title: CTC.127268.20CTC.1

description:
Sample name: 127268.20CTC.1
Matched array sample Accession Number: GSM998040
Matched array sample name: 127268_20CTC


title: CTC.127201.20CTC

status: Public on Apr 01 2018

type: RNA

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

country: USA

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

description:
Sample name: 127201.20CTC
Matched array sample Accession Number: GSM998039
Matched array sample name: 127201_5CTC

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA).

data_processing:
Amplification curves were processed using SDS 2.4 and analyzed using RQ Manager 1.2.1 to obtain mean cycle threshold (Ct) of the triplicate measurements for each gene.
The mean Ct for ACTB and RPS18 was used to calculate for the ∆Cts

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: Circulating Tumor Cells

label_protocol:
Reverse transcription (RT) and preamplification were performed using Taqman® PreAmp Cells-to-CT™ kit (Ambion, Texas) following manufacturer’s instructions with some modification. These steps were performed in the same tube the cells were sorted into to avoid any loss of nucleic acids.  RT was performed on total RNA in the whole cell lysate (11µL) by adding 12.5µL of 2X RT buffer, 1.25µL of 20X RT enzyme and 0.25µL of nuclease free water and incubated in a thermal cycler for 60 min at 37°C and 5 min at 95°C to inactivate the RT enzyme. Specific transcript preamplification was performed by adding 50µL of Taqman® PreAmp Master and 25µL of the Custom PreAmp Pool to the RT reaction mix (25µL) and incubated in a thermal cycler for 10 min at 95°C followed by 14 cycles at 95°C for 15 sec and 60°C for 4 min. The Custom PreAmp Pool contained 63 Taqman® assays. The same set of Taqman® assays were also printed onto the TLDA card and used for subsequent RT-PCR. The primers for RPS18 were not included in the custom pool due to the already high expression level of this gene. Note that each assay contained specific primers for transcript specific preamplification.
Preamplified cDNA was diluted to 1/32 by adding 12.5µL of cDNA from the completed RT reaction to 187.5µL of nuclease free water and 200µL of Taqman® Universal PCR Master Mix (no UNG). Two samples were loaded in each TLDA card (100 µL per port; 4 ports per sample). RT-PCR was performed using the ABI PRISM 7900HT.

extract_protocol: Cells were sorted into reaction tubes containing 9.5µL of lysis buffer and 0.5 µL of DNAse. Lysis reaction was carried out for 5 min at room temperature and 1µL of Stop solution was added and incubated for 2 min and immediately placed on ice. Whole cell lysates were then stored in -80°C until further use.

treatment_protocol: Cell isolation via IE/FACS: If a patient had ≥1 CTC/mL the remaining volume of blood was subjected to immunomagnetic enrichment and fluorescence activated cell sorting (IE/FACS) within 24-32 hr after blood draw. In the initial step, magnetic beads coated with EpCAM mAb are used to enrich for tumor cells. Enriched samples are then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+/CD45-) from leukocytes (CD45+/EpCAM-) during sorting. This procedure allows for the isolation of small pools cells, which can be subjected to downstream molecular analyses.

tag: sample type

value: Test

tag: diagnosis

value: Breast cancer

tag: tumor stage

value: Metastatic

tag: gender

value: Female

tag: tissue

value: Peripheral Blood

tag: cell type

value: Circulating Tumor Cells

tag: matched leukocyte sample


title: CTC.127055.50CD45

source_name: Blood Leukocytes

value: Control

value: Blood Leukocytes


title: CTC.126958.20CTC


title: CTC.126976.24CD45


title: CTC.127055.20CTC


title: CTC.128099.20CTC.1.T2

value: no pair


title: CTC.126958.50CD45


title: CTC.127201.50CD45


title: CTC.128099.50CD45.1


title: CTC.128099.20CTC.1.T3


title: CTC.128148.12CTC


title: CTC.126850.50CD45


title: CTC.126850.14CTC


title: CTC.126976.16CTC

description:
Sample name: 126976.16CTC
Matched array sample Accession Number: GSM998038
Matched array sample name: 126976_20CTC


title: CTC.126750.20CTC.1


title: CTC.126750.50CD45


title: CTC.126746.20CTC.T6


title: CTC.126746.50CD45.1


title: CTC.126632.11CTC.T4


title: CTC.126632.18CTC


title: CTC.126746.20CTC.1.T4


title: CTC.126721.20CTC.1

description:
Sample name: 126721.20CTC.1
Matched array sample Accession Number: GSM998036
Matched array sample name: 126721_20CTC


title: CTC.126746.20CTC.1

description:
Sample name: 126746.20CTC.1
Matched array sample Accession Number: GSM998037
Matched array sample name: 126746_20CTC


title: CTC.126703.20CTC.1

description:
Sample name: 126703.20CTC.1
Matched array sample Accession Number: GSM998035
Matched array sample name: 126703_20CTC


title: CTC.126703.50CD45.1


title: CTC.126632.50CD45


title: CTC.126624.20CTC.1.T4


title: CTC.126624.20CTC.1.T2


title: CTC.126563.50CD45


title: CTC.126608.20CTC.1.A1

description:
Sample name: 126608.20CTC.1.A1
Matched array sample Accession Number: GSM998033
Matched array sample name: 126608_20CTC


title: CTC.126608.50CD45.1


title: CTC.126423.50CD45


title: CTC.126320.19CTC.T2


title: CTC.126149.50CD45


title: CTC.126149.20CTC.2.T5


title: CTC.126624.20CTC.T3


title: CTC.126358.20CTC

description:
Sample name: 126358.20CTC
Matched array sample Accession Number: GSM998030
Matched array sample name: 126358_20CTC


title: CTC.126423.20CTC.1

description:
Sample name: 126423.20CTC.1
Matched array sample Accession Number: GSM998031
Matched array sample name: 126423_20CTC


title: CTC.126358.50CD45


title: CTC.126320.50CD45.T2


title: CTC.126563.20CTC.1

description:
Sample name: 126563.20CTC.1
Matched array sample Accession Number: GSM998032
Matched array sample name: 126563_20CTC


title: CTC.126624.50CD45.1


title: CTC.126624.20CTC.1

description:
Sample name: 126624.20CTC.1
Matched array sample Accession Number: GSM998034
Matched array sample name: 126624_20CTC


title: CTC.126149.20CTC.1.T3

description:
Sample name: 126149.20CTC.1.T3
Matched array sample Accession Number: GSM998029
Matched array sample name: 126149_20CTC


title: CTC.126149.20CTC.1.T4


title: CTC.126149.20CTC.2


title: CTC.125796.50CD45


title: CTC.126139.20CTC


title: CTC.125323.50CD45


title: CTC.125301.50CD45.A2


title: CTC.126149.20CTC.1.T2


title: CTC.125904.16CTC


title: CTC.125263.20CTC.1

description:
Sample name: 125263.20CTC.1
Matched array sample Accession Number: GSM998027
Matched array sample name: 125263_20CTC


title: CTC.125904.50CD45


title: CTC.125301.14CTC.A2


title: CTC.125263.50CD45


title: CTC.125122.50CD45


title: CTC.125233.20CTC.A1


title: CTC.125233.50CD45.A1


title: CTC.125183.50CD45.A1


title: CTC.125796.20CTC.1

description:
Sample name: 125796.20CTC.1
Matched array sample Accession Number: GSM998028
Matched array sample name: 125796_20CTC


title: CTC.125796.20CTC.T2


title: CTC.125323.10CTC


title: CTC.125051.20CTC.1

description:
Sample name: 125051.20CTC.1
Matched array sample Accession Number: GSM998026
Matched array sample name: 125051_20CTC


title: CTC.125051.20CTC.1.T2


title: CTC.125051.50CD45


title: CTC.124759.50CD45.T2.A1


title: CTC.125122.19CTC


title: CTC.125054.15CTC


title: CTC.124828.20CTC


title: CTC.124828.17CTC.T3


title: CTC.124828.20CTC.T2

description:
Sample name: 124828.20CTC.T2
Matched array sample Accession Number: GSM998025
Matched array sample name: 124828_14CTC


title: CTC.125183.20CTC.A1


title: CTC.124578.20CTC.2


title: CTC.125054.50CD45


title: CTC.124551.50CD45


title: CTC.124759.13CTC.T2.A1


title: CTC.124551.20CTC.1


title: CTC.124523.50CD45


title: CTC.124523.20CTC.1.T3

description:
Sample name: 124523.20CTC.1.T3
Matched array sample Accession Number: GSM998024
Matched array sample name: 124523_20CTC


title: CTC.124228.20CTC.T4


title: CTC.124437.20CTC

description:
Sample name: 124437.20CTC
Matched array sample Accession Number: GSM998023
Matched array sample name: 124437_5CTC


title: CTC.123680.50CD45.T2


title: CTC.123781.50CD45


title: CTC.123808.14CTC.T2


title: CTC.123834.20CTC


title: CTC.123781.20CTC.1


title: CTC.124437.50CD45


title: CTC.123834.20CTC.1.T2

description:
Sample name: 123834.20CTC.1.T2
Matched array sample Accession Number: GSM998020
Matched array sample name: 123834_20CTC


title: CTC.124088.20CTC.1

description:
Sample name: 124088.20CTC.1
Matched array sample Accession Number: GSM998021
Matched array sample name: 124088_20CTC


title: CTC.124523.20CTC.T2.A1


title: CTC.124504.18CTC


title: CTC.124504.50CD45


title: CTC.124523.20CTC.1


title: CTC.123547.50CD45


title: CTC.124088.50CD45


title: CTC.124228.20CTC.T3.A1


title: CTC.123680.20CTC.1.T2


title: CTC.123562.20CTC.1

description:
Sample name: 123562.20CTC.1
Matched array sample Accession Number: GSM998018
Matched array sample name: 123562_20CTC


title: CTC.123625.20CTC

description:
Sample name: 123625.20CTC
Matched array sample Accession Number: GSM998019
Matched array sample name: 123625_13CTC


title: CTC.124228.20CTC.2

description:
Sample name: 124228.20CTC.2
Matched array sample Accession Number: GSM998022
Matched array sample name: 124228_20CTC


title: CTC.124228.20CTC.2.T2


title: CTC.123760.14CTC.T2


title: CTC.123760.20CTC.T4


title: CTC.124228.18CTC.T5


title: CTC.123544.15CTC

description:
Sample name: 123544.15CTC
Matched array sample Accession Number: GSM998016
Matched array sample name: 123544_5CTC


title: CTC.123490.50CD45


title: CTC.123490.20CTC.1.T2


title: CTC.123547.20CTC.1

description:
Sample name: 123547.20CTC.1
Matched array sample Accession Number: GSM998017
Matched array sample name: 123547_20CTC


title: CTC.123544.50CD45


title: CTC.123490.20CTC


title: CTC.123190.10CTC


title: CTC.123412.20CTC.1

description:
Sample name: 123412.20CTC.1
Matched array sample Accession Number: GSM998015
Matched array sample name: 123412_20CTC


title: CTC.123036.50CD45


title: CTC.123074.17CTC


title: CTC.123328.50CD45


title: CTC.123328.20CTC.1

description:
Sample name: 123328.20CTC.1
Matched array sample Accession Number: GSM679633
Matched array sample name: 123328_20CTC


title: CTC.122504.20CD45


title: CTC.123024.20CTC.1.T2

description:
Sample name: 123024.20CTC.1.T2
Matched array sample Accession Number: GSM679631
Matched array sample name: 123024_20CTC


title: CTC.122478.20CTC.1.T3


title: CTC.122743.10CTC


title: CTC.122309.20CTC


title: CTC.122306.50CD45.A1


title: CTC.122504.20CTC


title: CTC.122504.20CTC.T2


title: CTC.122030.20CTC.1

description:
Sample name: 122030.20CTC.1
Matched array sample Accession Number: GSM679623
Matched array sample name: 122030_20CTC


title: CTC.122306.20CTC.1.A1

description:
Sample name: 122306.20CTC.1.A1
Matched array sample Accession Number: GSM998014
Matched array sample name: 122306_20CTC


