counts.txt

data_processing:
The reads were trimmed and clipped for quality control in Trimmomatic (v0.36).
Read quality was checked for each sample using FastQC v0.10.1.
High quality reads were then imported into STAR (v2.4.0.1) for alignment into BAM files.
The function summarizeOverlaps from the GenomicAlignments package (v1.16.0) was used to count the reads from BAM files.
DESeq (v1.32.0) was then used to get differential expression genes on the raw counts.
Alignment was done using the transcriptome hg38 (from UCSC)
Genome_build: hg38
Supplementary_files_format_and_content: txt file includes raw read counts.

source_name: diffuse intrinsic pontine glioma

growth_protocol: SF7761 cells were cultured in tumor stem media (TSM) consisting of all the following components from Invitrogen: Neurobasal-A medium (1:1), D-MEM/F-12 (1:1),  HEPES Buffer Solution (10 mM), MEM Sodium Pyruvate Solution (1 mM), MEM Non-Essential Amino Acids (0.1 mM), GlutaMAX-I Supplement (1:100), Antibiotic-Antimycotic (1X), B-27 Supplement Minus Vitamin A (1X), except all the growth factors, human-basic FGF (20 ng/mL), human-EGF (20 ng/mL), human PDGF-AA (10 ng/mL), human PDGF-BB (10 ng/mL) from Shenandoah Biotech, heparin (2 ug/mL) from StemCell Technologies and N-2 Supplement and L-Glutamine from Invitrogen.

extract_protocol:
RNA from cell lines were extracted with a RNeasy Plus RNA kit (Qiagen) and the purity of the RNA isolated was examined using an Agilent 2100 bioanalyzer.
mRNA libraries were made from the isolated pure RNA and RNA sequencing was performed using Nova-Seq.

treatment_protocol: The small-molecule inhibitor used in this study is PTC-028 (orb181369, Biorbyt). This drug was dissolved in DMSO to make stock concentrations to use in in vitro experiments.Stable knockdown of genes was carried out using shRNAs targeting different genes. Briefly, the cells (~100,000/well) were seeded onto a 6-well plate and the cells were transduced with the lentiviral shRNA using polybrene (polybrene final concentration of 8 ng/ml). Transduced cells were selected using puromycin (2µg/ml) and the cells were routinely maintained in the cell culture medium containing 1µg/ml of puromycin. ShRNAs targeting BMI1 was obtained from transOMIC technologies and from the Functional Genomic Core Facility at the University of Colorado, Denver.

tag: passage

tag: agent


title: VZA01701R.H19


title: VZA01701R.H18


title: SF7761_BMI1_shRNA_1-8


title: DIPG4_BMI1_shRNA_3-9

growth_protocol: SU-DIPG04 cells were cultured in tumor stem media (TSM) consisting of all the following components from Invitrogen: Neurobasal-A medium (1:1), D-MEM/F-12 (1:1),  HEPES Buffer Solution (10 mM), MEM Sodium Pyruvate Solution (1 mM), MEM Non-Essential Amino Acids (0.1 mM), GlutaMAX-I Supplement (1:100), Antibiotic-Antimycotic (1X), B-27 Supplement Minus Vitamin A (1X), except all the growth factors, human-basic FGF (20 ng/mL), human-EGF (20 ng/mL), human PDGF-AA (10 ng/mL), human PDGF-BB (10 ng/mL) from Shenandoah Biotech and the heparin (2 ug/mL) from StemCell Technologies.


title: DIPG4_Control_shRNA


title: VZA01701R.H15


title: DIPG4_BMI1_shRNA_1-8


title: VZA01701R.H11


title: VZA01701R.H13


title: VZA01701R.H10


title: VZA01701R.H09


title: VZA01701R.H08


title: Blood_Platelets_Vumc-GBM-378 [Vumc-GBM-378-TR1347]


title: VZA01701R.H17


title: VZA01701R.H16


title: VZA01701R.H14


title: VZA01701R.H12


title: VZA01701R.H06


title: VZA01701R.H04


title: SF7761_Control_shRNA


title: VZA01701R.H05


title: VZA01701R.H07


title: VZA01701R.H03


title: VZA01701R.H02


title: VZA01701R.H01


title: VZA01701R.G24


title: VZA01701R.G23


title: VZA01701R.G22


title: VZA01701R.G20


title: VZA01701R.G21


title: VZA01701R.G19


title: mdR-H460

city: Seoul

first: Yourae

last: Hong

address: 81, Irwon-ro

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

data_processing:
Fastq data was aligned to a human genome reference (GRCh38) and the unique molecular identifier (UMI) counts was quantified using CellRanger 3.0.2 pipeline (10X Genomics).
Afterwards, all analyses were performed using an R package of SEURAT 3.0 version with custom parameters in subset command: H460 with nFeature_RNA > 200, nFeature < 5,000, and percent.mt < 10; mdR-H460 with nFeature_RNA > 200, nFeature RNA < 5,000, and percent.mt < 10; ldR-H460 with nFeature_RNA > 200, nFeature RNA < 4,000, and percent.mt < 10.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the cellranger pipeline are given. Three files each represent gene symbols, cell barcodes, and UMI count matrix.

molecule: polyA RNA

source_name: mid-term dR-H460 cell line

growth_protocol: Preparation of Reprogrammed cancer (R-cancer) cells  1. Gamma irradiation of human fibroblasts and preparation of conditioned medium  Human fibroblast cells (Millipore) were seeded in the 100 mm dish in complete DMEM medium at 37°C and 5% CO2. At 90% confluence, cells were detached and total 1x107 cells suspended in 50 ml DMEM medium without serum. The suspended cells were irradiated in the gamma radiation chamber for 5 minutes at 60 Grays by using Gammacell 3000 elan (MDS Nordion, Ottawa, Canada). After suspended in freezing medium (Reprocell, Beltsville, MD), the irradiated human fibroblasts were kept frozen in the liquid nitrogen tank until use.  To prepare conditioned medium, irradiated human fibroblasts were thawed, and 5 x 106 cells in 10 ml of complete DMEM medium were seeded in a T75 flask. After overnight incubation at 37°C and 5% CO2, the medium was changed into bFGF-Pluriton medium. After further 48 h-incubation, culture supernatant was collected, and the collection of culture supernatant after change with fresh FGF-Pluriton medium was repeated until 6 cycles. All collected culture supernatants were pooled and employed as con-Pluriton medium which was transferred to 15 ml conical tubes, and kept at -80°C until use.  2. Feeder layer formation and transfer of target cancer cells onto the feeder layer  For the preparation of gelatin-coated 6-well plates, 1 ml of 0.2% gelatin (Sigma-Aldrich, St. Louis, MO) in phosphate buffered saline (PBS) was employed, and the coating plate was incubated for 30 minute at 37°C. Irradiated human fibroblasts (Millipore) were thawed, and seeded on the gelatin-coated plates at a density of 2.5 x 105 cells in complete DMEM media per well of 6-well plates. The cells were incubated overnight at 37°C and 5% CO2, and the Pluriton-R medium was added. The prepared fibroblasts were employed as the feeder layer.  To adapt the target cancer cells to the media change from complete RPMI to Pluriton medium, H460 and N87 cells were incubated in Pluriton-R medium for 5 days. Then, the Pluriton medium-adapted cancer cells were detached with trypsin-EDTA, and washed with PBS. The detached cancer cells were seeded on the feeder cell layer in Pluriton-R medium at a density of 2.5 x 105 per well.  3. Transfection of OSKM mRNAs to target cells on feeder layer  On the next day (day 1) after transfer of target cancer cells onto the feeder layer, media was changed into fresh Puriton-R medium. Then, transfection of mRNAs of OCT4, SOX2, KLF4 and MYC (OSKM) in mRNA reprogramming system (Stemgent) was performed. mRNA transfection complex (120 μL), which was prepared as the instruction of the system, was added to each well in a dropwise fashion, and the transfected cells was incubated for 4 h at 37°C and 5% CO2. After incubation, mRNA transfection complex was removed by aspiration, and freshly prepared Pluriton-R medium (2 ml) was added. Then the plate was incubated overnight at 37°C and 5% CO2. Transfection was repeated every day until day 8.  4. Transfer of target cancer cells on feeder layer to CTS- or CTS/Matrigel-coated plates  On day 8, CTS-coated (for the transfection of H460) or CTS/Matrigel-coated 6-well (for the transfection of N87) plate was prepared. For the preparation of CTS-coated plate, 1 ml of diluted CELLstartTM (1:50 in Dulbeco’s PBS) was added per well as the instruction (Gibco), and for the preparation of CTS/Matrigel-coated plate, 1 ml of diluted CELLstartTM and 1 ml diluted Matrigel solution [mixture of one vial of Magrigel stock solution (Corning, Corning, NY) and 25 ml of Pluriton medium] were mixed. Then, 1 ml of the mixture was added per well in a 6-well plate, and the plate was incubated for 30 minutes in clean bench and overnight at 4°C. To transfer target cancer cells to the prepared CTS- or CTS/Matrigel-coated plates, the cancer cells on the feeder layer were detached and seeded on CTS-coated (for H460) or CTS/Matrigel-coated plate (for N87) in con-Puriton-R medium.  5. Transfection of reprogramming factors to cancer cells on CTS- or CTS/Matrigel-coated plates  After incubation overnight of the cancer cells on CTS- or CTS/Matrigel-coated plates, transfection of OSKM was performed as described for the cancer cells on feeder cell layer. Con-Pluriton-R medium was replaced every other day until the transfection was finished on day 23. Typically, 6–12 R-cancer colonies were observed within the 3 weeks from the start of the transfection. From day 24, con-Pluriton-R-B18R medium was added to maintain R-cancer cells.  On day 30, distinct colonies were detached by scraping with a sterile Pasteur pipette under the light microscope in clean bench, and were transferred into freshly prepared Matrigel-coated 6-well plates in mTeSR1 medium (StemCell Technologies). For the preparation of Matrigel-coated plate, 1 ml of diluted Matrigel solution [mixture of one vial of Matrigel stock solution (Corning) and 25 ml of Pluriton medium] was added per well in a 6-well plate, and the plate was incubated for 30 minutes in clean bench and overnight at 4°C.  6. Maintenance of R-cancer cells   To maintain R-cancer cells in the undifferentiated state, R-cancer cells were cultured in mTeSR1 medium (StemCell Technologies) on six-well plates coated with Matrigel (BD Biosciences). On a daily basis, the medium was replaced. When R-cancer cells reached 80% confluence, Stempro Acutase (Life Technologies, Norwalk, CT) was treated to detach the cells from the surface, and the cells were divided at a ratio of 1:3. For long term maintenance, R-cancer cells were kept frozen at -70 °C. Thawed cells were cultured in con-Pluriton-R-B18R medium for 24 hr, and thereafter again in mTeSR1 medium.