title: CTC.122478.20CD45


title: CTC.122413.20CTC


title: CTC.122030.20CD45


title: CTC.122413.50CD45


title: CTC.123036.15CTC


title: CTC.122025.50CD45.T2


title: CTC.123024.50CD45.T2


title: CTC.121975.20CD45


title: CTC.121975.20CTC.1

description:
Sample name: 121975.20CTC.1
Matched array sample Accession Number: GSM679621
Matched array sample name: 121975_20CTC


title: CTC.121986.20CTC


title: CTC.122478.20CTC.1

description:
Sample name: 122478.20CTC.1
Matched array sample Accession Number: GSM679626
Matched array sample name: 122478_20CTC


title: CTC.121295.20CTC

description:
Sample name: 121295.20CTC
Matched array sample Accession Number: GSM679619
Matched array sample name: 121295_20CTC


title: CTC.121304.20CTC


title: CTC.121304.50CD45


title: CTC.121059.20CTC.1.T2


title: CTC.121276.20CD45


title: CTC.121276.20CTC


title: CTC.120850.20CTC.1.T3


title: CTC.121295.20CD45


title: CTC.121059.20CD45


title: CTC.120850.20CTC.1.T4

description:
Sample name: 120850.20CTC.1.T4
Matched array sample Accession Number: GSM679618
Matched array sample name: 120850_20CTC


title: CTC.121059.20CTC.1

description:
Sample name: 121059.20CTC.1
Matched array sample Accession Number: GSM1196061
Matched array sample name: 121059_20CTC


title: CTC.122025.20CTC.1.T2


title: CTC.120850.15CTC.T2


title: CTC.120850.20CTC.1


title: CTC.120850.20CD45


title: CTC.120447.20CTC


title: CTC.120670.20CTC.1.T2


title: CTC.120670.20CD45


title: CTC.120670.10CTC


title: CTC.120447.20CD45


title: CTC.120447.20CTC.1.T2


title: CTC.120670.20CTC.1.T3.A1

description:
Sample name: 120670.20CTC.1.T3.A1
Matched array sample Accession Number: GSM679616
Matched array sample name: 120670_20CTC


title: CTC.120660.50CD45


title: CTC.120153.20CD45


title: CTC.120153.20CTC.1.T2


title: CTC.120153.20CTC.1.T3

description:
Sample name: 120153.20CTC.1.T3
Matched array sample Accession Number: GSM679605
Matched array sample name: 120153_20ctc


title: CTC.120153.40CTC


title: CTC.120660.20CTC


title: CTC.119982.20CTC.1.T2


title: CTC.119982.20CD45


title: CTC.119982.20CTC.1

description:
Sample name: 119982.20CTC.1
Matched array sample Accession Number: GSM998013
Matched array sample name: 119982_20CTC


title: CTC.119826.20CTC.1

description:
Sample name: 119826.20CTC.1
Matched array sample Accession Number: GSM679600
Matched array sample name: 119826_20CTC


title: CTC.119063.20CTC


title: CTC.118273.50CD45


title: WT_6.cDNA.004.C93

type: SRA

city: Minneapolis

first: Jakub

last: Tolar

state: MN

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota, Twin Cities

library_source: transcriptomic

data_processing:
Reads were mapped to hg19 using Bowtie2 (version 2.2.4) and Tophat (version 2.0.9)
Two single-cell samples sequenced as population controls with high read counts were sub-sampled (random sub-sampling, 10% of total reads)
Gene expression levels were calculated using Cuffquant (Cufflinks version 2.2.1 with parameters -u -max-bundle-frags 10000000) and Cuffnorm (Cufflinks version 2.2.1)
FPKM values as estimated by Cufflinks were added a value of 1 (to avoid zeros) and log2 transformed
Lowly expressed genes (average log2 (FPKM) < 1.5) were excluded from further analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimted text file includes FPKM values

source_name: Human dermal fibroblasts

growth_protocol: Dermal fibroblasts from patients with recessive dystrophic epidermolysis bullosa and their human leukocyte antigen (HLA) matched healthy siblings were obtained from skin biopsies and cultured in DMEM high glucose (Thermo Fisher Scientific) containing 10% fetal bovine serum (MilliporeSigma), 1% Pen/Strep (Thermo Fisher Scientific), 1% L-glutamine (Thermo Fisher Scientific), and 1% MEM NEAA (Thermo Fisher Scientific). For sub-culture, the medium was removed and cells were washed with 1X PBS (Thermo Fisher Scientific) and detached using Trypsin/EDTA (Thermo Fisher Scientific).

extract_protocol:
Fibroblasts were collected by trypsinization and resuspended in 5 ul of fibroblast medium for loading into the C1 capture chip.
cDNA was created from selected cells using the SMARTer Ultra Low RNA kit designed for the C1 system (Clontech). mRNA libraries were constructed using the the Nextera XT kit (Illumina) according to the manufacturer’s protocol.

tag: disease

value: wild-type control

value: Fibroblast

tag: passage number

tag: c1 chip size

value: Large


title: WT_6.cDNA.004.C91


title: WT_6.cDNA.004.C95


title: WT_6.cDNA.004.C92


title: WT_6.cDNA.004.C90


title: WT_6.cDNA.004.C96


title: CTC.116285.20CTC.1

description:
Sample name: 116285.20CTC.1
Matched array sample Accession Number: GSM679560
Matched array sample name: 116285_20CTC


title: WT_6.cDNA.004.C88


title: WT_6.cDNA.004.C87


title: CTC.116285.20CD45


title: CTC.116875.20CTC


title: CTC.116285.20CTC.1.T3


title: CTC.117548.20CTC.1

description:
Sample name: 117548.20CTC.1
Matched array sample Accession Number: GSM679575
Matched array sample name: 117548_20CTC


title: WT_6.cDNA.004.C78


title: WT_6.cDNA.004.C75


title: WT_6.cDNA.004.C74


title: CTC.117494.20CD45


title: CTC.118273.20CTC.1


title: WT_6.cDNA.004.C70


title: WT_6.cDNA.004.C73


title: CTC.117494.20CTC.1

description:
Sample name: 117494.20CTC.1
Matched array sample Accession Number: GSM679572
Matched array sample name: 117494_20CTC


title: WT_6.cDNA.004.C68


title: WT_6.cDNA.004.C67


title: WT_6.cDNA.004.C62


title: WT_6.cDNA.004.C64


title: WT_6.cDNA.004.C82


title: WT_6.cDNA.004.C54


title: WT_6.cDNA.004.C52


title: WT_6.cDNA.004.C56


title: WT_6.cDNA.004.C51


title: WT_6.cDNA.004.C69


title: WT_6.cDNA.004.C57


title: WT_6.cDNA.004.C36


title: WT_6.cDNA.004.C49


title: WT_6.cDNA.004.C46


title: WT_6.cDNA.004.C47


title: WT_6.cDNA.004.C42


title: WT_6.cDNA.004.C34


title: WT_6.cDNA.004.C28


title: WT_6.cDNA.004.C27


title: WT_6.cDNA.004.C44


title: WT_6.cDNA.004.C37


title: WT_6.cDNA.004.C15


title: WT_6.cDNA.004.C12


title: WT_6.cDNA.004.C11


title: WT_6.cDNA.004.C60


title: WT_6.cDNA.004.C09


title: WT_6.cDNA.004.C05


title: WT_6.cDNA.004.C55


title: WT_6.cDNA.004.C02


title: WT_6.cDNA.004.C01


title: RDEB_6.cDNA.003.C96

value: RDEB


title: CTC.116285.20CTC.T2


title: WT_6.cDNA.004.C14


title: WT_6.cDNA.004.C32


title: WT_6.cDNA.004.C17


title: RDEB_6.cDNA.003.C90


title: RDEB_6.cDNA.003.C93


title: RDEB_6.cDNA.003.C89


title: RDEB_6.cDNA.003.C84


title: RDEB_6.cDNA.003.C94


title: RDEB_6.cDNA.003.C86


title: RDEB_6.cDNA.003.C74


title: RDEB_6.cDNA.003.C78


title: RDEB_6.cDNA.003.C81


title: RDEB_6.cDNA.003.C76


title: RDEB_6.cDNA.003.C75


title: RDEB_6.cDNA.003.C80


title: RDEB_6.cDNA.003.C71


title: RDEB_6.cDNA.003.C70


title: RDEB_6.cDNA.003.C72


title: RDEB_6.cDNA.003.C62


title: RDEB_6.cDNA.003.C59


title: RDEB_6.cDNA.003.C60


title: RDEB_6.cDNA.003.C56


title: RDEB_6.cDNA.003.C57


title: RDEB_6.cDNA.003.C87


title: RDEB_6.cDNA.003.C54


title: RDEB_6.cDNA.003.C53


title: RDEB_6.cDNA.003.C51


title: RDEB_6.cDNA.003.C52


title: RDEB_6.cDNA.003.C55


title: RDEB_6.cDNA.003.C44


title: RDEB_6.cDNA.003.C43


title: RDEB_6.cDNA.003.C26


title: RDEB_6.cDNA.003.C27


title: RDEB_6.cDNA.003.C33


title: RDEB_6.cDNA.003.C32


title: RDEB_6.cDNA.003.C37


title: RDEB_6.cDNA.003.C35


title: RDEB_6.cDNA.003.C67


title: RDEB_6.cDNA.003.C41


title: RDEB_6.cDNA.003.C21


title: RDEB_6.cDNA.003.C02


title: RDEB_6.cDNA.003.C07


title: RDEB_6.cDNA.003.C03


title: RDEB_6.cDNA.003.C12


title: RDEB_6.cDNA.003.C13


title: RDEB_6.cDNA.003.C19


title: RDEB_6.cDNA.003.C04


title: WT_5.cDNA.001.C94


title: WT_5.cDNA.001.C92


title: WT_5.cDNA.001.C91


title: WT_5.cDNA.001.C90


title: CTC.117548.20CTC.T2


title: WT_5.cDNA.001.C88


title: WT_5.cDNA.001.C87


title: WT_5.cDNA.001.C84


title: WT_5.cDNA.001.C82


title: WT_5.cDNA.001.C81


title: RDEB_6.cDNA.003.C38


title: WT_5.cDNA.001.C79


title: WT_5.cDNA.001.C68


title: WT_5.cDNA.001.C73


title: WT_5.cDNA.001.C66


title: WT_5.cDNA.001.C60


title: WT_5.cDNA.001.C62


title: WT_5.cDNA.001.C64


title: WT_5.cDNA.001.C78


title: WT_5.cDNA.001.C57


title: WT_5.cDNA.001.C56


title: WT_5.cDNA.001.C50


title: WT_5.cDNA.001.C54


title: WT_5.cDNA.001.C55


title: WT_5.cDNA.001.C51


title: WT_5.cDNA.001.C70


title: WT_5.cDNA.001.C48


title: WT_5.cDNA.001.C52


title: WT_5.cDNA.001.C36


title: WT_5.cDNA.001.C43


title: WT_5.cDNA.001.C28


title: WT_5.cDNA.001.C26


title: WT_5.cDNA.001.C25


title: WT_5.cDNA.001.C24


title: WT_5.cDNA.001.C40


title: WT_5.cDNA.001.C41


title: WT_5.cDNA.001.C38


title: WT_5.cDNA.001.C21


title: WT_5.cDNA.001.C18


title: WT_5.cDNA.001.C06


title: WT_5.cDNA.001.C29


title: WT_5.cDNA.001.C04


title: RDEB_5.cDNA.007.C95


title: WT_5.cDNA.001.C22


title: WT_5.cDNA.001.C75


title: WT_5.cDNA.001.C02


title: WT_5.cDNA.001.C17


title: WT_5.cDNA.001.C03


title: RDEB_5.cDNA.007.C92


title: RDEB_5.cDNA.007.C89


title: RDEB_5.cDNA.007.C88


title: RDEB_5.cDNA.007.C85


title: RDEB_5.cDNA.007.C72


title: RDEB_5.cDNA.007.C77


title: RDEB_5.cDNA.007.C70


title: RDEB_5.cDNA.007.C69


title: RDEB_5.cDNA.007.C71


title: WT_6.cDNA.004.C77


title: WT_5.cDNA.001.C15


title: RDEB_5.cDNA.007.C64


title: RDEB_5.cDNA.007.C67


title: RDEB_5.cDNA.007.C65


title: RDEB_5.cDNA.007.C93


title: RDEB_5.cDNA.007.C62


title: RDEB_5.cDNA.007.C60


title: RDEB_5.cDNA.007.C58


title: RDEB_5.cDNA.007.C86


title: RDEB_5.cDNA.007.C47


title: RDEB_5.cDNA.007.C45


title: RDEB_5.cDNA.007.C46


title: RDEB_5.cDNA.007.C41


title: RDEB_5.cDNA.007.C38


title: RDEB_5.cDNA.007.C48


title: RDEB_5.cDNA.007.C49


title: RDEB_5.cDNA.007.C74


title: RDEB_5.cDNA.007.C84


title: RDEB_5.cDNA.007.C35


title: RDEB_5.cDNA.007.C30


title: RDEB_5.cDNA.007.C29


title: RDEB_5.cDNA.007.C32


title: RDEB_5.cDNA.007.C28


title: RDEB_5.cDNA.007.C27


title: RDEB_5.cDNA.007.C24


title: RDEB_5.cDNA.007.C18


title: WT_5.cDNA.001.C33


title: RDEB_5.cDNA.007.C55


title: RDEB_5.cDNA.007.C14


title: RDEB_5.cDNA.007.C56


title: RDEB_5.cDNA.007.C13


title: RDEB_5.cDNA.007.C12


title: RDEB_5.cDNA.007.C05


title: RDEB_5.cDNA.007.C11


title: WT_4.cDNA.005.C92


title: RDEB_5.cDNA.007.C02


title: RDEB_5.cDNA.007.C03


title: WT_4.cDNA.005.C88


title: WT_4.cDNA.005.C83


title: WT_4.cDNA.005.C95


title: WT_4.cDNA.005.C93


title: WT_4.cDNA.005.C85


title: WT_4.cDNA.005.C74


title: WT_4.cDNA.005.C76


title: WT_4.cDNA.005.C78


title: RDEB_5.cDNA.007.C17


title: WT_4.cDNA.005.C71


title: WT_4.cDNA.005.C91


title: WT_4.cDNA.005.C65


title: WT_4.cDNA.005.C62


title: WT_4.cDNA.005.C67


title: RDEB_5.cDNA.007.C04


title: WT_4.cDNA.005.C61


title: WT_4.cDNA.005.C70


title: WT_4.cDNA.005.C43


title: WT_4.cDNA.005.C51


title: WT_4.cDNA.005.C38


title: WT_4.cDNA.005.C50


title: WT_4.cDNA.005.C47


title: WT_4.cDNA.005.C57


title: WT_4.cDNA.005.C46


title: WT_4.cDNA.005.C52


title: WT_4.cDNA.005.C20


title: WT_4.cDNA.005.C54


title: WT_4.cDNA.005.C56


title: WT_4.cDNA.005.C33


title: WT_4.cDNA.005.C31


title: WT_4.cDNA.005.C25


title: WT_4.cDNA.005.C18


title: WT_4.cDNA.005.C27


title: WT_4.cDNA.005.C19


title: WT_4.cDNA.005.C17


title: WT_4.cDNA.005.C16


title: WT_4.cDNA.005.C73


title: WT_4.cDNA.005.C79


title: WT_4.cDNA.005.C68


title: WT_4.cDNA.005.C14


title: WT_4.cDNA.005.C06


title: WT_4.cDNA.005.C15


title: WT_4.cDNA.005.C11


title: WT_4.cDNA.005.C30


title: WT_4.cDNA.005.C29


title: WT_4.cDNA.005.C04


title: WT_4.cDNA.005.C02


title: WT_4.cDNA.005.C05


title: RDEB_4.cDNA.004.C90


title: WT_4.cDNA.005.C01


title: RDEB_4.cDNA.004.C82


title: RDEB_4.cDNA.004.C92


title: WT_4.cDNA.005.C12


title: RDEB_4.cDNA.004.C83


title: RDEB_4.cDNA.004.C77


title: RDEB_4.cDNA.004.C81


title: RDEB_4.cDNA.004.C89


title: RDEB_4.cDNA.004.C8


title: RDEB_4.cDNA.004.C70


title: RDEB_4.cDNA.004.C75


title: RDEB_4.cDNA.004.C7


title: WT_4.cDNA.005.C08


title: RDEB_4.cDNA.004.C66


title: RDEB_4.cDNA.004.C64


title: RDEB_4.cDNA.004.C74


title: RDEB_4.cDNA.004.C69


title: RDEB_4.cDNA.004.C65


title: RDEB_4.cDNA.004.C6


title: RDEB_4.cDNA.004.C63


title: RDEB_4.cDNA.004.C51


title: RDEB_4.cDNA.004.C56


title: WT_4.cDNA.005.C03


title: RDEB_4.cDNA.004.C49


title: RDEB_4.cDNA.004.C50


title: RDEB_4.cDNA.004.C76


title: RDEB_4.cDNA.004.C41


title: RDEB_4.cDNA.004.C44


title: RDEB_4.cDNA.004.C42


title: RDEB_4.cDNA.004.C38


title: RDEB_4.cDNA.004.C48


title: RDEB_4.cDNA.004.C25


title: RDEB_4.cDNA.004.C12


title: WT_3.cDNA.002.C75


title: WT_3.cDNA.002.C84


title: WT_3.cDNA.002.C9


title: WT_3.cDNA.002.C90


title: WT_3.cDNA.002.C70


title: RDEB_4.cDNA.004.C34


title: WT_3.cDNA.002.C83


title: WT_3.cDNA.002.C82


title: RDEB_4.cDNA.004.C14


title: RDEB_4.cDNA.004.C13


title: RDEB_4.cDNA.004.C10


title: WT_3.cDNA.002.C91


title: RDEB_4.cDNA.004.C16


title: RDEB_4.cDNA.004.C22


title: WT_3.cDNA.002.C87


title: WT_3.cDNA.002.C77


title: WT_3.cDNA.002.C6


title: WT_3.cDNA.002.C79


title: WT_3.cDNA.002.C66


title: WT_3.cDNA.002.C51


title: WT_3.cDNA.002.C73


title: WT_3.cDNA.002.C7


title: WT_3.cDNA.002.C52


title: WT_3.cDNA.002.C49


title: WT_3.cDNA.002.C76


title: WT_3.cDNA.002.C4


title: WT_3.cDNA.002.C38


title: WT_3.cDNA.002.C60


title: WT_3.cDNA.002.C36


title: WT_3.cDNA.002.C35


title: WT_3.cDNA.002.C22


title: WT_3.cDNA.002.C25


title: WT_3.cDNA.002.C26


title: WT_3.cDNA.002.C21


title: WT_3.cDNA.002.C27


title: WT_3.cDNA.002.C31


title: WT_3.cDNA.002.C20


title: WT_3.cDNA.002.C3


title: WT_3.cDNA.002.C29


title: WT_3.cDNA.002.C11


title: RDEB_3.cDNA.003.C95


title: RDEB_3.cDNA.003.C96


title: RDEB_3.cDNA.003.C91


title: WT_3.cDNA.002.C34


title: WT_3.cDNA.002.C13


title: RDEB_3.cDNA.003.C88


title: RDEB_3.cDNA.003.C86


title: RDEB_3.cDNA.003.C92


title: WT_3.cDNA.002.C2


title: RDEB_3.cDNA.003.C8


title: RDEB_3.cDNA.003.C80


title: RDEB_3.cDNA.003.C82


title: RDEB_3.cDNA.003.C79


title: RDEB_3.cDNA.003.C78


title: Populus nigra root grown under  control condition (1.5 ppm)_rep2

city: tokat

first: Kubilay

last: Yıldırım

address: tasliciftlik kampusu

country: Turkey

institute: gaziosmanpasa university

description: Gene expression data from the roots of boron toxicity tolerant Black poplar genotype

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Robust Multiarray Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Populus nigra

source_name: 1.5ppm (control) boric acid treated root

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: One hundred hardwood cuttings of P.a (A.67.267) and P.n (N.62.191) (15 cm in length, 1-2 cm in diameter) were obtained from Poplar and Fast Growing Forest Trees Research Institute (İzmit/Turkey). Cuttings were firstly planted into the plastic bags (1 L) as a single cutting per bag on 15 April 2015. When the rooted cuttings had 15-20 mature leaves, the best growing 50 rooted cuttings/clone were selected and transferred individually to 20 L plastic pots (bottom closed) having five different soil boric acid concentrations (1.5, 5,10,15 and 20 ppm). Pots contained 5 kg perlite and soil mixture (4:1) (pH 7.1) that have 0.0062 dS/m EC, 1.9 % organic carbon and 1.48 (control) initial B concentration. In total, the experiment included 100 sapling for B toxicity treatment (2 different poplar clones x 5 soil B supply x 10 replications =100 pots). In two day intervals, the pots were weighted and transpired water replenished with tap water (B content; 0.068ppm) to keep the water content at constant level. Experiment was carried out for five weeks in a fully controlled greenhouse at the Gaziosmanpasa University (Tokat /Turkey) with a 25/22 °C day/night temperatures.

extract_protocol: Leaves and roots collected from control (1.5 ppm soil boron content) and toxic (10 ppm soil boron content) soil conditions were were utilized for total RNA isolation as described in Chang et al. (1993) with minor modifications as described in Le-Provost et al (2007).

tag: genotype

value: hyper boron accumulator

tag: age

value: one year old rooted cuttings

value: root

tag: treated with

value: 1.5ppm (control) boric acid


title: RDEB_3.cDNA.003.C74


title: RDEB_3.cDNA.003.C72


title: RDEB_3.cDNA.003.C6


title: RDEB_3.cDNA.003.C7


title: RDEB_3.cDNA.003.C73


title: RDEB_3.cDNA.003.C67


title: Populus nigra root grown under  control condition (1.5 ppm)_rep1

treatment_protocol: When the rooted cuttings had 15-20 mature leaves, the best growing 50 rooted cuttings/clone were selected and transferred individually to 20 L plastic pots (bottom closed) having five different soil boric acid concentrations (1.5, 5,10,15 and 20 ppm). Pots contained 5 kg perlite and soil mixture (4:1) (pH 7.1) that have 0.0062 dS/m EC, 1.9 % organic carbon and 1.48 (control) initial B concentration.


title: RDEB_3.cDNA.003.C70


title: RDEB_3.cDNA.003.C65


title: Populus nigra root grown under  boron toxicity (10 ppm)_rep2

source_name: 10 ppm (toxic) boric acid treated root

value: 10 ppm (toxic) boric acid


title: Populus nigra root grown under  boron toxicity (10 ppm)_rep1


title: Populus nigra leaf grown under  control condition (1.5 ppm)_rep2

description: Gene expression data from the leaves of boron toxicity tolerant Black poplar genotype

source_name: 1.5ppm (control) boric acid treated leaf

value: leaf


title: RDEB_3.cDNA.003.C63


title: RDEB_3.cDNA.003.C71


title: RDEB_3.cDNA.003.C64


title: RDEB_3.cDNA.003.C61


title: RDEB_3.cDNA.003.C69


title: RDEB_3.cDNA.003.C58


title: Populus alba leaf grown under control condition (1.5 ppm)_rep2

organism: Populus alba

value: Lower B accumulator


title: Populus alba leaf grown under  boron toxicity (10 ppm)_rep2

source_name: 10 ppm (toxic) boric acid treated leaf


title: Populus alba leaf grown under control condition (1.5 ppm)_rep1


title: RDEB_3.cDNA.003.C55


title: Populus nigra leaf grown under  boron toxicity (10 ppm)_rep1


title: Populus alba root grown under control condition (1.5 ppm)_rep2


title: RDEB_3.cDNA.003.C50


title: Populus alba root grown under  boron toxicity (10 ppm)_rep1


title: Populus alba root grown under  boron toxicity (10 ppm)_rep2


title: Populus nigra leaf grown under  boron toxicity (10 ppm)_rep2


title: Populus alba root grown under control condition (1.5 ppm)_rep1


title: RDEB_3.cDNA.003.C49


title: Populus nigra leaf grown under  control condition (1.5 ppm)_rep1


title: Populus alba leaf grown under  boron toxicity (10 ppm)_rep1


title: RDEB_3.cDNA.003.C44


title: RDEB_3.cDNA.003.C51


title: RDEB_3.cDNA.003.C48


title: RDEB_3.cDNA.003.C42


title: RDEB_3.cDNA.003.C38


title: RDEB_3.cDNA.003.C3


title: RDEB_3.cDNA.003.C37


title: RDEB_3.cDNA.003.C32


title: RDEB_3.cDNA.003.C35


title: RDEB_3.cDNA.003.C34


title: RDEB_3.cDNA.003.C30


title: RDEB_3.cDNA.003.C33


title: genomic DNA from WB92

type: genomic

city: Iowa City

first: Robert

middle: Alan

last: Philibert

state: IA

address: 500 Newton Rd

institute: University of Iowa

description:
drinker WB sample
SAMPLE 92

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
Genome Studios
The matrix_signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: drinkers_male_whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from WB samples using QIAamp DNA Blood Mini Kit according to standard instructions