extract_protocol:
For single cell transcriptome analysis, parent H460 cells, mdR-H460, and ldR-H460 cells were cultured in 75 mm flasks. Single cell suspensions in PBS were filtered through MACS SmartStrainer (30 μm).
3 cell lines were loaded into Chromium system (10x Genomics, Pleasanton, CA) targeting 5,000 cells, following the manufacturer’s instruction. Barcoded sequencing libraries were generated using Chromium Single Cell 3’ reagent kits (v2 chemistry) and sequenced using HiSeq 2500 platform (Illumina, San Diego, CA).

tag: parental cell line

value: H460 cell line


title: ldR-H460

source_name: long-term dR-H460 cell line


title: VZA01701R.G14


title: VZA01701R.G13


title: VZA01701R.G17


title: Blood_Platelets_107-005458 [TR3481-HD-NKI]

value: asymptomaticControls


title: VZA01701R.G16


title: Blood_Platelets_107-005463 [TR4039-HD-NKI]


title: Blood_Platelets_107-005423 [TR3296-HD-NKI]


title: VZA01701R.G18


title: VZA01701R.G15


title: Blood_Platelets_R-40 [MGH-R-40-RENAL-TR3209]

value: brainMeta


title: Blood_Platelets_107-005428 [TR3298-HD-NKI]


title: VZA01701R.G08


title: VZA01701R.G10


title: H460

source_name: H460 cell line


title: Blood_Platelets_107-005467 [TR4040-HD-NKI]


title: VZA01701R.G07


title: VZA01701R.G09


title: VZA01701R.G06


title: VZA01701R.G05


title: Blood_Platelets_107-005427 [TR3297-HD-NKI]


title: Blood_Platelets_107-005421 [TR3295-HD-NKI]


title: Blood_Platelets_107-005396 [TR3499-HD-NKI]


title: Blood_Platelets_107-005431 [TR3299-HD-NKI]


title: Blood_Platelets_107-005419 [TR3294-HD-NKI]


title: Blood_Platelets_107-005432 [TR3300-HD-NKI]


title: Blood_Platelets_107-005453 [TR3477-HD-NKI]


title: VZA01701R.G12


title: VZA01701R.G11


title: VZA01701R.G03


title: Blood_Platelets_107-005410 [TR3431-HD-NKI]


title: Blood_Platelets_107-005408 [TR3429-HD-NKI]


title: VZA01701R.F24


title: VZA01701R.G02


title: VZA01701R.F22


title: VZA01701R.F20


title: Blood_Platelets_107-005413 [TR3432-HD-NKI]


title: Blood_Platelets_107-005398 [TR3423-HD-NKI]


title: Blood_Platelets_107-005409 [TR3430-HD-NKI]


title: VZA01701R.F21


title: Blood_Platelets_HC441 [VUMC-HC441-HD-TR3445]


title: Blood_Platelets_107-005406 [TR3428-HD-NKI]


title: Blood_Platelets_HC423 [VUMC-HC423-HD-TR3444]


title: VZA01701R.F17


title: Blood_Platelets_HC440 [VUMC-HC440-HD-TR3446]


title: Blood_Platelets_HC426 [VUMC-HC426-HD-TR3324]


title: Blood_Platelets_HC428 [VUMC-HC428-HD-TR3325]


title: VZA01701R.F16


title: Blood_Platelets_107-005390 [TR3498-HD-NKI]


title: VZA01701R.G04


title: Blood_Platelets_HC425 [VUMC-HC425-HD-TR3322]


title: VZA01701R.F15


title: VZA01701R.F14


title: VZA01701R.G01


title: Blood_Platelets_HC434 [VUMC-HC434-HD-TR3320]


title: VZA01701R.F23


title: Blood_Platelets_HC438 [VUMC-HC438-HD-TR3321]


title: VZA01701R.F12


title: Blood_Platelets_HC439 [VUMC-HC439-HD-TR3319]


title: VZA01701R.F19


title: VZA01701R.F11


title: VZA01701R.F13


title: Blood_Platelets_NKI-107-005500-HD-TR3288 [NKI-107-005500-HD-TR3288]


title: Blood_Platelets_NKI-107-005484-HD-TR3285 [NKI-107-005484-HD-TR3285]


title: VZA01701R.F18


title: Blood_Platelets_NKI-107-005456-HD-TR3479 [NKI-107-005456-HD-TR3479]


title: VZA01701R.F04


title: VZA01701R.F09


title: Blood_Platelets_NKI-107-005495-HD-TR3286 [NKI-107-005495-HD-TR3286]


title: Blood_Platelets_NKI-107-005497-HD-TR3287 [NKI-107-005497-HD-TR3287]


title: VZA01701R.F05


title: VZA01701R.F10


title: Blood_Platelets_HC442 [VUMC-HC442-HD-TR3323]


title: VZA01701R.F08


title: Blood_Platelets_NKI-107-005462-HD-TR3283 [NKI-107-005462-HD-TR3283]


title: Blood_Platelets_NKI-107-005461-HD-TR3482 [NKI-107-005461-HD-TR3482]


title: VZA01701R.F07


title: VZA01701R.F02


title: VZA01701R.F06


title: Blood_Platelets_NKI-107-005450-HD-TR3476 [NKI-107-005450-HD-TR3476]


title: Blood_Platelets_NKI-107-005455-HD-TR3478 [NKI-107-005455-HD-TR3478]


title: Blood_Platelets_NKI-107-005472-HD-TR3284 [NKI-107-005472-HD-TR3284]


title: VZA01701R.F03


title: VZA01701R.F01


title: Blood_Platelets_NKI-107-005448-HD-TR3290 [NKI-107-005448-HD-TR3290]


title: Blood_Platelets_NKI-107-005440-HD-TR3289 [NKI-107-005440-HD-TR3289]


title: VZA01701R.E23


title: VZA01701R.E24


title: Blood_Platelets_NKI-107-005437-HD-TR3475 [NKI-107-005437-HD-TR3475]


title: VZA01701R.E22


title: Blood_Platelets_NKI-107-005436-HD-TR3474 [NKI-107-005436-HD-TR3474]


title: VZA01701R.E21


title: VZA01701R.E20


title: Blood_Platelets_NKI-107-005433-HD-TR3301 [NKI-107-005433-HD-TR3301]


title: VZA01701R.E19


title: Blood_Platelets_NKI-107-005404-HD-TR3427 [NKI-107-005404-HD-TR3427]


title: VZA01701R.E18


title: Blood_Platelets_NKI-107-005415-HD-TR3291 [NKI-107-005415-HD-TR3291]


title: Blood_Platelets_NKI-107-005397-HD-TR3500 [NKI-107-005397-HD-TR3500]


title: VZA01701R.E16


title: Blood_Platelets_NKI-107-005417-HD-TR3293 [NKI-107-005417-HD-TR3293]


title: Blood_Platelets_NKI-107-005389-HD-TR3460 [NKI-107-005389-HD-TR3460]


title: VZA01701R.E17


title: Blood_Platelets_NKI-107-005402-HD-TR3425 [NKI-107-005402-HD-TR3425]


title: VZA01701R.E13


title: VZA01701R.E15


title: VZA01701R.E14


title: VZA01701R.E11


title: VZA01701R.E12


title: Blood_Platelets_NKI-107-005385-HD-TR3458 [NKI-107-005385-HD-TR3458]


title: Blood_Platelets_NKI-107-005400-HD-TR3424 [NKI-107-005400-HD-TR3424]


title: Blood_Platelets_NKI-107-005384-HD-TR3457 [NKI-107-005384-HD-TR3457]


title: VZA01701R.E09


title: Blood_Platelets_NKI-107-005379-HD-TR3455 [NKI-107-005379-HD-TR3455]


title: VZA01701R.E08


title: VZA01701R.E10


title: Blood_Platelets_NKI-107-005371-HD-TR3451 [NKI-107-005371-HD-TR3451]


title: Blood_Platelets_NKI-107-005370-HD-TR3396 [NKI-107-005370-HD-TR3396]


title: VZA01701R.E07


title: Blood_Platelets_NKI-107-005414-HD-TR3433 [NKI-107-005414-HD-TR3433]


title: VZA01701R.E06


title: Blood_Platelets_NKI-107-005364-HD-TR3395 [NKI-107-005364-HD-TR3395]


title: VZA01701R.E05


title: Blood_Platelets_NKI-107-005386-HD-TR3497 [NKI-107-005386-HD-TR3497]


title: Blood_Platelets_NKI-107-005356-HD-TR3393 [NKI-107-005356-HD-TR3393]


title: VZA01701R.E02


title: VZA01701R.E03


title: VZA01701R.E01


title: Blood_Platelets_NKI-107-005314-HD-TR3349 [NKI-107-005314-HD-TR3349]


title: VZA01701R.D24


title: Blood_Platelets_NKI-107-005315-HD-TR3386 [NKI-107-005315-HD-TR3386]


title: Blood_Platelets_NKI-107-005354-HD-TR3392 [NKI-107-005354-HD-TR3392]


title: Blood_Platelets_NKI-107-005309-HD-TR3345 [NKI-107-005309-HD-TR3345]


title: Blood_Platelets_NKI-107-005313-HD-TR3348 [NKI-107-005313-HD-TR3348]


title: Blood_Platelets_NKI-107-005311-HD-TR3347 [NKI-107-005311-HD-TR3347]

description: Please note that the mapped and counted intron-spanning reads from the uploaded FASTQ file do not match the data in the count matrix. This has to do to with an error in the processing of our sequencing files. This error was noted once all RNA-seq data had been processed and analyzed in the associated publication. We apologies for this inconvenience.


title: VZA01701R.D22


title: VZA01701R.D21


title: Blood_Platelets_NKI-107-005310-HD-TR3346 [NKI-107-005310-HD-TR3346]


title: VZA01701R.D23


title: Blood_Platelets_NKI-107-005295-HD-TR3343 [NKI-107-005295-HD-TR3343]


title: VZA01701R.D20


title: Blood_Platelets_NKI-107-005304-HD-TR3344 [NKI-107-005304-HD-TR3344]


title: VZA01701R.D19


title: VZA01701R.D18


title: Blood_Platelets_NKI-107-005292-HD-TR3342 [NKI-107-005292-HD-TR3342]


title: Blood_Platelets_NKI-107-005289-HD-TR3341 [NKI-107-005289-HD-TR3341]


title: Blood_Platelets_NKI-107-005287-HD-TR3339 [NKI-107-005287-HD-TR3339]


title: VZA01701R.D16


title: VZA01701R.D17


title: VZA01701R.E04


title: Blood_Platelets_HC0161 [VUMC-HC0161-DOT-HD-48h-TR3137]


title: VZA01701R.D15


title: VZA01701R.D14


title: Blood_Platelets_HC0151 [VUMC-HC0151-DOT-HD-48h-TR3136]


title: Blood_Platelets_HC0094 [VUMC-HC0094-DOT-HD-48h-TR3095]


title: Blood_Platelets_HC0083 [VUMC-HC0083-DOT-HD-48h-TR3093]


title: VZA01701R.D11


title: VZA01701R.D10


title: VZA01701R.D09


title: VZA01701R.D12


title: VZA01701R.D08


title: VZA01701R.D13


title: Blood_Platelets_HC0049 [VUMC-HC0049-DOT-HD-48h-TR3086]


title: Blood_Platelets_HC0131 [VUMC-HC0131-DOT-HD-48h-TR3069]


title: Blood_Platelets_HC0097 [VUMC-HC0097-DOT-HD-48h-TR3098]


title: VZA01701R.D06


title: Blood_Platelets_HC0095_48h [VUMC-HC0095-DOT-HD-48h-TR3096]


title: Blood_Platelets_HC0068 [VUMC-HC0068-DOT-HD-48h-TR3090]


title: Blood_Platelets_HC0056_48h [VUMC-HC0056-DOT-HD-48h-TR3089]


title: VZA01701R.D05


title: Blood_Platelets_HC0140 [VUMC-HC0140-DOT-HD-48h-TR3071]


title: Blood_Platelets_HC0129 [VUMC-HC0129-DOT-HD-48h-TR3068]


title: Blood_Platelets_HC0175 [VUMC-HC0175-DOT-HD-48h-TR3108]


title: VZA01701R.D02


title: VZA01701R.D04


title: VZA01701R.D01


title: Blood_Platelets_HC0054 [VUMC-HC0054-DOT-HD-48h-TR3088]


title: Blood_Platelets_HC0053_48h [VUMC-HC0053-DOT-HD-48h-TR3087]


title: Blood_Platelets_HC0172 [VUMC-HC0172-DOT-HD-48h-TR3107]


title: VZA01701R.C23


title: Blood_Platelets_HC0171_48h [VUMC-HC0171-DOT-HD-48h-TR3106]


title: VZA01701R.C21


title: Blood_Platelets_HC0139_48h [VUMC-HC0139-DOT-HD-48h-TR3070]


title: VZA01701R.C19


title: Blood_Platelets_HC0166 [VUMC-HC0166-DOT-HD-48h-TR3105]


title: VZA01701R.D07


title: VZA01701R.C18


title: VZA01701R.C22


title: VZA01701R.C20


title: Blood_Platelets_HC0125 [VUMC-HC0125-DOT-HD-48h-TR3067]


title: VZA01701R.C17


title: VZA01701R.C16


title: Blood_Platelets_HC0096 [VUMC-HC0096-DOT-HD-48h-TR3097]


title: Blood_Platelets_HC0143 [VUMC-HC0143-DOT-HD-48h-TR3072]


title: Blood_Platelets_HC0069 [VUMC-HC0069-DOT-HD-48h-TR3094]


title: Blood_Platelets_HC0118 [VUMC-HC0118-DOT-HD-48h-TR3066]


title: VZA01701R.C15


title: VZA01701R.D03


title: Blood_Platelets_HC0146_48h [VUMC-HC0146-DOT-HD-48h-TR3074]


title: VZA01701R.C14


title: VZA01701R.C13


title: VZA01701R.C24


title: Blood_Platelets_HC0144 [VUMC-HC0144-DOT-HD-48h-TR3073]


title: Blood_Platelets_HC0103 [VUMC-HC0103-DOT-HD-48h-TR3065]


title: VZA01701R.C12


title: Blood_Platelets_HC0082 [VUMC-HC0082-DOT-HD-48h-TR3092]


title: Blood_Platelets_HC0102 [VUMC-HC0102-DOT-HD-48h-TR3064]


title: VZA01701R.C11


title: Blood_Platelets_31P [TR4033-MS-MGH]


title: VZA01701R.C10


title: Blood_Platelets_29P [TR3989-MS-MGH]


title: VZA01701R.C09


title: Blood_Platelets_24P [TR3924-MS-MGH]


title: VZA01701R.C06


title: VZA01701R.C07


title: Blood_Platelets_21P [TR3921-MS-MGH]


title: Blood_Platelets_3P [TR3848-MS-MGH]


title: VZA01701R.C04


title: VZA01701R.C03


title: VZA01701R.C01


title: Blood_Platelets_4P [TR3849-MS-MGH]


title: VZA01701R.C05


title: VZA01701R.B24


title: Blood_Platelets_11P [TR3852-MS-MGH]


title: Blood_Platelets_18P [TR3854-MS-MGH]


title: VZA01701R.B23


title: Blood_Platelets_25P [TR3925-MS-MGH]


title: VZA01701R.B22


title: Blood_Platelets_22P [TR3922-MS-MGH]


title: Blood_Platelets_19P [TR3920-MS-MGH]


title: VZA01701R.B21


title: Blood_Platelets_26P [TR3926-MS-MGH]


title: Blood_Platelets_5P [TR3850-MS-MGH]


title: Blood_Platelets_1P [TR3846-MS-MGH]


title: VZA01701R.B20


title: VZA01701R.C08


title: Blood_Platelets_23P [TR3923-MS-MGH]


title: VZA01701R.B19


title: Blood_Platelets_2P [TR3847-MS-MGH]


title: Blood_Platelets_6P [TR3851-MS-MGH]


title: VZA01701R.C02


title: Blood_Platelets_30P [TR3990-MS-MGH]


title: VZA01701R.B17


title: Control3

city: Los Angeles

first: Kinji

last: Asahina

state: CA

address: 1333 San Pablo Street

department: Pathology

institute: University of Southern California

data_processing:
Partek Flow software used for basecalling.
Read were aligned by STAR algorithm. Sequenced reads were normalized with the RPKM method.
Supplementary_files_format_and_content: Processed data.xlsx

organism: Mus musculus

source_name: Pancreas

extract_protocol:
Pancreas tissues were collected from mice. Total RNAs were extracted using an RNeasy kit.
Library construction was carried out using the TruSeqRNA Sample Prep kit.

tag: strain

tag: tissue

value: Pancreas

tag: age

value: 7 months

tag: genotype

value: Kras overexpression


title: Blood_Platelets_15P [TR3853-MS-MGH]


title: Control2


title: VZA01701R.B15


title: VZA01701R.B14


title: VZA01701R.B16


title: Alcohol3


title: Blood_Platelets_VU624 T0 [TR3677-GBM-VUMC]


title: Blood_Platelets_VU609 T6 [TR4035-GBM-VU]


title: Blood_Platelets_VU604 T4 [TR3716-GBM-VUMC]


title: All5

data_processing:
Partek Flow software used for basecalling.
Read were aligned by STAR algorithm. Sequenced reads were normalized with the Upper quartile method.


title: Alcohol1


title: Blood_Platelets_550 T10 [TR3744-GBM-VUMC]


title: Alcohol2


title: Control1


title: VZA01701R.B12


title: VZA01701R.B18


title: All6


title: Blood_Platelets_518 T6 [TR3736-GBM-VUMC]


title: All1


title: All3


title: VZA01701R.B11


title: All2


title: Blood_Platelets_VU584 T0 [TR3815-GBM-VUMC]


title: VZA01701R.B10


title: Blood_Platelets_VU578 T3 [TR3812-GBM-VUMC]


title: VZA01701R.B09


title: Normal1

value: wild type


title: Blood_Platelets_VU578 T2 [TR3811-GBM-VUMC]


title: All4


title: VZA01701R.B08


title: Blood_Platelets_VU578 T0 [TR3809-GBM-VUMC]


title: Blood_Platelets_VU666 T0 [TR3690-GBM-VUMC]


title: VZA01701R.B13


title: VZA01701R.B07


title: Blood_Platelets_VU604 T0 [TR3712-GBM-VUMC]


title: Normal3


title: VZA01701R.B05


title: VZA01701R.B06


title: Blood_Platelets_VU648 T0 [TR3687-GBM-VUMC]


title: VZA01701R.B04


title: Normal2


title: VZA01701R.B03


title: TAMR OSMI-1 3_b

type: RNA

city: Helsinki

first: Harri

last: Itkonen

address: Haartmaninkatu

country: Finland

institute: University of Helsinki

description:
Biological replicate 3, technical replicate 2
SAMPLE 16

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data processing and analysis was performed using GenomeStudio V2011.1.