value: Male

tag: disease state

value: case; drinkers

value: whole blood (WB)


title: genomic DNA from WB94

description:
drinker WB sample
SAMPLE 94


title: RDEB_3.cDNA.003.C26


title: genomic DNA from WB90

description:
drinker WB sample
SAMPLE 90


title: RDEB_3.cDNA.003.C24


title: RDEB_3.cDNA.003.C43


title: RDEB_3.cDNA.003.C27


title: genomic DNA from WB93

description:
non-drinker WB sample
SAMPLE 93

source_name: non-drinkers_male_whole blood

value: control; non-drinkers


title: genomic DNA from WB89

description:
non-drinker WB sample
SAMPLE 89


title: RDEB_3.cDNA.003.C46


title: genomic DNA from WB88

description:
drinker WB sample
SAMPLE 88


title: RDEB_3.cDNA.003.C28


title: RDEB_3.cDNA.003.C23


title: RDEB_3.cDNA.003.C16


title: genomic DNA from WB91

description:
non-drinker WB sample
SAMPLE 91


title: genomic DNA from WB87

description:
non-drinker WB sample
SAMPLE 87


title: genomic DNA from WB82

description:
non-drinker WB sample
SAMPLE 82

source_name: non-drinkers_female_whole blood

value: Female


title: genomic DNA from WB84

description:
non-drinker WB sample
SAMPLE 84


title: RDEB_3.cDNA.003.C20


title: genomic DNA from WB80

description:
drinker WB sample
SAMPLE 80


title: RDEB_3.cDNA.003.C31


title: RDEB_3.cDNA.003.C13


title: genomic DNA from WB78

description:
non-drinker WB sample
SAMPLE 78


title: genomic DNA from WB83

description:
drinker WB sample
SAMPLE 83

source_name: drinkers_female_whole blood


title: genomic DNA from WB79

description:
drinker WB sample
SAMPLE 79


title: genomic DNA from WB75

description:
drinker WB sample
SAMPLE 75


title: genomic DNA from WB86

description:
non-drinker WB sample
SAMPLE 86


title: genomic DNA from WB81

description:
non-drinker WB sample
SAMPLE 81


title: RDEB_3.cDNA.003.C10


title: genomic DNA from WB76

description:
non-drinker WB sample
SAMPLE 76


title: genomic DNA from WB77

description:
drinker WB sample
SAMPLE 77


title: WT_2.cDNA.003.C93


title: genomic DNA from WB73

description:
drinker WB sample
SAMPLE 73


title: WT_2.cDNA.003.C94


title: RDEB_3.cDNA.003.C11


title: WT_2.cDNA.003.C92


title: WT_2.cDNA.003.C90


title: WT_2.cDNA.003.C91


title: WT_2.cDNA.003.C88


title: WT_2.cDNA.003.C86


title: WT_2.cDNA.003.C85


title: genomic DNA from WB85

description:
drinker WB sample
SAMPLE 85


title: WT_2.cDNA.003.C80


title: WT_2.cDNA.003.C81


title: genomic DNA from WB74

description:
non-drinker WB sample
SAMPLE 74


title: RDEB_3.cDNA.003.C17


title: genomic DNA from WB71

description:
non-drinker WB sample
SAMPLE 71


title: WT_2.cDNA.003.C79


title: WT_2.cDNA.003.C76


title: genomic DNA from WB68

description:
drinker WB sample
SAMPLE 68


title: genomic DNA from WB67

description:
non-drinker WB sample
SAMPLE 67


title: WT_2.cDNA.003.C74


title: WT_2.cDNA.003.C73


title: WT_2.cDNA.003.C69


title: genomic DNA from WB72

description:
non-drinker WB sample
SAMPLE 72


title: WT_2.cDNA.003.C96


title: WT_2.cDNA.003.C68


title: WT_2.cDNA.003.C64


title: WT_2.cDNA.003.C58


title: WT_2.cDNA.003.C59


title: WT_2.cDNA.003.C56


title: genomic DNA from WB70

description:
drinker WB sample
SAMPLE 70


title: genomic DNA from WB69

description:
non-drinker WB sample
SAMPLE 69


title: genomic DNA from WB65

description:
non-drinker WB sample
SAMPLE 65


title: WT_2.cDNA.003.C52


title: genomic DNA from WB63

description:
drinker WB sample
SAMPLE 63


title: genomic DNA from WB62

description:
non-drinker WB sample
SAMPLE 62


title: WT_2.cDNA.003.C49


title: WT_2.cDNA.003.C47


title: genomic DNA from WB58

description:
non-drinker WB sample
SAMPLE 58


title: genomic DNA from WB54

description:
drinker WB sample
SAMPLE 54


title: genomic DNA from WB57

description:
drinker WB sample
SAMPLE 57


title: genomic DNA from WB56

description:
non-drinker WB sample
SAMPLE 56


title: genomic DNA from WB66

description:
drinker WB sample
SAMPLE 66


title: WT_2.cDNA.003.C46


title: genomic DNA from WB53

description:
non-drinker WB sample
SAMPLE 53


title: WT_2.cDNA.003.C45


title: WT_2.cDNA.003.C54


title: WT_2.cDNA.003.C44


title: genomic DNA from WB59

description:
drinker WB sample
SAMPLE 59


title: WT_2.cDNA.003.C42


title: genomic DNA from WB45

description:
drinker WB sample
SAMPLE 45


title: genomic DNA from WB55

description:
non-drinker WB sample
SAMPLE 55


title: genomic DNA from WB64

description:
drinker WB sample
SAMPLE 64


title: WT_2.cDNA.003.C41


title: genomic DNA from WB61

description:
drinker WB sample
SAMPLE 61


title: genomic DNA from WB52

description:
drinker WB sample
SAMPLE 52


title: genomic DNA from WB43

description:
drinker WB sample
SAMPLE 43


title: WT_2.cDNA.003.C37


title: genomic DNA from WB51

description:
non-drinker WB sample
SAMPLE 51


title: WT_2.cDNA.003.C33


title: genomic DNA from WB49

description:
non-drinker WB sample
SAMPLE 49


title: genomic DNA from WB44

description:
non-drinker WB sample
SAMPLE 44


title: genomic DNA from WB50

description:
drinker WB sample
SAMPLE 50


title: genomic DNA from WB47

description:
drinker WB sample
SAMPLE 47


title: WT_2.cDNA.003.C34


title: WT_2.cDNA.003.C32


title: genomic DNA from WB42

description:
non-drinker WB sample
SAMPLE 42


title: WT_2.cDNA.003.C31


title: WT_2.cDNA.003.C20


title: genomic DNA from WB41

description:
drinker WB sample
SAMPLE 41


title: WT_2.cDNA.003.C19


title: WT_2.cDNA.003.C16


title: WT_2.cDNA.003.C14


title: genomic DNA from WB40

description:
non-drinker WB sample
SAMPLE 40


title: WT_2.cDNA.003.C17


title: WT_2.cDNA.003.C18


title: genomic DNA from WB48

description:
drinker WB sample
SAMPLE 48


title: genomic DNA from WB46

description:
non-drinker WB sample
SAMPLE 46


title: WT_2.cDNA.003.C07


title: genomic DNA from WB38

description:
drinker WB sample
SAMPLE 38


title: genomic DNA from WB39

description:
non-drinker WB sample
SAMPLE 39


title: WT_2.cDNA.003.C05


title: WT_2.cDNA.003.C03


title: genomic DNA from WB60

description:
non-drinker WB sample
SAMPLE 60


title: RDEB_2.cDNA.004.C95


title: genomic DNA from WB33

description:
drinker WB sample
SAMPLE 33


title: genomic DNA from WB34

description:
drinker WB sample
SAMPLE 34


title: RDEB_2.cDNA.004.C94


title: genomic DNA from WB35

description:
non-drinker WB sample
SAMPLE 35


title: genomic DNA from WB32

description:
drinker WB sample
SAMPLE 32


title: RDEB_2.cDNA.004.C92


title: genomic DNA from WB36

description:
drinker WB sample
SAMPLE 36


title: RDEB_2.cDNA.004.C91


title: RDEB_2.cDNA.004.C90


title: WT_2.cDNA.003.C08


title: RDEB_2.cDNA.004.C89


title: genomic DNA from WB28

description:
drinker WB sample
SAMPLE 28


title: genomic DNA from WB29

description:
non-drinker WB sample
SAMPLE 29


title: RDEB_2.cDNA.004.C88


title: RDEB_2.cDNA.004.C93


title: genomic DNA from WB31

description:
non-drinker WB sample
SAMPLE 31


title: genomic DNA from WB25

description:
non-drinker WB sample
SAMPLE 25


title: genomic DNA from WB23

description:
drinker WB sample
SAMPLE 23


title: RDEB_2.cDNA.004.C87


title: RDEB_2.cDNA.004.C86


title: RDEB_2.cDNA.004.C84


title: RDEB_2.cDNA.004.C85


title: genomic DNA from WB22

description:
non-drinker WB sample
SAMPLE 22


title: genomic DNA from WB20

description:
non-drinker WB sample
SAMPLE 20


title: genomic DNA from WB17

description:
drinker WB sample
SAMPLE 17


title: genomic DNA from WB21

description:
drinker WB sample
SAMPLE 21


title: genomic DNA from WB14

description:
drinker WB sample
SAMPLE 14


title: genomic DNA from WB27

description:
non-drinker WB sample
SAMPLE 27


title: RDEB_2.cDNA.004.C82


title: genomic DNA from WB24

description:
non-drinker WB sample
SAMPLE 24


title: genomic DNA from WB15

description:
non-drinker WB sample
SAMPLE 15


title: genomic DNA from WB30

description:
drinker WB sample
SAMPLE 30


title: RDEB_2.cDNA.004.C78


title: RDEB_2.cDNA.004.C76


title: RDEB_2.cDNA.004.C75


title: RDEB_2.cDNA.004.C74


title: genomic DNA from WB18

description:
non-drinker WB sample
SAMPLE 18


title: genomic DNA from WB26

description:
drinker WB sample
SAMPLE 26


title: RDEB_2.cDNA.004.C73


title: genomic DNA from WB16

description:
drinker WB sample
SAMPLE 16


title: RDEB_2.cDNA.004.C72


title: WT_2.cDNA.003.C01


title: genomic DNA from WB19

description:
drinker WB sample
SAMPLE 19


title: genomic DNA from WB10

description:
drinker WB sample
SAMPLE 10


title: Colon biopsy from UC [3F07_14072200093]

city: Cambridge

first: William

last: Gordon

address: 1 Portland Street

institute: Pfizer Inc

description:
SAMPLE 117
RNA from Ulcerative Colitis biopsies

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Primeview 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings

label: biotin

source_name: Human Colon Tissue Biopsy_Non-lesional

label_protocol: Biotinylated cRNA were prepared according to the standard Nugen protcol from 1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiazol extraction of total RNA was performed according to the manufacturer's instructions with on column DNASE digestion

treatment_protocol: Colon biopsies were placed in RNAlater and stored at -80 until processed

tag: patient id

tag: Sex

value: Ulcerative Colitis

tag: tissue state

value: Non-lesional

tag: hospital site

value: Children's Hospital Boston - Snapper

tag: hybe kit

value: Nugen Ovation V2

tag: tissue location

value: Intestine;Rectum

tag: secondary id


title: RDEB_2.cDNA.004.C70

value: RDEB

value: Fibroblast

value: Large


title: genomic DNA from WB37

description:
non-drinker WB sample
SAMPLE 37

tag: gender

tag: tissue


title: genomic DNA from WB11

description:
non-drinker WB sample
SAMPLE 11


title: RDEB_2.cDNA.004.C71

tag: cell type


title: genomic DNA from WB12

description:
drinker WB sample
SAMPLE 12


title: genomic DNA from WB8

description:
non-drinker WB sample
SAMPLE 8


title: skin at black, biological rep3

city: Shihezi

first: dai

last: rong

state: Xinjiang

address: Wuyi Road No. 221

department: Animal husbandry and veterinary institute

country: China

institute: XinJiang Academy of Agricultural and Reclamation Science

description: Whole-transcript Expression data from skin of white coat in Chinese Merino