label: biotin

source_name: breast cancer cells

label_protocol: Standard label protocol

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS. TAMR cells were grown in DMEM medium without phenol red, supplemented with 10% CFS.

extract_protocol: Trizol RNA isolation, dilution in nuclease-free water. RNA integrity number (RIN) analysis was performed for quality control.

treatment_protocol: Cells were treated with either OGT inhibitor OSMI-1, or DMSO for control at 40μM concentration for 24 hours.

value: OGT inhibitor OSMI-1

value: TAMR (tamoxifen-resistant)


title: Blood_Platelets_VU584 T2 [TR3817-GBM-VUMC]


title: TAMR OSMI-1 2

description:
Biological replicate 2
SAMPLE 14


title: TAMR OSMI-1 1

description:
Biological replicate 1
SAMPLE 13


title: TAMR ctrl 3

description:
Biological replicate 3
SAMPLE 12

value: control


title: MCF7 OSMI-1 3

description:
Biological replicate 3
SAMPLE 8

value: MCF7 (tamoxifen-sensitive)


title: MCF7 OSMI-1 2_b

description:
Biological replicate 2, technical replicate 2
SAMPLE 7


title: VZA01701R.B02


title: TAMR ctrl 1

description:
Biological replicate 1
SAMPLE 9


title: TAMR ctrl 2_a

description:
Biological replicate 2, technical replicate 1
SAMPLE 10


title: TAMR OSMI-1 3_a

description:
Biological replicate 3, technical replicate 1
SAMPLE 15


title: Blood_Platelets_VU578 T5 [TR3814-GBM-VUMC]


title: VZA01701R.B01


title: Blood_Platelets_VU639 T1 [TR3685-GBM-VUMC]


title: Blood_Platelets_VU782 T0 [TR3726-GBM-VUMC]


title: VZA01701R.A24


title: VZA01701R.A23


title: Blood_Platelets_VU578 T1 [TR3810-GBM-VUMC]


title: MCF7 OSMI-1 2_a

description:
Biological replicate 2, technical replicate 1
SAMPLE 6


title: Blood_Platelets_VU671 T0 [TR3770-GBM-VUMC]


title: MCF7 OSMI-1 1

description:
Biological replicate 1
SAMPLE 5


title: TAMR ctrl 2_b

description:
Biological replicate 2, technical replicate 2
SAMPLE 11


title: Blood_Platelets_VU604 T2 [TR3714-GBM-VUMC]


title: VZA01701R.A21


title: Blood_Platelets_VU595 T4 [TR3711-GBM-VUMC]


title: MCF7 ctrl 1

description:
Biological replicate 1
SAMPLE 1


title: VZA01701R.A20


title: MCF7 ctrl 2_b

description:
Biological replicate 2, technical replicate 2
SAMPLE 3


title: Blood_Platelets_508 T7 [TR3734-GBM-VUMC]


title: VZA01701R.A19


title: Blood_Platelets_VU595 T2 [TR3709-GBM-VUMC]


title: VZA01701R.A22


title: VZA01701R.A18


title: Blood_Platelets_508 T2 [TR3732-GBM-VUMC]


title: Blood_Platelets_504 T3 [TR3731-GBM-VUMC]


title: VZA01701R.A17


title: MCF7 ctrl 3

description:
Biological replicate 3
SAMPLE 4


title: MCF7 ctrl 2_a

description:
Biological replicate 2, technical replicate 1
SAMPLE 2


title: Blood_Platelets_VU594 T1 [TR3704-GBM-VUMC]


title: SON WKY 1

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

hyb_protocol: Following fragmentation, sample were hybridized to Rat Genome 230 plus 2.0 GeneChip® arrays for 16 hours in the Affymetrix GeneChip® Hybridization Oven 6400 (Affymetrix). Following hybridization, the GeneChip® arrays were stained and washed on the GeneChip® Fluidics Station 400 (Affymetrix), and fluorescent signals were detected using the Affymetrix GeneChip® Scanner 3000 (Affymetrix).

data_processing: These data were initially documented using Affymetrix Microarray Suite software (MAS 5.0), which generates an expression report file that lists the quality control parameters. All of these parameters were scrutinized to ensure that array data had reached the necessary quality standards (42). Data were uploaded into GeneSpring software version 7.0 (Agilent) for normalization and high-level analysis (42).

label: Biotin

organism: Rattus norvegicus

source_name: 12-week WKY

label_protocol: Samples that met quality control criteria were used as templates for cRNA synthesis and Biotin labelling, incorporating a single round of linear amplification using the Ambion Message Amp II aRNA kit (Ambion).

extract_protocol: RNA was extracted using QIAzol Lysis Reagent (Qiagen) and the aqueous phase was removed after centrifugation through a Phase Lock Gel column (Eppendorf). Total RNA was purified with RNeasy Micro Kit MinElute Spin Columns (Qiagen).

treatment_protocol: Untreated animals

value: Normotensive


title: SON WKY 5

scan_protocol: fluorescent signals were detected using the Affymetrix GeneChip® Scanner 3000 (Affymetrix).


title: VZA01701R.A15


title: SON WKY 3


title: Blood_Platelets_VU591 T3 [TR3702-GBM-VUMC]


title: SON SHR 4

source_name: 12-week SHR

value: Hypertensive


title: SON SHR 1


title: SON WKY 4


title: VZA01701R.A16

value: colorectal carcinoma


title: VZA01701R.A14


title: SON SHR 2


title: PVN SHR 3


title: SON WKY 2


title: SON SHR 3


title: PVN SHR 5


title: PVN WKY 2


title: PVN SHR 2


title: PVN SHR 4


title: PVN SHR 1


title: Blood_Platelets_548 T2 [TR3738-GBM-VUMC]


title: PVN WKY 3


title: PVN WKY 5


title: PVN WKY 4


title: PVN WKY 1


title: VZA01701R.A13


title: Blood_Platelets_508 T8 [TR3735-GBM-VUMC]


title: Blood_Platelets_VU595 T3 [TR3710-GBM-VUMC]


title: VZA01701R.A12

value: X-ray 5Gy


title: VZA01701R.A11


title: Blood_Platelets_508 T3 [TR3733-GBM-VUMC]


title: PBS injected healthy control, biological rep 3

city: Glasgow

first: Jonathan

last: Cavanagh

address: 120 University Place

department: Immunology

institute: University of Glasgow

description: Gene expression in the brain of healthy control mice, 48 hours after PBS injection

hyb_protocol: Fragmented cDNA samples were then hybridized to GeneChip Mouse Gene 1.0 ST Arrays using GeneTitan hybridization

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data generated using GeneSpring GX software were normalized using RMA16. The normalized data were subsequently analyzed using t-test to determine the significance of each gene in LPS-treated mice compared with vehicle-treated controls.

source_name: Whole brain RNA, 48hr after PBS injection (i.p.)

label_protocol: cDNA  fragmentation and labelling was performed using a GeneChip WT Terminal Labelling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: C57BL/6 mice (7 to 8 weeks old, 20 to 25 g) were purchased from Harlan Laboratories. Mice were maintained in specific pathogen-free conditions in standard caging in the Central Research Facility at the University of Glasgow. Mice were givin 1 week to acclimatise prior to treatment.

extract_protocol: Whole brain tissue was snap frozen and stored at -80°C until use. Under RNase-free conditions, brains were homogenized using the TissueLyser LT (Qiagen, Hilden, Germany). RNA was extracted from homogenized tissue using Trizol® (Life Technologies, Invitrogen, Carlsbad, CA, USA) as described by the manufacturers. Isolated RNA was further purified and genomic DNA removed using an RNeasy Mini Kit (Qiagen, Hilden, Germany). Red blood cells were lysed from blood samples using red blood cell lysis buffer (Miltenyi, Cologne, Germany). Under RNase-free conditions, RNA was isolated and genomic DNA was removed from PBLs using an RNeasy Micro Kit (Qiagen, Hilden, Germany).

treatment_protocol: Male C57BL6 mice were injected (i.p.) with 4mg/kg LPS (Escherichia coli serotype 055:B5) or PBS (n=3/group).

tag: Sex

value: Male

value: Brain


title: VZA01701R.A10


title: LPS injected healthy control, biological rep 1

description: Gene expression in the brain, 48 hours after the induction of systemic inflammation by LPS injection

source_name: Whole brain RNA, 48hr after LPS injection (i.p.)


title: LPS injected healthy control, biological rep 2


title: Blood_Platelets_VU635 T1 [TR3682-GBM-VUMC]

value: GBM


title: LPS injected healthy control, biological rep 3


title: VZA01701R.A09


title: Blood_Platelets_VU624 T4 [TR3680-GBM-VUMC]


title: VZA01701R.A08


title: Blood_Platelets_VU729 T3 [TR3725-GBM-VUMC]


title: VZA01701R.A06


title: Blood_Platelets_VU729 T1 [TR3724-GBM-VUMC]


title: Blood_Platelets_VU703 T3 [TR3722-GBM-VUMC]


title: VZA01701R.A05


title: PBS injected healthy control, biological rep 2


title: VZA01701R.A04


title: Blood_Platelets_VU635 T0 [TR3681-GBM-VUMC]


title: VZA01701R.A07


title: PBS injected healthy control, biological rep 1


title: Blood_Platelets_551 T3 [TR3745-GBM-VUMC]


title: VZA01701R.A03


title: Blood_Platelets_VU703 T0 [TR3696-GBM-VUMC]


title: VZA01701R.A02


title: Blood_Platelets_550 T9 [TR3743-GBM-VUMC]


title: VZA01701R.A01


title: Blood_Platelets_550 T6 [TR3741-GBM-VUMC]


title: HCA00102.O16

value: malignant melanoma


title: Blood_Platelets_550 T4 [TR3740-GBM-VUMC]


title: Blood_Platelets_VU648 T2 [TR3689-GBM-VUMC]


title: HCA00102.O15


title: HCA00102.O14


title: genomic DNA from malignant melanoma clinical sample 1413M

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: Malignant melanoma clinical sample.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip Kit using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from primary cell culture or clinical samples using QIAamp DNA FFPE Tissue Kit according to standard instructions.

tag: gender

value: Female

tag: disease state

value: lymph node

tag: stage (ajcc 7th)


title: genomic DNA from malignant melanoma clinical sample 1206P

description: Malignant melanoma clinical sample.

value: skin


title: genomic DNA from primary melanocyte culture

description: Healthy control.

source_name: primary melanocyte culture PMC P5

value: healthy

value: skin (melanocyte culture)


title: genomic DNA from malignant melanoma clinical sample 1611P

description: Malignant melanoma clinical sample.


title: MB231cells Q_DES_18 h-rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: The amplified DNA was then fragmented, precipitated, and resuspended prior to hybridization to BeadChips for 17 hours at 48°C.

scan_protocol: The slides were washed and stained as per the standard Illumina HD methylation protocol. Finally, the arrays were scanned with an Illumina iScan.

data_processing: For EPIC BeadChip DNA methylome analysis, Methylation Module from Illumina Genome Studio was used.

source_name: MB231cells Q_DES_18 h

label_protocol: DNA methylation analysis was conducted using Infinium Methylation EPIC BeadChip arrays (Illumina, San Diego, CA) following the Illumina InfiniumHD methylation protocol.  Starting with 200ng of bisulfite converted DNA; samples were amplified for 22 hours at 37°C using random priming.

growth_protocol: MB231cells were seeded in 60 x 15 mm dishes with 5% sFBS medium and starved for 2 days.

extract_protocol: Genomic DNA DNA (400-500 ng) was extracted from MB231 stable cells using a Tissue Blood Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Bisulfite treatment was performed using using the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA) following the manufacturer’s instructions.

treatment_protocol: After changing to fresh 5% sFBS medium, cells were treated with vehicle control (DMSO, final concentration < 0.01%), 100 nM E2 or DES for 18 hours.

value: breast

tag: genotype/variation

value: Q mutation

value: 18 hours DES


title: genomic DNA from malignant melanoma clinical sample 1114P

description: Malignant melanoma clinical sample.


title: MB231cells R_E2_18 h-rep1

source_name: MB231cells R_E2_18 h

value: R mutation

value: 18 hours E2


title: Blood_Platelets_VU639 T0 [TR3684-GBM-VUMC]

tag: group


title: genomic DNA from malignant melanoma clinical sample 1515P

description: Malignant melanoma clinical sample.


title: MB231cells R_veh_18 h-rep3

source_name: MB231cells R_veh_18 h

tag: cell line

value: veh


title: genomic DNA from malignant melanoma clinical sample 1404P

description: Malignant melanoma clinical sample.


title: MB231cells R_veh_18 h-rep2

tag: treatment


title: HCA00102.O13

tag: cell id

tag: cell type

tag: time point


title: MB231cells Q_DES_18 h-rep1


title: MB231cells Q_veh_18 h-rep3

source_name: MB231cells Q_veh_18 h


title: MB231cells Q_DES_18 h-rep2


title: MB231cells R_E2_18 h-rep3


title: MB231cells R_veh_18 h-rep1


title: MB231cells R_DES_18 h-rep2

source_name: MB231cells R_DES_18 h


title: Blood_Platelets_VU594 T3 [TR3706-GBM-VUMC]

source_name: Thrombocytes


title: HCA00102.O12

source_name: DNTR-seq mRNA

tag: cell count


title: genomic DNA from malignant melanoma clinical sample 1308P

description: Malignant melanoma clinical sample.


title: HCA00102.O11


title: genomic DNA from malignant melanoma clinical sample 1208P

description: Malignant melanoma clinical sample.


title: MB231cells Q_veh_18 h-rep2


title: MB231cells R_DES_18 h-rep1


title: HCA00102.O10


title: MB231cells Q_E2_18 h-rep1

source_name: MB231cells Q_E2_18 h


title: MB231cells WT_DES_18 h-rep3

source_name: MB231cells WT_DES_18 h

value: WT


title: Control [204013970051_R06C01]

city: Bangkok

first: Monnat

last: Pongpanich

address: Phayathai Road

country: Thailand

institute: Chulalongkorn University

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 8

hyb_protocol: Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
Normalized signal intensity and genotype were computed using Illumina’s GenomeStudio v.2 software.
Genotype: AA,AB,BB,or NC (no call)

label: cy3, cy5

source_name: Peripheral blood leucocytes

label_protocol: Illumina protocol

extract_protocol: Extraction of genomic DNA from peripheral blood leucocytes was performed using a standard protocol

value: Control


title: MB231cells R_DES_18 h-rep3


title: Blood_Platelets_VU782 T2 [TR3728-GBM-VUMC]


title: MB231cells R_E2_18 h-rep2


title: BAFME1 [204013970051_R03C01]

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 7

value: Male


title: BAFME1 [204013970051_R05C01]

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 1


title: BAFME1 [202966740033_R02C01]

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 2


title: Blood_Platelets_VU594 T2 [TR3705-GBM-VUMC]


title: HCA00102.O09


title: MB231cells Q_E2_18 h-rep2


title: BAFME1 [202966740033_R01C01]

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 6


title: HCA00102.O08

value: colorectal carcinoma


title: BAFME1 [204013970051_R02C01]

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 5


title: MB231cells Q_veh_18 h-rep1


title: BAFME1 [204013970051_R01C01]

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 4


title: Control [204013970051_R04C01]

description:
Genomic DNA extracted from peripheral blood leucocytes was genotyped using Infinium OmniZhongHua BeadChips.
SAMPLE 3


title: Blood_Platelets_VU782 T1 [TR3727-GBM-VUMC]

value: GBM


title: HCA00102.O06


title: 68 PBMC_HIV_Negative

city: Nashville

first: John

last: Koethe

state: TN

address: 1211 Medical Center Drive

department: Internal Medicine

institute: VUMC

data_processing:
Reads were quality-filtered and passed through a demultiplexing tool to assign reads to individual wells and to the 3’ end and 5’ end
Reads for the individual single-cells were demultiplexed using plate-id (30 nt), and cell barcode (6 nt).
The reads were further demultiplexed as either 3’ or 5’ using primer sequence (30 nt) and the reminder 45 nt sequences were aligned to the GRCh38 human reference genome (Ensembl rel. 92) using the CLC Genomics Workbench (CLC Bio) (v.11, QIAGEN Bioinformatics).
An eight nucleotide UMI tag and mapping coordinates were used to remove PCR-duplicate reads.
Gene-specific read counts were calculated using HTSeq-count using the latest Gencode annotations and the 3’ and 5’ counts were summed.
Genome_build: GRCh38 human reference genome (Ensembl rel. 92)
Supplementary_files_format_and_content: tab-delimited text files

source_name: Peripheral blood monocytes

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: individual

value: Subject 17

tag: hiv status

value: HIV-negative

tag: diabetes status

value: Diabetic

value: untreated

value: Peripheral blood monocytes


title: 69 Adipose Tissue_HIV_Negative

source_name: Adipose tissue

value: Subject 15

tag: tissue

value: adipose


title: Blood_Platelets_VU590 T1 [TR3698-GBM-VUMC]


title: Blood_Platelets_VU591 T1 [TR3700-GBM-VUMC]


title: Blood_Platelets_VU729 T0 [TR3723-GBM-VUMC]


title: Blood_Platelets_VU595 T0 [TR3707-GBM-VUMC]


title: HCA00102.O05


title: 66 Adipose Tissue_HIV_Negative


title: 67 PBMC_HIV_Negative


title: HCA00102.O07


title: Blood_Platelets_VU609 T7 [TR3721-GBM-VUMC]


title: MB231cells Q_E2_18 h-rep3

value: breast

value: Q mutation


title: HCA00102.O04


title: 65 Adipose Tissue_HIV_Negative


title: MB231cells WT_DES_18 h-rep2

value: 18 hours DES


title: 64 PBMC_HIV_Negative

value: Subject 16


title: HCA00102.O03


title: 62 Adipose Tissue_HIV_Negative


title: 63 PBMC_HIV_Negative


title: 61 Adipose Tissue_HIV_Negative


title: Blood_Platelets_VU609 T2 [TR3719-GBM-VUMC]


title: MB231cells WT_DES_18 h-rep1


title: Blood_Platelets_VU609 T4 [TR3720-GBM-VUMC]


title: HCA00102.O01


title: HCA00102.O02


title: 60 PBMC_HIV_Negative


title: 59 PBMC_HIV_Negative


title: 57 Adipose Tissue_HIV_Negative


title: 56 PBMCs_HIV_Positive

value: Subject 14

value: HIV-positive


title: HCA00102.M16

value: malignant melanoma


title: 55 PBMCs_HIV_Positive


title: Blood_Platelets_550 T7 [TR3742-GBM-VUMC]


title: Blood_Platelets_VU609 T0 GBM mogelijk apart variant [TR3717-GBM-VUMC]


title: Blood_Platelets_548 T4 [TR3739-GBM-VUMC]


title: HCA00102.M15


title: 54 Adipose Tissue_HIV_Positive


title: 52 PBMC_HIV_Negative

value: Subject 13


title: HCA00102.M13


title: 58 Adipose Tissue_HIV_Negative


title: 48 PBMC_HIV_Negative

value: Subject 12


title: 51 PBMC_HIV_Negative


title: 50  Adipose Tissue_HIV_Negative


title: Blood_Platelets_VU635 T2 [TR3683-GBM-VUMC]

value: GBM


title: Blood_Platelets_493 T4 [TR3730-GBM-VUMC]


title: Blood_Platelets_423 T8 [TR3729-GBM-VUMC]