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner3000.

data_processing: The data were analyzed with Significance analysis of microarray (SAM) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Ovis aries

source_name: Chinese Merino skin of black/brown coat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Six healthy adult Chinese Merino (Junken type) were selected from the farm of Xinjiang Academy of Agricultural and Reclamation Science (Xinjiang, China) for sample collection. All sheep were housed in one group under the normal condition with free access to food and water.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Skin excision was performed under xylazine hydrochloride anesthesia, and all efforts were made to minimize the sheep's suffering. The skin samples (1 cm × 1 cm) from the body side were collected under local anesthesia and immediately stored in liquid nitrogen.

tag: breed

value: Chinese Merino (Junken type)

value: skin

tag: phenotype

value: black coat


title: Colon biopsy from UC [3G05_14072200104]

description:
SAMPLE 118
RNA from Ulcerative Colitis biopsies

tag: disease

value: Intestine;Colon;Ascending


title: genomic DNA from WB6

description:
non-drinker WB sample
SAMPLE 6

value: Male


title: skin at black, biological rep2


title: skin at black, biological rep1


title: RDEB_2.cDNA.004.C68

tag: passage number

tag: c1 chip size


title: genomic DNA from WB7

description:
drinker WB sample
SAMPLE 7

value: case; drinkers


title: RDEB_2.cDNA.004.C83


title: Colon biopsy from UC [3F06_14072200098]

description:
SAMPLE 116
RNA from Ulcerative Colitis biopsies

tag: age


title: RDEB_2.cDNA.004.C67


title: RDEB_2.cDNA.004.C63


title: Colon biopsy from UC [2G09_14072200086]

description:
SAMPLE 113
RNA from Ulcerative Colitis biopsies


title: genomic DNA from WB5

description:
drinker WB sample
SAMPLE 5

tag: disease state

value: whole blood (WB)


title: RDEB_2.cDNA.004.C64


title: Colon biopsy from UC [3G07_14072200103]

description:
SAMPLE 119
RNA from Ulcerative Colitis biopsies

tag: patient id


title: RDEB_2.cDNA.004.C61


title: genomic DNA from WB9

description:
non-drinker WB sample
SAMPLE 9

value: control; non-drinkers


title: skin at white, biological rep1

source_name: Chinese Merino skin of white coat

value: white coat


title: genomic DNA from WB13

description:
non-drinker WB sample
SAMPLE 13


title: skin at white, biological rep3

description: Whole-transcript Expression data from skin of black/brown coat in Chinese Merino


title: RDEB_2.cDNA.004.C60


title: Colon biopsy from UC [2F09_14072200079]

description:
SAMPLE 112
RNA from Ulcerative Colitis biopsies

tag: Sex

value: Female

value: Ulcerative Colitis

value: Intestine;Colon;Descending


title: Colon biopsy from UC [1G07_14072200045]

description:
SAMPLE 109
RNA from Ulcerative Colitis biopsies

tag: tissue state

value: Non-lesional

value: Children's Hospital Boston - Snapper

value: Nugen Ovation V2

value: Intestine;Colon;Transverse


title: genomic DNA from WB2

description:
non-drinker WB sample
SAMPLE 2


title: RDEB_2.cDNA.004.C59

value: RDEB

value: Fibroblast

value: Large


title: genomic DNA from WB3

description:
drinker WB sample
SAMPLE 3


title: Colon biopsy from UC [2D08_14072200064]

description:
SAMPLE 111
RNA from Ulcerative Colitis biopsies

tag: hospital site

value: Intestine;Rectum


title: Colon biopsy from UC [2C07_14072200056]

description:
SAMPLE 110
RNA from Ulcerative Colitis biopsies

tag: hybe kit


title: genomic DNA from WB1

description:
drinker WB sample
SAMPLE 1


title: genomic DNA from WB4

description:
non-drinker WB sample
SAMPLE 4


title: RDEB_2.cDNA.004.C58


title: RDEB_2.cDNA.004.C57


title: RDEB_2.cDNA.004.C54


title: 7day treatment_control

city: Sendai

first: Satoshi

last: Naramoto

address: 2-1-1, Katahira

country: Japan

institute: Tohoku University

hyb_protocol: Hybridization, washing, staining were conducted with Fluids Station 450 as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Scanning was conducted with GeneChip Scanner 3000 7G as described in the Gene Chip Expression Analysis Technical Manual (Affymetrix).

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
RMA

organism: Arabidopsis thaliana

source_name: 7day DEX treated arabidopsis

label_protocol: Biotinylated cRNA were prepared with GenChip One-Cycle Target labeling and Control Reagents (Affymetrix).

growth_protocol: Arabidopsis seedlings  grow on 23 degree for 1week.

extract_protocol: Trizol extraction of total RNA was performed according to the manufa

treatment_protocol: 10uM DEX is treated for 4hr, 8hr, 12hr, 1day, 2day, 3day, 5day, and 7day.

value: whole seedlings


title: Colon biopsy from UC [3B04_14072200092]

description:
SAMPLE 114
RNA from Ulcerative Colitis biopsies

value: Male

tag: tissue location


title: RDEB_2.cDNA.004.C69


title: 7day treatment

source_name: 7day DEX treated arabidopsis expressing KOBU


title: Colon biopsy from UC [1G04_14072200042]

description:
SAMPLE 107
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Ascending

tag: secondary id


title: 5day treatment

source_name: 5day DEX treated arabidopsis expressing KOBU


title: Colon biopsy from UC [1G06_14072200044]

description:
SAMPLE 108
RNA from Ulcerative Colitis biopsies


title: RDEB_2.cDNA.004.C52


title: 5day treatment_control

source_name: 5day DEX treated arabidopsis


title: 3day treatment

source_name: 3day DEX treated arabidopsis expressing KOBU


title: Colon biopsy from UC [1F07_14072200038]

description:
SAMPLE 106
RNA from Ulcerative Colitis biopsies


title: RDEB_2.cDNA.004.C51

source_name: Human dermal fibroblasts


title: 2day treatment_control

source_name: 2day DEX treated arabidopsis


title: RDEB_2.cDNA.004.C50


title: Colon biopsy from UC [1E07_14072200031]

description:
SAMPLE 104
RNA from Ulcerative Colitis biopsies


title: 1day treatment

source_name: 1day DEX treated arabidopsis expressing KOBU


title: Colon biopsy from UC [3C08_14072200097]

description:
SAMPLE 115
RNA from Ulcerative Colitis biopsies


title: Colon biopsy from UC [1E08_14072200032]

description:
SAMPLE 105
RNA from Ulcerative Colitis biopsies


title: RDEB_2.cDNA.004.C48


title: 3day treatment_control

source_name: 3day DEX treated arabidopsis


title: 2day treatment

source_name: 2day DEX treated arabidopsis expressing KOBU


title: 1day treatment_control

source_name: 1day DEX treated arabidopsis


title: RDEB_2.cDNA.004.C47


title: 12hr treatment

source_name: 12hr DEX treated arabidopsis expressing KOBU


title: Colon biopsy from UC [1E06_14072200030]

description:
SAMPLE 103
RNA from Ulcerative Colitis biopsies


title: RDEB_2.cDNA.004.C46


title: 12hr treatment_control

source_name: 12hr DEX treated arabidopsis


title: RDEB_2.cDNA.004.C45


title: Colon biopsy from UC [1E03_14072200027]

description:
SAMPLE 102
RNA from Ulcerative Colitis biopsies


title: Colon biopsy from UC [1D05_14072200022]

description:
SAMPLE 101
RNA from Ulcerative Colitis biopsies


title: 4hr treatment

source_name: 4hr DEX treated arabidopsis expressing KOBU


title: 4hr treatment_control

source_name: 4hr DEX treated arabidopsis


title: 8hr treatment

source_name: 8hr DEX treated arabidopsis expressing KOBU


title: skin at white, biological rep2

description: Whole-transcript Expression data from skin of white coat in Chinese Merino

source_name: Chinese Merino skin of white coat

value: Chinese Merino (Junken type)

value: skin


title: RDEB_2.cDNA.004.C44


title: Matrigel, biological rep3

city: HOUSTON

first: Kazuharu

last: Kai

state: TX

address: 2130 West Holcombe Blvd. Life Science Plaza

department: Translational Molecular Pathology

institute: MD Anderson Cancer Center

description: Gene expression data from SUM149 cells cultured in Matrigel condition for 2 days

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instructions

data_processing: Data obtained from the six microarrays were normalized by the robust multiarray average (RMA) method using R statistical software version 2.10.1 and BioConductor software.

source_name: SUM149 cells cultured in Matrigel

label_protocol: Using 200 ng of total RNA, cRNA was prepared using a one-cycle target labeling and control reagents kit (Affymetrix).

growth_protocol: Single suspended SUM149 cells were plated in monolayer and Matrigel-coated dishes and cultured for 2 days. Cell suspension in Matrigel contained 2% Matrigel.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen). The integrity of the obtained RNA was assessed using the Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: Monolayer cultured SUM149 cells were tripsinized and tripsion was neutralized with 10% FBS containing medium. Matrigel cultured SUM149 cells were recovered by using Cell Recovery Solution (Corning).

tag: cell line

tag: culture

value: matrigel

value: Inflammatory breast cancer

tag: gender


title: Matrigel, biological rep2

scan_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instructions

value: Female


title: Matrigel, biological rep1


title: Colon biopsy from UC [1C03_14072200013]

description:
SAMPLE 99
RNA from Ulcerative Colitis biopsies

source_name: Human Colon Tissue Biopsy_Non-lesional

value: Ulcerative Colitis


title: Colon biopsy from UC [1C02_14072200012]

description:
SAMPLE 98
RNA from Ulcerative Colitis biopsies

value: Non-lesional

value: Intestine;Colon;Descending


title: Monolayer, biological rep3

description: Gene expression data from SUM149 cells cultured in Monolayer condition for 2 days

source_name: SUM149 cells cultured in monolayer

value: monolayer


title: RDEB_2.cDNA.004.C42

tag: cell type


title: Monolayer, biological rep2


title: Colon biopsy from UC [1C04_14072200014]

description:
SAMPLE 100
RNA from Ulcerative Colitis biopsies

value: Children's Hospital Boston - Snapper

value: Nugen Ovation V2


title: Colon biopsy from UC [3G08_14072200100]

description:
SAMPLE 97
RNA from Ulcerative Colitis biopsies

source_name: Human Colon Tissue Biopsy_Lesional

value: Lesional


title: KDR+PDGFRα+ at day5

city: Kyoto

first: Jun

middle: K

last: Yamashita

address: 54 Kawahara-cho, Shogoin, Sakyo-ku,

department: Department of Stem Cell Differentiation

institute: Center for iPS Cell Research and Application (CiRA)

description: Gene expression of KP d5

hyb_protocol: Labeled cDNA was hybridized with Human Genome U133 Plus2.0 Array (Affymetrix) by GeneChip Hybridization Control Kit (Affymetrix) and GeneChip Fluidics Station 450 (Affymetrix) at 45 oC for 16 hours.

scan_protocol: Arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed by GeneChip Operating Software (Affymetrix). The raw data were normalized using the MAS5 algorithm (Median score of the gene expressions: 500).