title: 49  Adipose Tissue_HIV_Negative


title: HCA00102.M12


title: 47 PBMC_HIV_Negative


title: 53 Adipose Tissue_HIV_Positive


title: HCA00102.M11


title: 46  Adipose Tissue_HIV_Negative


title: 45  Adipose Tissue_HIV_Negative


title: 44 PBMCs_HIV_Positive

value: Subject 11


title: Blood_Platelets_VU620 T1 [TR3676-GBM-VUMC]


title: Blood_Platelets_VU591 T0 [TR3699-GBM-VUMC]


title: HCA00102.M14


title: MB231cells WT_E2_18 h-rep3

source_name: MB231cells WT_E2_18 h

value: WT

value: 18 hours E2


title: 43 PBMCs_HIV_Positive

value: Diabetic

value: untreated


title: HCA00102.M09


title: 42 Adipose Tissue_HIV_Positive


title: HCA00102.M10


title: HCA00102.M08

value: colorectal carcinoma


title: 40 PBMCs_HIV_Positive

value: Subject 10

value: Non-diabetic

value: Peripheral blood monocytes


title: HCA00102.M07


title: Blood_Platelets_VU609 T8 [TR3674-GBM-VUMC]


title: 39 PBMCs_HIV_Positive


title: Blood_Platelets_VU703 T1 [TR3697-GBM-VUMC]


title: 41 Adipose Tissue_HIV_Positive

value: adipose


title: 38 Adipose Tissue_HIV_Positive


title: Blood_Platelets_VU671 T2 [TR3695-GBM-VUMC]


title: MB231cells WT_veh_18 h-rep1

source_name: MB231cells WT_veh_18 h

value: breast

value: veh


title: 36 PBMCs_HIV_Positive

value: Subject 9

value: HIV-positive


title: HCA00102.M06


title: 37 Adipose Tissue_HIV_Positive


title: Blood_Platelets_VU609 T1 [TR3718-GBM-VUMC]


title: MB231cells WT_E2_18 h-rep1


title: 35 PBMCs_HIV_Positive


title: HCA00102.M05


title: Blood_Platelets_VU 666 T3 [TR3693-GBM-VUMC]


title: 33 Adipose Tissue_HIV_Positive


title: 32 PBMCs_HIV_Positive

value: Subject 8


title: Blood_Platelets_VU604 T3 [TR3715-GBM-VUMC]


title: HCA00102.M04


title: MB231cells WT_veh_18 h-rep2


title: 31 PBMCs_HIV_Positive


title: HCA00102.M03


title: 30 Adipose Tissue_HIV_Positive


title: 34 Adipose Tissue_HIV_Positive


title: 29 Adipose Tissue_HIV_Positive


title: HCA00102.M02


title: 28 PBMCs_HIV_Positive

value: Subject 7


title: Blood_Platelets_523 T1 [TR3737-GBM-VUMC]

value: GBM


title: Blood_Platelets_VU639 T2 [TR3686-GBM-VUMC]


title: 27 Adipose Tissue_HIV_Positive


title: 25 Adipose Tissue_HIV_Positive


title: 24 Adipose Tissue_HIV_Positive

value: Subject 6


title: 26 Adipose Tissue_HIV_Positive


title: HCA00102.K16

value: malignant melanoma


title: Blood_Platelets_VU624 T2 [TR3679-GBM-VUMC]


title: 22 PBMCs_HIV_Positive


title: 23 Adipose Tissue_HIV_Positive


title: HCA00102.K14


title: 21 PBMCs_HIV_Positive


title: MB231cells WT_E2_18 h-rep2

value: WT

value: 18 hours E2


title: Blood_Platelets_VU591 T2 [TR3701-GBM-VUMC]


title: 20 Adipose Tissue_HIV_Positive

value: Subject 5

value: Diabetic

value: untreated


title: MB231cells WT_veh_18 h-rep3


title: HCA00102.K13


title: 19 PBMCs_HIV_Positive


title: 17 PBMCs_HIV_Positive


title: 18 PBMCs_HIV_Positive


title: Blood_Platelets_VU620 T0 [TR3675-GBM-VUMC]


title: Blood_Platelets_VU624 T1 [TR3678-GBM-VUMC]


title: HCA00102.K12


title: 15 Adipose Tissue_HIV_Positive

value: Subject 4

value: Non-diabetic


title: 14 PBMCs_HIV_Positive

value: Peripheral blood monocytes


title: 12 Adipose Tissue_HIV_Positive

value: Subject 3

value: adipose


title: HCA00102.K10


title: 13 PBMCs_HIV_Positive


title: Blood_Platelets_VU604 T1 [TR3713-GBM-VUMC]


title: Blood_Platelets_VU666 T1 [TR3691-GBM-VUMC]


title: 10 PBMCs_HIV_Positive


title: 9 PBMCs_HIV_Positive


title: HCA00102.M01

value: colorectal carcinoma


title: HCA00102.K08


title: Blood_Platelets_VU590 T0 [TR3819-GBM-VUMC]


title: Blood_Platelets_VU584 T3 [TR3818-GBM-VUMC]


title: 6 Adipose Tissue_HIV_Positive

value: Subject 2

value: HIV-positive


title: Blood_Platelets_VU584 T1 [TR3816-GBM-VUMC]


title: 7 PBMCs_HIV_Positive


title: HCA00102.K07


title: 5 Adipose Tissue_HIV_Positive


title: Blood_Platelets_VU578 T4 [TR3813-GBM-VUMC]


title: HCA00102.K06


title: Blood_Platelets_VU666 T2 [TR3692-GBM-VUMC]


title: 4 PBMCs_HIV_Positive

value: Subject 1


title: Blood_Platelets_VU648 T1 [TR3688-GBM-VUMC]

value: GBM


title: 16 Adipose Tissue_HIV_Positive


title: HCA00102.K11


title: 3 PBMCs_HIV_Positive


title: HCA00102.K05


title: 11 Adipose Tissue_HIV_Positive


title: 1 Adipose Tissue_HIV_Positive


title: NIR_Gli1_rep2

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

description: NIR 2 GLI1 ChIP

library_source: genomic

data_processing:
Adaptor sequences were removed using Cutadapt tool before alignment with STAR2 algorithm using human hg38 reference and PCR replicates were removed using SAMtools.
After peak detection, the list of enriched regions were created. These peaks were used to identify consensus binding motif, nearest genomic features/locations such as intron, exon, 5’UTR, 3’UTR, and intra-gene or out-of-gene locations.
Genome_build: hg38
Supplementary_files_format_and_content: bedgrpah

source_name: SUM1315 cells

growth_protocol: SUM1315 cells were grown in complete media prior to irradiation or mock irradiation.

extract_protocol:
ChIP done and DNA extracted using SimpleChIP Plus kit (Cell Signaling Technologies, 9005S)
Done by external vendor (GENEWIZ). Library was constructed with NEBNext Ultra DNA Library Prep with Beads Size Selection following manufacturer’s recommendations. Briefly, the ChIP DNA was end repaired and adapters were ligated after adenylation of the 3’ends. Adapter-ligated DNA was size selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as real time PCR (Applied Biosystems, Carlsbad, CA, USA).
ChIP-Seq done by external vendor (GENEWIZ). The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).  Sequencing was performed using a 2x150 Paired End (PE) configuration.  Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

treatment_protocol: Dishes were exposed to 4 Gy ionizing radiation as indicated using an X-ray irradiator and chromatin was crosslinked and harvested 4 hours later for ChIP. GLI1 pull-down was done using 3 ug of C-1 antibody (Santa Cruz).

tag: 4 gy ionizing radiation

value: No

tag: gli1 antibody (c-1, santa cruz)

value: Yes

tag: 2% input control


title: HCA00102.K09

value: malignant melanoma


title: HCA00102.K04


title: 8 PBMCs_HIV_Positive


title: NIR_Gli1_rep1

description: NIR 1 GLI1 ChIP


title: HCA00102.K03


title: C9-TTR-ILI-M

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

data_processing:
Sequences were trimmed to the first base with a quality score <3 and then paired.  Sequences with less than 300 and more than 600 nucleotides and paired reads with an expected error >3 were excluded from the analysis.
Processing of aw-reads was performed using IMNGS to operational taxonomic units of 97% sequence similarity
Following analyses were performed using R using edgeR
Supplementary_files_format_and_content: Comma-delimited text with the counts for each samples and OTUS

source_name: biopsy

extract_protocol:
Biopsies were resuspended in 180 μl TET buffer and 20mg lysozyme. Samples were incubated for 1h at 37ºC and vortexed with 25 μl Proteinase K before incubating at 56ºC for 3h. Buffer B3  was added followed by a heat treatment. Two washing steps were performed before eluting DNA, concentrations and purity were checked using NanoDrop One (Thermo Fisher Scientific)
V3-V4 regions of the 16S rRNA gene were amplified using standard protocols  with forward and reverse primers 341F-785R. Following the manufacter’s protocol with a pooled samples in paired-end modus (PE275)
Paired sequencing on a MiSeq system (Illumina, San Diego, CA)

tag: Sex

value: FEMALE

value: NO

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

tag: time

value: C

tag: patient id

tag: afected area

tag: involved

value: HEALTHY

tag: active area

tag: transplant

value: Baseline

tag: surgery

tag: age diagnostic

tag: age sample


title: NIR_rep2

description: NIR 2 input

tag: 4 gy ionizing radiation

tag: gli1 antibody (c-1, santa cruz)


title: C9-TTR-CA-M

tag: Sex

tag: treatment

value: ASCENDING COLON


title: NIR_rep1

description: NIR 1 input

tag: 2% input control


title: C9-TTR-SIG-M

tag: cdai

tag: pcr

tag: sescd global

value: SIGMOID COLON


title: TS62_THP-1_R

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

data_processing:
Library strategy: 4C-seq
Sequencing data was deconvoluted using cutadapt v1.18. Reads were mapped and analysis performed using 4Cseqpipe (van de Werken et al. 2012).
Genome_build: hg19

growth_protocol: THP-1 and derived cell lines were cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

extract_protocol:
4C primer sequences and enzyme combinations were selected using the University of Chicago online tool (http://mnlab.uchicago.edu/4Cpd) with co-ordinates from the ABCB1 promoter active in THP-1_R cells (hg38, chr7:87,598,302-87,601,399). 4C sequencing was performed according to the protocol developed by Splinter et al. (6). Briefly, 107 cells were cross-linked with 2% formaldehyde for 10 minutes at room temperature before the reaction was quenched with 0.125M glycine. Cells were lysed with buffer containing 50mM Tris–HCl pH7.5, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TX-100 and 1x complete protease inhibitors (Roche, #11245200). The cross-linked nuclear preparation was then incubated with DpnII. Digestion was confirmed by reversing crosslinking for an aliquot and running on a 0.6% agarose gel. Samples were then ligated overnight at 16°C using T4 DNA ligase (Roche, #799009). Ligation efficiency was again confirmed with 0.6% agarose gel. Crosslinking was reversed and DNA extracted using phenol-chloroform. Samples were then subjected to a second digestion using Csp6I. Ligation was again performed overnight at 16°C using T4 DNA ligase. DNA was then extracted using phenol-chloroform and purified with a QIAquick PCR purification kit (Qiagen, #28104).
PCR primers were designed to incorporate 4C primers with a barcode and Illumina adapter sequences: Non-reading primer: CAAGCAGAAGACGGCATACGAGATAGGGTAGGTATTCCACTTTT; Reading primer (THP-1_S): AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGCCAATGAGATACCAGGTCTGATC; Reading primer (THP-1_R):  AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCTTGTAGAGATACCAGGTCTGATC. PCR was performed with Expand Long Template Polymerase (Roche, #11759060001) using 3.2μg of 4C template product and then purified using a High Pure PCR Product Purification Kit (Roche. #11732676001). Library quality was assessed using a 2100 Bioanalyzer (Agilent Technologies). Samples were sequenced with 10% phiX using a MiSeq desktop sequencing system (Illumina) with 75bp single-end settings generating a mean of 1.4M reads per sample.

tag: cell type

tag: phenotype

value: Resistant


title: TS77_THP1_R (targeted resequencing)

data_processing:
FASTQ files were aligned against the GRCh38/hg38 reference human genome using LAST after training the aligner with a subsample of 10,000 reads. Structural variant calling was performed using NanoSV (Stancu et al. 2017).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
Genomic DNA was extracted from 5x10e6 cells using a QIAamp DNA mini kit (Qiagen, Manchester, UK).
1μg of genomic DNA was sheared with a g-TUBETM (Covaris, Inc., 520079) using 50μl sample volume and a 30s spin at 11,000rpm followed by inversion and a further 30s at 11,000rpm. Barcoded libraries were prepared from 45μl of fragmented DNA using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK‐LSK108) according to a 1D Sequence Capture protocol with the following modifications: the pre-hybridization PCR was replaced by a custom PCR with 6 cycles using Herculase II fusion DNA polymerase (Agilent). The subsequent AMPure XP purification was performed using a 0.6x bead to sample volume ratio. All purified product was used for the hybridization, which was performed using a SureSelect Target Enrichment System following the manufacturer’s protocol (https://www.agilent.com). The oligonucleotide library was designed using the online Agilent SureDesign service (https://earray.chem.agilent.com/suredesign/home.htm). The library targeted a 500kb region that included ABCB1 and upstream neighboring genes (RUNDC3B, SLC25A40, DBF4 and ADAM22; chr7: 87,132,949-87,632,948 hg19). Following pull-down, the post-capture amplification was replaced by a custom PCR with 14 cycles as described above. Amplified libraries were quantified by Qubit (Invitrogen) and TapeStation 2200 (Agilent Technologies). An additional amplification was performed using 10 cycles of PCR and the product was quantified. Amplified libraries were again quantified by Qubit and 1μg of each library used for the End-prep. AMPure XP purification was performed using a 0.47x bead to sample ratio. Four end-prepped libraries were pooled into one adapter ligation reaction using 125ng of each, as measured by Tapestation. A 0.47x bead to sample ratio was used for the AMPure XP bead binding. Target enriched DNA from THP-1_R was sequenced using a MiSeq desktop sequencing system (Illumina) with 1% phiX and 251bp, paired-end settings generating 1.92M reads.

tag: cell line


title: IR_Gli1_rep2

description: IR 2 GLI1 ChIP


title: Blood_Platelets_VU594 T0 [TR3703-GBM-VUMC]

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

tag: group


title: C8-TTR-SIG-M

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

tag: involved

tag: active area


title: C7-TTR-SIG-M

tag: Sex

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: C8-TTR-CA-M

tag: treatment

tag: cdai

tag: pcr

tag: sescd global


title: C8-TTR-ILI-M


title: 2 Adipose Tissue_HIV_Positive

tag: individual

tag: hiv status

tag: diabetes status

value: Diabetic

value: untreated

tag: tissue

value: adipose


title: HCA00102.I16

data_processing:
https://github.com/EngeLab/DNTRseq
Genome_build: hg38
Supplementary_files_format_and_content: mRNA read counts summarized over genes; DNA read counts summarized over genomic bins

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: IR_Gli1_rep1

description: IR 1 GLI1 ChIP

tag: 4 gy ionizing radiation

tag: gli1 antibody (c-1, santa cruz)

tag: 2% input control


title: HCA00102.K01

value: colorectal carcinoma


title: C7-TTR-ILI-M

tag: Sex

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: IR_rep2

description: IR 2 input


title: C6-TTR-SIG-M

value: MALE

tag: treatment

tag: cdai

tag: pcr

tag: sescd global


title: IR_rep1

description: IR 1 input

tag: 4 gy ionizing radiation

tag: gli1 antibody (c-1, santa cruz)

value: No

tag: 2% input control


title: HCA00102.I13

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C6-TTR-ILI-M

tag: Sex

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

tag: involved

tag: active area


title: TS62_THP-1_S

tag: phenotype

value: Sensitive


title: C6-TTR-CA-M

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: HCA00102.K02

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C5-TTR-CA-M

tag: Sex

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area


title: C4-TTR-SIG-M

tag: treatment

tag: cdai

tag: pcr

tag: involved

tag: active area


title: C4-TTR-CA-M

tag: sescd global

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: C3-TTR-SIG-M


title: HCA00102.I11

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: HCA00102.I15


title: C9-TTR-SIG; healthy

data_processing:
Quality filtering was performed using cutadapt v. 1.7.1
Reads were mapped against the human reference genome using the STAR aligner v.2.5.2a
Read counts per gene were obtained using RSEM program v.1.2.31 and the Ensembl gtf annotation file.
Following analyses were performed using R using edgeR
Genome_build: Ensembl gtf annotation file (release GRCh38.10)
Supplementary_files_format_and_content: Tab-delimited text with the counts for each sample

extract_protocol:
Tissue RNA was isolated by Rneasy Kit (Qiagen, Spain) according to the manufacturer's instructions. RNA were quantified by NanoDrop spectrophotometer (NanoDrop Technologies, USA). The purity and integrity of the total RNA was assessed via 2100 Bioanalyzer (Agilent, Germany). All RNA samples analyzed had a RNA Integrity Number ≥ 7.
Barcoded RNA sequencing libraries were prepared from 100 ng total RNA using Illumina’s TruSeq stranded mRNA kit according to the manufacturer’s instructions.
Libraries were subjected to paired-end sequencing (101 bp) on a HighSeq-4000 platform (Illumina, San Diego, CA).

tag: disease state

value: healthy

tag: Sex

value: FEMALE

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: affected area


title: C9-TTR-CA; healthy

tag: treatment

value: NO

tag: cdai

tag: pcr

tag: sescd global

tag: involved

tag: active area


title: C9-TTR-ILI; healthy

value: ILEUM

value: C

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: HCA00102.I10

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C3-TTR-CA-M

tag: Sex

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

value: HEALTHY

value: Baseline


title: C7-TTR-CA-M

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

value: ASCENDING COLON

tag: involved


title: C20-TTR-SIG-M

value: SIGMOID COLON

tag: active area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: C20-TTR-ILI-M


title: HCA00102.I09

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: HCA00102.I14


title: C8-TTR-ILI; healthy

tag: disease state

tag: Sex

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: affected area


title: C8-TTR-SIG; healthy

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

tag: involved

tag: active area


title: C19-TTR-SIG-M

tag: afected area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: C20-TTR-CA-M

tag: Sex


title: HCA00102.I08

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C19-TTR-ILI-M

tag: treatment

tag: sescd local

tag: exact location

tag: time

tag: patient id


title: C8-TTR-CA; healthy

tag: disease state

tag: cdai

tag: pcr

tag: sescd global

tag: affected area

tag: involved

tag: active area


title: C18-TTR-SIG-M

tag: Sex

tag: afected area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: HCA00102.I07