source_name: KDR+PDGFRα+ at day5

label_protocol: Samples were labeled with Cy3 using Bioarray HighYield RNA transcript labeling kit (T7) (Enzo Life Science)

growth_protocol: KDR+PDGFRα+ (KP) cells were induced with the addition of 100 ng/mL of Activin A  for 24 hours, followed by 10 ng/mL human bone morphogenetic protein 4 (BMP4) and 10 ng/mL hbFGF for 2 to 3 days. In addition, we purified KP cells at day5 and re-cultrued them under 10% serum condition for 14 days to induce cardiomyocytes.

extract_protocol: RNA was extracted using RNeasy Mini kit (QIAGEN). Total RNA was reverse transcribed into cDNA via Superscript II Reverse Transcriptase (Life technology).

treatment_protocol: Cells were dissociated by incubation with Accumax (Innovative Cell Technologies) and washed by PBS twice.

value: KP d5


title: Accuracy_V9-125

city: Rochester

first: Numrah

middle: Mohammadali

last: Fadra

state: Minnesota

address: 200 2nd Street SW

department: Health Sciences Research

institute: Mayo Clinic

data_processing:
Base calling was performed by the instrument computer using Illumina Real Time Analysis (RTA) software that is integrated with HiSeq Control Software (HCS) and provides a summary of quality statistics as per Illumina's acceptance criteria for sequencing. CASAVA 1.8.2 was used for de-multiplexing and conversion of base calls to paired-end FASTQ files
RNA-Seq data was analyzed using the MAP-RSeq(http://www.ncbi.nlm.nih.gov/pubmed/24972667) pipeline v 1.2 which uses TopHat 2.0.6 to align reads to the human reference GRCh37  without alternative haplotypes. During alignment,TopHat was supplied transcript models from UCSC (March 2012 version) available from Illumina’s iGenomes Project. For the degraded KU812 samples we obtained > 13 million reads per sample and for the degraded UHR and clinical samples we obtained > 80 million reads per sample. Fusion calling was performed using TopHat-Fusion (http://www.ncbi.nlm.nih.gov/pubmed/21835007) with a minimum of 5 fusion supporting reads required. The following samples did not have any fusions reported  thus the processed files (fusion reports) for these samples will not be included in the submission although the raw sequenicng files for these samples will be available . Sample names V10-136, V10-144,V1-1,V12-158,V12-159,V12-163,V3-40,V3-58,V63RPT,V6-79,V6-80,V8-113,V9-124,V9-126
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fusions found in each sample with annotations on the 5' and 3' gene partners, exons, syupporting read information and genomic breakpoints for each fusion

source_name: Bladder

extract_protocol:
RNA quality [RNA Integrity Number (RIN)] was assessed on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit and quantified with a Qubit® 2.0 fluorometer with the Qubit® RNA BR Assay Kit. The TruSeq® RNA Sample Preparation v2 Kit (Illumina, San Diego, CA) was used for isolation of polyadenylated mRNA with oligo-dT beads, second strand cDNA synthesis and NGS library preparation
Paired-end, 101 bp sequencing was performed on a HiSeq 2500 (Illumina) instrument in Rapid Run mode.

tag: histology

value: Bladder Transitional Cell Carcinoma

tag: rin score


title: Accuracy_V9-126

source_name: Breast

value: Breast Adenocarcinoma


title: Colon biopsy from UC [3G06_14072200109]

description:
SAMPLE 96
RNA from Ulcerative Colitis biopsies

tag: disease

value: Intestine;Colon;Sigmoid


title: RDEB_2.cDNA.004.C41

source_name: Human dermal fibroblasts

value: RDEB

value: Fibroblast

tag: passage number

tag: c1 chip size

value: Large


title: Cardiomyocytes derived from KDR+PDGFRα+ at day5

description: Gene expression of CMs d5-19

value: CMs d5-19


title: KDR+PDGFRα+ at day4

description: Gene expression of KP d4

source_name: KDR+PDGFRα+ at day4

value: KP d4


title: KDR+PDGFRα+ at day3

description: Gene expression of KP d3

source_name: KDR+PDGFRα+ at day3

value: KP d3


title: Accuracy_V9-124

source_name: Colon

value: Colon Adenocarcinoma


title: 8hr treatment_control

source_name: 8hr DEX treated arabidopsis

tag: tissue

value: whole seedlings


title: RDEB_2.cDNA.004.C40


title: Colon biopsy from UC [3G03_14072200089]

description:
SAMPLE 95
RNA from Ulcerative Colitis biopsies

tag: patient id

value: Female

value: Ulcerative Colitis

tag: age

value: Intestine;Cecum


title: Accuracy_V9-123

source_name: Soft Tissue

value: Synovial Sarcoma


title: PPV_V8-118

source_name: Bone

value: Osteosarcoma


title: PPV_V8-117

source_name: Soft Tissue, Muscle

value: Rhabdomyosarcoma


title: Monolayer, biological rep1

value: monolayer

value: Inflammatory breast cancer


title: Accuracy_V8-116

source_name: Pleural Effusion

value: Large Cell Immunoblastic Lymphoma


title: RDEB_2.cDNA.004.C38

value: RDEB


title: Colon biopsy from UC [3E09_14072200091]

description:
SAMPLE 94
RNA from Ulcerative Colitis biopsies

tag: Sex

tag: tissue state

value: Lesional

value: Children's Hospital Boston - Snapper

value: Nugen Ovation V2


title: PPV_V8-107

source_name: Retroperitoneum

value: Liposarcoma


title: RDEB_2.cDNA.004.C39

value: Fibroblast

value: Large


title: Accuracy_V8-113

source_name: Thigh

value: Lipoblastoma


title: RDEB_2.cDNA.004.C37


title: Accuracy_V8-105

source_name: Perineum

value: Epitheliod Sarcoma


title: Accuracy_V8-106


title: PPV_V7-96

source_name: Papillary Thyroid

value: Papillary Thyroid Carcinoma


title: Accuracy_V7-95

source_name: Lymph node

value: Large Diffuse B-cell Lymphoma


title: RDEB_2.cDNA.004.C33


title: Colon biopsy from UC [3E08_14072200107]

description:
SAMPLE 93
RNA from Ulcerative Colitis biopsies

source_name: Human Colon Tissue Biopsy_Lesional

value: Male

value: Ulcerative Colitis

tag: hospital site

tag: hybe kit

value: Intestine;Colon;Sigmoid


title: Colon biopsy from UC [3E07_14072200095]

description:
SAMPLE 92
RNA from Ulcerative Colitis biopsies

value: Female

tag: tissue location

value: Intestine;Rectum

tag: secondary id


title: Accuracy_V7-93


title: Colon biopsy from UC [3D07_14072200110]

description:
SAMPLE 91
RNA from Ulcerative Colitis biopsies


title: Undifferentiated iPSCs

description: Gene expression of Und. iPSCs

source_name: Undifferentiated iPSCs

value: Undifferentiated iPSCs


title: PPV_V6-89

source_name: Peritoneal Effusion

value: Diffuse Histiocytic Lymphoma


title: Colon biopsy from UC [3D05_14072200106]

description:
SAMPLE 90
RNA from Ulcerative Colitis biopsies

value: Lesional


title: PPV_V6-86

source_name: Prostate

value: Prostate Adenocarcinoma


title: RDEB_2.cDNA.004.C31

source_name: Human dermal fibroblasts

value: RDEB


title: Colon biopsy from UC [3D04_14072200099]

description:
SAMPLE 89
RNA from Ulcerative Colitis biopsies

value: Children's Hospital Boston - Snapper

value: Nugen Ovation V2


title: Accuracy_V6-83

source_name: Peripheral Blood

value: Chronic Myeloid Leukemia


title: RDEB_2.cDNA.004.C30

value: Fibroblast

value: Large


title: OT1 only (2)

city: Melbourne

first: Stephin

middle: J

last: Vervoort

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
OT1_2
17-OT1

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package
The Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression. Genes with read counts under 10 were filtered before Limma analysis.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts

organism: Mus musculus

growth_protocol: 10 percent FCS in DMEM + Pen/Strep

extract_protocol:
RNA was extracted using the Nucleospin® RNA extraction kit (Macherey-Nagel, Bethlehem, PA) as per the manufacturer's instructions.
cDNA libraries were prepared using the QuantSeq 3' mRNA seq kit, Lexogen.

tag: cell line

tag: treatment


title: OT1 only (3)

description:
OT1_3
18-OT1


title: OT1 only (1)

description:
OT1_1
16-OT1


title: RDEB_2.cDNA.004.C34

tag: cell type


title: RDEB_2.cDNA.004.C29


title: mc38 only (3)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_3
15-MC38

value: only


title: RDEB_2.cDNA.004.C28


title: mc38 only (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_2
14-MC38


title: RDEB_2.cDNA.004.C32


title: Accuracy_V6-80

source_name: Right Temporal Mass

tag: histology

value: Brain Tumor, NOS


title: Accuracy_V6-84

source_name: colon

value: Cholangiocarcinoma

tag: rin score


title: Accuracy_V6-79

source_name: Soft Tissue , leg

value: Angiofibroma


title: mc38 only (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_1
13-MC38


title: Colon biopsy from UC [3C03_14072200094]

description:
SAMPLE 87
RNA from Ulcerative Colitis biopsies

value: Male

tag: disease

value: Ulcerative Colitis

value: Intestine;Colon;Transverse


title: RDEB_2.cDNA.004.C27

tag: passage number


title: Colon biopsy from UC [3B05_14072200090]

description:
SAMPLE 84
RNA from Ulcerative Colitis biopsies

value: Female

value: Intestine;Cecum


title: mc38 + OT1 + PD1 (3)

description:
OTI_PD1_3
12-PD1-OT1-3


title: RDEB_2.cDNA.004.C25

tag: c1 chip size


title: Colon biopsy from UC [3C07_14072200096]

description:
SAMPLE 88
RNA from Ulcerative Colitis biopsies

value: Lesional

value: Intestine;Colon;Sigmoid


title: Accuracy_V63RPT

value: Acute Promyelocytic Leukemia


title: Colon biopsy from UC [3B10_14072200102]

description:
SAMPLE 86
RNA from Ulcerative Colitis biopsies

value: Children's Hospital Boston - Snapper

value: Intestine;Rectum


title: Colon biopsy from UC [3B03_14072200101]

description:
SAMPLE 83
RNA from Ulcerative Colitis biopsies

value: Nugen Ovation V2


title: PPV_V6-81

source_name: Soft Tissue , Thigh

value: Epitheliod Sarcoma


title: PPV_V3-71

value: Prostate Adenocarcinoma


title: Colon biopsy from UC [3B08_14072200105]

description:
SAMPLE 85
RNA from Ulcerative Colitis biopsies


title: mc38 + OT1 + PD1 (2)

description:
OTI_PD1_2
11-PD1-OT1-2


title: RDEB_2.cDNA.004.C23

value: RDEB

value: Fibroblast

value: Large


title: RDEB_2.cDNA.004.C24


title: mc38 treated with co colture sup (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
Sup2
10-ck-260517-Sup-2

value: treatedwithcocolturesup


title: Colon biopsy from UC [2G10_14072200087]

description:
SAMPLE 82
RNA from Ulcerative Colitis biopsies


title: Accuracy_V3-58

source_name: Lung

value: Normal (lung)


title: Colon biopsy from UC [2G06_14072200083]

description:
SAMPLE 81
RNA from Ulcerative Colitis biopsies

value: Ulcerative Colitis


title: mc38 + OT1 + PD1 (1)

description:
OTI_PD1_1
10-PD1-OT1-1


title: RDEB_2.cDNA.004.C21


title: PPV_V3-56

source_name: 10 cell lines

value: Universal Human Reference RNA* (Agilent)


title: Colon biopsy from UC [2G05_14072200082]

description:
SAMPLE 80
RNA from Ulcerative Colitis biopsies

value: Male


title: RDEB_2.cDNA.004.C20


title: mc38 treated with co colture sup (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
Sup1
9-ck-260517-Sup-1


title: RDEB_2.cDNA.004.C19


title: mc38 + OT1 + isotype (3)

description:
OT1 isotype 3
9-Isotype-OT1-3


title: Accuracy_V3-40

value: B-cell lymphoma


title: Accuracy_V3-42


title: PPV_V23-231

source_name: Left Teres Major Muscle Mass

value: Perinuerioma


title: Accuracy_V3-65

value: Anaplastic Large T-Cell Lymphoma


title: Colon biopsy from UC [2F11_14072200081]