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: C19-TTR-CA-M

tag: cdai

tag: pcr

tag: sescd local

tag: exact location

tag: time

tag: patient id


title: HCA00102.I12


title: HCA00102.I06


title: C18-TTR-CA-M

tag: Sex

tag: sescd global

tag: afected area

tag: involved

tag: active area


title: C18-TTR-ILI-M

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: C7-TTR-SIG; healthy

tag: disease state

tag: treatment

tag: affected area


title: C7-TTR-ILI; healthy

tag: cdai

tag: pcr


title: C17-TTR-ILI-M

tag: sescd local

tag: exact location


title: HCA00102.I04

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C17-TTR-CA-M

tag: Sex

tag: sescd global

tag: time

tag: patient id

tag: afected area

tag: involved

tag: active area


title: HCA00102.I05

tag: treatment


title: C16-TTR-SIG-M

tag: cdai

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: HCA00102.I03

tag: cell id

tag: cell type


title: HCA00102.K15

tag: cell line

tag: time point


title: C7-TTR-CA; healthy

tag: disease state

tag: Sex

tag: pcr

tag: sescd local

tag: exact location

tag: affected area


title: C6-TTR-ILI; healthy

tag: sescd global

tag: time

tag: patient id

tag: involved

tag: active area


title: C6-TTR-SIG; healthy

tag: treatment

tag: cdai

tag: transplant

tag: surgery

tag: age diagnostic


title: HCA00102.I02

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C16-TTR-ILI-M

tag: Sex

tag: pcr

tag: sescd local

tag: exact location

tag: afected area

tag: age sample


title: C15-TTR-ILI-M

tag: sescd global

tag: time

tag: patient id

tag: involved

tag: active area


title: C16-TTR-CA-M

tag: treatment

tag: cdai

tag: transplant

tag: surgery

tag: age diagnostic


title: C6-TTR-CA; healthy

tag: disease state

tag: affected area


title: C15-TTR-CA-M

tag: Sex

tag: pcr


title: C15-TTR-SIG-M

tag: sescd local

tag: exact location


title: HCA00102.I01

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C14-TTR-SIG-M

tag: sescd global

tag: time

tag: patient id

tag: afected area

tag: involved

tag: active area

tag: age sample


title: DR 56 hpf Rep5 [5-56-R]

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

institute: UCL

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 using trimgalore
Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters --outSAMtype BAM Unsorted --outSAMunmapped Within
Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates
Count files were created using htseq -count (v0.6.1) and modelled using DESeq2
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

organism: Danio rerio

source_name: dorsal retina_56 hpf

growth_protocol: zebrafish were harvested at appropriate time points (hpf), retinal regions dissected

extract_protocol:
RNA was extracted using Qiagen Rneasy FFPE kit and quantified
RNA-seq libraries were constructed using the SMARTer low input  kit using standard protocols

tag: hpf

tag: tissue

value: dorsal retina


title: HCA00102.G16

extract_protocol:
Individual live cells were FACS-sorted into 384-well plates with lysis buffer, snap-frozen and stored at -80 degrees C.
After splitting each cell, separate mRNA- (*R suffix) and DNA-libraries (*D suffix) were constructed. As comparison, a set of cells had mRNA libraries prepared with Smart-Seq2 (no suffix).
Barcoded libraries were sequenced paired-end (37bp x 2) on an Illumina NextSeq.

tag: treatment


title: C5-TTR-CA; healthy

tag: disease state

tag: Sex

tag: cdai

tag: pcr

tag: sescd local

tag: affected area

tag: transplant

tag: surgery

tag: age diagnostic


title: C14-TTR-ILI-M

tag: sescd global

tag: exact location

tag: time

tag: patient id


title: C4-TTR-SIG; healthy

tag: involved

tag: active area

tag: age sample


title: OF 56 hpf Rep5 [5-56-0]

source_name: optic fissure retina_56 hpf

tag: hpf

tag: tissue

value: optic fissure retina


title: HCA00102.G15

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: C14-TTR-CA-M

tag: Sex

tag: cdai

tag: pcr

tag: sescd local

tag: afected area

tag: transplant

tag: surgery


title: C17-TTR-SIG-M

tag: sescd global

tag: exact location

tag: time

tag: patient id

tag: involved

tag: active area

tag: age diagnostic


title: DR 48 hpf Rep5 [5-48-R]

source_name: dorsal retina_48 hpf

tag: hpf

tag: tissue


title: HCA00102.G14

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: C4-TTR-CA; healthy

tag: disease state

tag: Sex

tag: cdai

tag: pcr

tag: sescd local

tag: affected area

tag: transplant

tag: age sample


title: C3-TTR-SIG; healthy

tag: sescd global

tag: exact location

tag: time

tag: patient id

tag: involved

tag: active area

tag: surgery

tag: age diagnostic


title: C13-TTR-SIG-M

tag: treatment

tag: afected area


title: HCA00102.G13

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C12-TTR-SIG-M

tag: Sex

tag: cdai

tag: pcr

tag: sescd local

tag: transplant


title: C3-TTR-CA; healthy

tag: disease state

tag: sescd global

tag: exact location

tag: time

tag: patient id

tag: affected area

tag: age sample


title: C13-TTR-ILI-M

tag: treatment

tag: afected area

tag: involved

tag: active area

tag: surgery

tag: age diagnostic


title: HCA00102.G12

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: OF 32 hpf Rep5 [5-32-0]

source_name: optic fissure retina_32 hpf

tag: hpf

tag: tissue


title: DR 32 hpf Rep5 [5-32-R]

source_name: dorsal retina_32 hpf


title: DR 56 hpf Rep4 [4-56-R]


title: HCA00102.G10


title: C12-TTR-ILI-M

tag: Sex

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: transplant


title: C20-TTR-ILI; healthy

tag: disease state

tag: treatment

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: surgery

tag: age sample


title: OF 56 hpf Rep4 [4-56-O]

tag: hpf

tag: tissue


title: C12-TTR-CA-M

tag: Sex

tag: cdai

tag: afected area

tag: age diagnostic


title: C11-TTR-SIG-M

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location


title: C20-TTR-CA; healthy

tag: disease state

tag: treatment

tag: time

tag: transplant


title: HCA00102.G09

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: DR 48 hpf Rep4 [4-48-R]

tag: hpf

tag: tissue


title: HCA00102.G08


title: C11-TTR-ILI-M

tag: Sex

tag: cdai

tag: patient id

tag: afected area

tag: involved

tag: active area

tag: surgery

tag: age sample


title: C19-TTR-ILI; healthy

tag: disease state

tag: treatment

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: affected area

tag: age diagnostic


title: OF 48 hpf Rep5 [5-48-O]

source_name: optic fissure retina_48 hpf

tag: hpf

tag: tissue


title: HCA00102.G06

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: OF 48 hpf Rep4 [4-48-O]


title: C19-TTR-CA; healthy

tag: Sex

tag: cdai

tag: patient id

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age sample


title: C11-TTR-CA-M

tag: treatment

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: afected area


title: DR 32 hpf Rep4 [4-32-R]

tag: hpf

tag: tissue


title: C10-TTR-SIG-M

tag: Sex

tag: age diagnostic


title: C10-TTR-ILI-M

tag: cdai

tag: patient id


title: C20-TTR-SIG; healthy

tag: disease state

tag: affected area

tag: involved

tag: active area


title: C18-TTR-SIG; healthy

tag: treatment

tag: transplant

tag: surgery

tag: age sample


title: HCA00102.G05

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: OF 32 hpf Rep4 [4-32-O]

tag: hpf

tag: tissue


title: HCA00102.G04


title: C19-TTR-SIG; healthy

tag: Sex

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: age diagnostic


title: DR 56 hpf Rep3 [3-56-R]


title: C10-TTR-CA-M

tag: treatment

tag: patient id

tag: afected area

tag: involved

tag: active area

tag: transplant

tag: surgery


title: C18-TTR-ILI; healthy

tag: disease state

tag: affected area

tag: age sample


title: HCA00102.G03

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: OF 56 hpf Rep3 [3-56-O]

tag: hpf

tag: tissue


title: DR 48 hpf Rep3 [3-48-R]


title: C17-TTR-SIG; healthy

tag: Sex

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: age diagnostic


title: C18-TTR-CA; healthy

tag: disease state

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age sample


title: C1-TTR-SIG-M

tag: Sex

tag: afected area


title: C1-TTR-CA-M

tag: treatment

tag: cdai


title: OF 48 hpf Rep3 [3-48-O]

tag: hpf

tag: tissue


title: HCA00102.G01

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: HCA00102.G07


title: 36-T26-TTR-IH-M

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

value: Post

tag: age diagnostic


title: DR 32 hpf Rep3 [3-32-R]


title: HCA00102.E16


title: C17-TTR-CA; healthy

tag: disease state

tag: Sex

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age sample


title: OF 32 hpf Rep3 [3-32-O]

tag: hpf

tag: tissue


title: C16-TTR-ILI; healthy

tag: treatment

tag: cdai

tag: pcr


title: DR 56 hpf Rep2 [2-56-R]


title: HCA00102.E15

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 35-T52-TTR-CII-M

tag: Sex

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

value: COLON

value: INVOLVED

value: INACTIVE

tag: age diagnostic


title: OF 56 hpf Rep2 [2-56-O]

tag: hpf

tag: tissue


title: HCA00102.E14

tag: treatment


title: HCA00102.G02

value: colorectal carcinoma


title: HCA00102.E13

value: malignant melanoma


title: C15-TTR-ILI; healthy

tag: disease state

value: healthy

value: MALE

tag: cdai

tag: pcr

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age sample


title: C15-TTR-SIG; healthy

tag: Sex

value: NO

tag: sescd global

tag: sescd local

tag: exact location


title: HCA00102.G11

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 35-T106-TR-CII-M

value: FEMALE

tag: treatment

value: YES

tag: cdai

tag: time

tag: patient id

tag: afected area

tag: age diagnostic


title: OF 48 hpf Rep2 [2-48-O]

tag: hpf

tag: tissue


title: 35-T26-TTR-CIA-M

tag: Sex

tag: pcr

tag: involved

tag: active area

value: ACTIVE

tag: transplant

tag: surgery

tag: age sample


title: C17-TTR-ILI; healthy

tag: disease state

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

value: C

tag: affected area

value: HEALTHY

value: Baseline


title: C16-TTR-CA; healthy

tag: treatment

tag: cdai

value: ASCENDING COLON

tag: time

tag: patient id


title: HCA00102.E11

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C14-TTR-SIG; healthy

tag: Sex

tag: pcr

value: SIGMOID COLON

tag: involved

tag: active area

tag: transplant

tag: age diagnostic


title: 36-T26-TTR-CI-M

tag: sescd global

tag: sescd local

tag: exact location

value: TRANSVERSE COLON

tag: afected area

value: COLON

value: Post

tag: surgery

tag: age sample