description:
SAMPLE 79
RNA from Ulcerative Colitis biopsies

value: Female

value: Lesional


title: RDEB_2.cDNA.004.C17


title: mc38 + IFN gamma + TNF (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
TNF_IFN_2
8-ck-260517-TNFplusIFNgamma-2

value: IFNgammaTNF


title: Colon biopsy from UC [2F07_14072200077]

description:
SAMPLE 78
RNA from Ulcerative Colitis biopsies

value: Children's Hospital Boston - Snapper

value: Nugen Ovation V2

value: Intestine;Rectum


title: RDEB_2.cDNA.004.C12

value: RDEB


title: RDEB_2.cDNA.004.C11

value: Fibroblast


title: Accuracy_V1-26

value: Acute Promyelocytic Leukemia


title: Colon biopsy from UC [2F05_14072200075]

description:
SAMPLE 77
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Ascending


title: mc38 + OT1 + isotype (2)

description:
OT1 isotype 2
8-Isotype-OT1-2


title: Colon biopsy from UC [2E11_14072200074]

description:
SAMPLE 76
RNA from Ulcerative Colitis biopsies


title: mc38 + IFN gamma + TNF (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
TNF_IFN_1
7-ck-260517-TNFplusIFNgamma-1


title: Colon biopsy from UC [2E05_14072200068]

description:
SAMPLE 74
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Sigmoid


title: Colon biopsy from UC [2E08_14072200071]

description:
SAMPLE 75
RNA from Ulcerative Colitis biopsies

value: Ulcerative Colitis

value: Intestine;Cecum


title: mc38 + OT1 + isotype (1)

description:
OT1 isotype 1
7-Isotype-OT1-1


title: PPV_V12-165

value: Prostate Adenocarcinoma


title: RDEB_2.cDNA.004.C08

value: Large


title: PPV_V12-164

value: Small Cell Lung Cancer


title: mc38 + IFN gamma (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
IFN_2
6-ck-260517-IFNgamma-2

value: IFNgamma


title: Colon biopsy from UC [2D10_14072200066]

description:
SAMPLE 72
RNA from Ulcerative Colitis biopsies

value: Male

value: Intestine;Colon;Descending


title: Colon biopsy from UC [2D11_14072200067]

description:
SAMPLE 73
RNA from Ulcerative Colitis biopsies

value: Lesional


title: Accuracy_V12-163

value: Normal Prostate


title: mc38 untreated (3)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_OT1_PD1_3
6-PD1-MC38-3

value: untreated


title: RDEB_2.cDNA.004.C05


title: Accuracy_V12-162

value: Acute Myeloid Leukemia


title: mc38 + IFN gamma (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
IFN_1
5-ck-260517-IFNgamma-1


title: mc38 + anti PD1 (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_OT1_PD1_2
5-PD1-MC38-2


title: RDEB_2.cDNA.004.C04

value: RDEB


title: Accuracy_V12-161

source_name: Soft Tissue, Mesenchymal

value: Chondrosarcoma


title: RDEB_2.cDNA.004.C10

value: Fibroblast


title: Colon biopsy from UC [2D07_14072200063]

description:
SAMPLE 71
RNA from Ulcerative Colitis biopsies

value: Female

value: Children's Hospital Boston - Snapper

value: Nugen Ovation V2


title: PPV_V12-160

source_name: Soft Tissue, Leg

value: Synovial Sarcoma


title: mc38 + TNF (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
TNF_2
4-ck-260517-TNF-2

value: TNF


title: RDEB_2.cDNA.004.C03

value: Large


title: Colon biopsy from UC [2C11_14072200060]

description:
SAMPLE 69
RNA from Ulcerative Colitis biopsies

value: Ulcerative Colitis

value: Intestine;Cecum


title: PPV_V12-159


title: Colon biopsy from UC [2D05_14072200061]

description:
SAMPLE 70
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Sigmoid


title: mc38 + anti PD1 (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_OT1_PD1_1
4-PD1-MC38-1


title: Accuracy_V12-158


title: RDEB_2.cDNA.004.C06


title: RDEB_2.cDNA.004.C01


title: mc38 + TNF (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
TNF_1
3-ck-260517-TNF-1


title: Colon biopsy from UC [2B10_14072200052]

description:
SAMPLE 67
RNA from Ulcerative Colitis biopsies

value: Male

value: Intestine;Colon;Descending


title: WT_1.cDNA.002.C94

value: wild-type control

value: Medium


title: mc38 + Isotype (3)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_OT1_3
3-Isotype-MC38-3

value: Isotype


title: Colon biopsy from UC [2C10_14072200059]

description:
SAMPLE 68
RNA from Ulcerative Colitis biopsies

value: Lesional

value: Intestine;Rectum


title: PPV_V12-157

value: Prostate Adenocarcinoma


title: PPV_V1-17

value: Acute Promyelocytic Leukemia


title: WT_1.cDNA.002.C75

value: Fibroblast


title: Colon biopsy from UC [2B07_14072200049]

description:
SAMPLE 65
RNA from Ulcerative Colitis biopsies

value: Children's Hospital Boston - Snapper

value: Nugen Ovation V2


title: mc38 untreated (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
UT_2
2-ck-260517-Untreated-2

value: untreated


title: WT_1.cDNA.002.C74


title: Accuracy_V11-154

value: Acute Myeloid Leukemia


title: Colon biopsy from UC [2B08_14072200050]

description:
SAMPLE 66
RNA from Ulcerative Colitis biopsies

value: Ulcerative Colitis


title: mc38 + Isotype (2)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_OT2_2
2-Isotype-MC38-2


title: RDEB_2.cDNA.004.C02

value: RDEB

value: Large


title: Colon biopsy from UC [1F05_14072200036]

description:
SAMPLE 63
RNA from Ulcerative Colitis biopsies

value: Female

value: Intestine;Colon;Sigmoid


title: Colon biopsy from UC [1G08_14072200046]

description:
SAMPLE 64
RNA from Ulcerative Colitis biopsies

value: Male


title: mc38 untreated (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
UT_1
1-ck-260517-Untreated-1


title: WT_1.cDNA.002.C71

value: wild-type control

value: Medium


title: WT_1.cDNA.002.C72


title: Accuracy_V11-152

value: Non Small Cell Lung Cancer


title: mc38 + Isotype (1)

description:
170605_NB501056_0018_AH2FYTBGX3_MC38_coculture_normalizedcounts.csv
MC38_OT1_1
1-Isotype-MC38-1

value: Isotype


title: WT_1.cDNA.002.C62


title: Ado gRNA 2 TNF 6 hour(2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO2_TNF6_2
CK 24

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package
The Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression. Genes with read counts lower than 10 were removed before Limma analysis.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts

value: TNF 6 hour

tag: grna

value: Ado gRNA 2

tag: genotype

value: Ado KO


title: Ado gRNA 2 TNF 6 hour(1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO2_TNF6_1
CK 23


title: WT_1.cDNA.002.C61

value: Fibroblast


title: PPV_V11-151

source_name: Nasal septum

value: Squamous Cell Carcinoma


title: Accuracy_V11-150

value: Prostate Adenocarcinoma


title: Colon biopsy from UC [1E04_14072200028]

description:
SAMPLE 62
RNA from Ulcerative Colitis biopsies

tag: patient id

value: Lesional

value: Children's Hospital Boston - Snapper

tag: age

value: Nugen Ovation V2

value: Intestine;Rectum


title: Ado gRNA 1 TNF 6 hour(2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO1_TNF6_2
CK 22

value: Ado gRNA 1


title: Colon biopsy from UC [1E02_14072200026]

description:
SAMPLE 61
RNA from Ulcerative Colitis biopsies

tag: Sex

value: Ulcerative Colitis

tag: tissue state


title: Colon biopsy from UC [1C08_14072200018]

description:
SAMPLE 59
RNA from Ulcerative Colitis biopsies

value: Male

tag: hospital site

tag: hybe kit

value: Intestine;Colon;Ascending


title: PPV_V11-149


title: WT_1.cDNA.002.C57

value: wild-type control

value: Medium


title: PPV_V11-153

value: Non Small Cell Lung Cancer


title: Accuracy_V1-1

source_name: Various Cell lines (Universal Human Reference)

value: Universal Human Reference RNA*  (Clone Tech)


title: Ado gRNA 1 TNF 6 hour(1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO1_TNF6_1
CK 21

value: TNF 6 hour


title: WT_1.cDNA.002.C55


title: PPV_V1-11

value: Tumor, NOS


title: Control gRNA 2 TNF 6 hour (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C2_TNF6_2
CK 20

value: Control gRNA 2

value: control


title: Accuracy_V10-144

source_name: Breast

value: Breast Adenocarcinoma


title: WT_1.cDNA.002.C49

value: Fibroblast


title: Control gRNA 2 TNF 6 hour (1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C2_TNF6_1
CK 19


title: Colon biopsy from UC [1C05_14072200015]

description:
SAMPLE 58
RNA from Ulcerative Colitis biopsies

source_name: Human Colon Tissue Biopsy_Lesional

value: Female

value: Lesional

value: Children's Hospital Boston - Snapper

tag: tissue location

value: Intestine;Colon;Sigmoid

tag: secondary id


title: Colon biopsy from UC [1B08_14072200011]

description:
SAMPLE 57
RNA from Ulcerative Colitis biopsies

value: Ulcerative Colitis

value: Nugen Ovation V2

value: Intestine;Colon;Transverse


title: Accuracy_V10-143

value: Synovial Sarcoma


title: WT_1.cDNA.002.C29

value: wild-type control

value: Medium


title: Colon biopsy from UC [1D03_14072200020]

description:
SAMPLE 60
RNA from Ulcerative Colitis biopsies

value: Male


title: Control gRNA 1 TNF 6 hour (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C1_TNF6_2
CK 18

tag: cell line

tag: treatment

value: TNF 6 hour

value: Control gRNA 1


title: Colon biopsy from UC [3G04_14072200116]

description:
SAMPLE 56
RNA from Ulcerative Colitis biopsies

source_name: Human Colon Tissue Biopsy_Non-lesional

value: Non-lesional

value: Brigham and Womens


title: Accuracy_V10-140

source_name: Retroperitoneum

tag: histology

value: Sarcoma


title: Colon biopsy from UC [3F09_14072200115]

description:
SAMPLE 55
RNA from Ulcerative Colitis biopsies


title: WT_1.cDNA.002.C60

source_name: Human dermal fibroblasts

tag: cell type

value: Fibroblast


title: Ado gRNA 2 TNF 1 hour (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO2_TNF1_2
CK 16

value: TNF 1 hour

value: Ado gRNA 2

value: Ado KO


title: WT_1.cDNA.002.C26

tag: disease


title: Control gRNA 1 TNF 6hour(1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C1_TNF6_1
CK 17

value: control


title: Accuracy_V10-135

value: Normal

tag: rin score


title: WT_1.cDNA.002.C18

tag: passage number

tag: c1 chip size


title: Accuracy_V10-133

source_name: Thyroid


title: Colon biopsy from UC [3F04_14072200125]

description:
SAMPLE 54
RNA from Ulcerative Colitis biopsies

value: Female

value: Ulcerative Colitis

value: Nugen Ovation V2

value: Intestine;Colon;Ascending


title: Ado gRNA 2 TNF 1 hour (1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO2_TNF1_1
CK 15

tag: grna

tag: genotype


title: Colon biopsy from UC [3E06_14072200118]

description:
SAMPLE 53
RNA from Ulcerative Colitis biopsies

tag: patient id

tag: age

value: Intestine;Colon;Transverse


title: Colon biopsy from UC [3E05_14072200117]

description:
SAMPLE 52
RNA from Ulcerative Colitis biopsies

tag: Sex

value: Male

tag: tissue state


title: WT_1.cDNA.002.C16

value: wild-type control

value: Medium


title: Colon biopsy from UC [3E04_14072200114]

description:
SAMPLE 51
RNA from Ulcerative Colitis biopsies

value: Non-lesional

tag: hospital site

tag: hybe kit

value: Intestine;Colon;Descending


title: WT_1.cDNA.002.C15


title: px0494-TTCTCCA_deep

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
Basecalls performed using Illumina's CASAVA software, version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The first 6 bases were trimmed using Trimgalore v0.4.0 and Cutadapt v1.2.1 using the parameters --clip_R1 6 --clip_R2 6 –paired. Trimmed fastq files were aligned using Novoalign version V3.02.10 (www.novocraft.com) to the mouse assembly GRCm38 (mm10). Alignments were done in paired-end mode using the options -b4 (non-directional), -t 20,3 (optimized for SNP concordance), –a (adapter trimming), --hlimit 8 (homopolymer filter), and -H 20 (removes trailing bases with quality ? 20), and –u8 (penalty for unconverted CHG or CHH cytosine) as recommended by Novoalign. Aligned reads were output into the BAM format and sorted using SAMtools V0.1.17. Duplicates were marked with Picard V1.31 (http://picard.sourceforge.net).
Methylation of each cytosine was called using SAMtools mpileup (-B -C 0 -q 30 -d 500) followed by Novomethyl V1.01 (-o Consensus -%) (www.novocraft.com). Cytosine calls with Phred quality score ?15 were discarded. Methylation percentage of each CpG di-nucleotide (found by searching the genome with a custom java script) was calculated by taking a weighted average of each cytosine using the map command from the bedtools suite (Quinlan and Hall, 2010). In most cases, only one base within a CpG dinucleotide had coverage; in these cases, the methylation information of the covered base was extrapolated to the other base.
Genome_build: hg19
Supplementary_files_format_and_content: bed file for CpG methylation. Columns are as follows: chr, start, end, fractional methylation, methylated C's, total C's, # of CpGs covered in the dinucleotide (1=just one, 2=both C and G covered)

source_name: CD49f Hematopoetic stem cell

extract_protocol:
Sorted cells were lysed in 96 well plates in 4 uL of lysis buffer (20 mM Tris-HCl, pH 8.0, 20 mM KCl, 0.3% Triton-X 100, 1 mg/mL Qiagen Protease) for 30 minutes at 50 degrees.
The lysed cells were then spiked-in with 1 uL of 60 fg/uL purified T7 phage DNA (GeneON). The DNA mixture was then bisulfite converted with the MethylEdge Bisulfite Conversion kit (Promega) using a modified bead-based protocol which enables automation (Domanico et al., 2013): 5 uL of the lysis/spike-in mixture was combined with 32.5 uL of MethylEdge Conversion reagent and incubated at 98°C for 8 minutes and 54°C for 60 minutes in a PCR machine. After incubation, the plate was briefly spun down and placed on an Agilent Bravo robot for subsequent steps. The 37.5 uL of bisulfite converted DNA was mixed with 180 uL of MethylEdge Binding Buffer and 1.8 uL of 20 mg/mL MagSi-DNA allround magnetic silica beads (MagnaMedics) and incubated at room temperature for 15 minutes. The beads were then collected on a magnet for 3 minutes and washed twice with 220 uL of 80% ethanol for 30 seconds while on the magnet. 60 uL of MethylEdge desulfonation buffer was added and incubated for 15 minutes. The desulfonation buffer was then removed and the beads were washed twice with 100 uL of 80% ethanol. The beads were then air-dried for 1 minute, resuspended in 20 uL of Qiagen elution buffer, and incubated at 56°C in a shaking incubator at 2,000 rpm for 15 minutes. The beads were then collected on a magnet for 30 seconds and the supernatant containing the DNA was removed. The bisulfite-converted ssDNA from above was added directly into a mixture containing 1.25 uL of 10 mM dNTPs and 1 uL of 500 uM random hexamers (3’ phosphothioate). The reactions were incubated at 98°C for 1 minute and snap frozen on ice for 2 minutes. A mastermix of 0.5 uL of 50 U/uL Klenow fragment [3’?5’ exo-] (NEB M0212M), and 2.5 uL of 10X NEB Buffer 2 was added on ice and mixed well. The reactions incubated in a PCR machine as follows: 4?C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes. The entire reaction was denatured again at 98?C for 1 minute and snap frozen on ice for 2 minutes. The reaction was transferred on a pre-chilled CoolRack by robot into a new plate containing 5 uL mixture of 20 uM random hexamers (3’ phosphothioate), 0.5 mM dNTPs, 1X NEB buffer and 25 U of Klenow fragment [3’?5’ exo-]. The wells were mixed well and the reaction was cycled once again: 4?C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes, and heat-inactivated at 70°C for 10 minutes. 20 uL of Qiagen Elution Buffer was added to each reaction to make it up to 50 uL, and each reaction was purified using 50 uL of Sera-Mag beads before proceeding to the standard illumina adapter ligation library construction protocol. The 25 uL of cleaned-up adapter-ligated fragments were PCR amplified in 50 uL containing 1 U of Phusion U Hot Start DNA Polymerase (Life Technologies F-555S), 1X HF buffer, 3% DMSO, 200 uM dNTPs, 0.5 uM PCR primer 1.0 (need sequence) (IDT), and corresponding 0.5 uM indexing PCR primer 2.0. The reactions were incubated in a PCR machine as follows: initial 98?C for 1 minute; 10 cycles of 98?C for 30 seconds, 65?C for 15 seconds, 72?C for 15 seconds; and a final extension of 72?C for 5 minutes. The 50 uL reaction was cleaned up with 40 uL of Sera-Mag beads and eluted in 15 uL.

tag: type

value: single-cell

tag: donor

tag: markers


title: Control gRNA 2 TNF 1 hour (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C2_TNF1_1
CK 12

tag: cell line

tag: treatment

value: Control gRNA 2


title: WT_1.cDNA.002.C08

tag: disease

tag: cell type

value: Fibroblast


title: Colon biopsy from UC [3D03_14072200126]

description:
SAMPLE 50
RNA from Ulcerative Colitis biopsies

value: Brigham and Womens

tag: tissue location

tag: secondary id


title: Accuracy_V10-136

source_name: Brain

tag: histology

value: Brain Tumor, NOS

tag: rin score


title: px0494-TTCGAAA_deep


title: WT_1.cDNA.002.C06

tag: passage number

tag: c1 chip size


title: Control gRNA 2 TNF 1 hour (1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C2_TNF1_2
CK 11

value: TNF 1 hour

tag: grna

tag: genotype

value: control


title: px0494-TGGCGCA_deep


title: WT_1.cDNA.002.C01


title: Control gRNA 1 TNF 1 hour (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C1_TNF1_2
CK 10

value: Control gRNA 1


title: px0494-TTAGGCA_deep


title: Colon biopsy from UC [2E09_14072200072]

description:
SAMPLE 48
RNA from Ulcerative Colitis biopsies

tag: patient id

tag: Sex

value: Ulcerative Colitis

tag: tissue state

tag: hospital site

tag: age


title: Colon biopsy from UC [2D06_14072200062]

description:
SAMPLE 46
RNA from Ulcerative Colitis biopsies

value: Female

tag: hybe kit

value: Nugen Ovation V2


title: RDEB_1.cDNA.001.C93

value: RDEB


title: Control gRNA 1 TNF 1hour(1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C1_TNF1_1
CK 9

tag: cell line

tag: treatment


title: px0494-TGCTGGA_deep

tag: type

tag: donor

tag: markers


title: Ado gRNA 1 TNF 1 hour (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO1_TNF1_2
CK 14

value: Ado gRNA 1

value: Ado KO


title: Colon biopsy from UC [2G11_14072200088]

description:
SAMPLE 49
RNA from Ulcerative Colitis biopsies

tag: disease

tag: tissue location

value: Intestine;Colon;Ascending

tag: secondary id


title: px0494-TGCCATA_deep


title: Colon biopsy from UC [2E07_14072200070]

description:
SAMPLE 47
RNA from Ulcerative Colitis biopsies

value: Male

value: Non-lesional

value: Intestine;Colon;Sigmoid


title: Colon biopsy from UC [2C06_14072200055]

description:
SAMPLE 44
RNA from Ulcerative Colitis biopsies


title: Ado gRNA 1 TNF 1hour(1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO1_TNF1_1
CK 13


title: Ado gRNA 2 untreated (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO2_UT_2
CK 8

value: untreated

value: Ado gRNA 2


title: Colon biopsy from UC [2C09_14072200058]

description:
SAMPLE 45
RNA from Ulcerative Colitis biopsies

value: Brigham and Womens


title: Ado gRNA 1 untreated (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO1_UT_2
CK 6


title: RDEB_1.cDNA.001.C89

tag: cell type

value: Fibroblast

tag: passage number

tag: c1 chip size

value: Medium


title: RDEB_1.cDNA.001.C87


title: Ado gRNA 1 untreated (1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO1_UT_1
CK 5

tag: grna

tag: genotype


title: Ado gRNA 2 untreated (1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
KO2_UT_1
CK 7


title: RDEB_1.cDNA.001.C92


title: RDEB_1.cDNA.001.C84


title: Control gRNA 2 untreated (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C2_UT_2
CK 4

value: Control gRNA 2

value: control


title: px0494-TCGAAGA_deep

value: single-cell


title: px0494-TCGGCAA_deep


title: px0494-TCCCGAA_deep


title: RDEB_1.cDNA.001.C83


title: px0494-TGACCAA_deep


title: Control gRNA 2 untreated (1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C2_UT_1
CK 3


title: RDEB_1.cDNA.001.C90


title: RDEB_1.cDNA.001.C82


title: Control gRNA 1 untreated (2)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C1_UT_2
CK 2

value: Control gRNA 1


title: Colon biopsy from UC [2B09_14072200051]

description:
SAMPLE 43
RNA from Ulcerative Colitis biopsies

tag: patient id

tag: Sex

value: Female

value: Ulcerative Colitis

tag: tissue state

value: Nugen Ovation V2


title: px0494-TGAATGA_deep


title: Colon biopsy from UC [2B05_14072200047]

description:
SAMPLE 41
RNA from Ulcerative Colitis biopsies

tag: hospital site

tag: age

tag: hybe kit


title: Colon biopsy from UC [1G02_14072200040]

description:
SAMPLE 39
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Transverse


title: Colon biopsy from UC [2B06_14072200048]

description:
SAMPLE 42
RNA from Ulcerative Colitis biopsies


title: Colon biopsy from UC [1D07_14072200024]

description:
SAMPLE 38
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Descending


title: RDEB_1.cDNA.001.C81

value: RDEB


title: px0494-TATAATA_deep

tag: type


title: Colon biopsy from UC [1G05_14072200043]

description:
SAMPLE 40
RNA from Ulcerative Colitis biopsies

value: Male

value: Non-lesional


title: RDEB_1.cDNA.001.C77


title: Control gRNA 1 untreated (1)

description:
171123_NB501056_0081_AHWWTVBGX3_normalizedcountdata.csv
C1_UT_1
CK 1

tag: cell line

tag: treatment

value: untreated


title: Colon biopsy from UC [1B05_14072200008]

description:
SAMPLE 36
RNA from Ulcerative Colitis biopsies

tag: disease


title: Colon biopsy from UC [1D02_14072200019]

description:
SAMPLE 37
RNA from Ulcerative Colitis biopsies

tag: tissue location

value: Intestine;Colon;Ascending


title: cCLP rep4

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by HTSeq 1.0.6.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: cCLP

growth_protocol: cCLP were cultured on OP9 in KIDMEM with Flt3L and low dose of IL-7.

extract_protocol:
RNA was extracted by TRIZOL reagent (Thermo Fischer Scientific) from 1x105 cells of FACS-sorted Lin-IL7R+Flk2+CD27+Ly6d- cCLP cultured in vitro for 2 months, or from freshly isolated CLP ex vivo.
The TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (RS-122-2201, Illumina) was used to prepare cDNA libraries from 100 ng total RNA according to the low sample protocol (RS-122-9007DOC Part #15031048 Rev. E). The resulting cDNA libraries were paired-end (2 x75 nt) sequenced on a NextSeq500 Illumina device using the NextSeq 500/550 Mid output Kit v2 with 150 cycles.

tag: strain

value: cCLP (Lin-Flk2+IL7R+CD27+Ly6d-) cultured in vitro for 2 months

tag: tissue of origin

value: bone marrow


title: RDEB_1.cDNA.001.C72

tag: cell type

value: Fibroblast

tag: passage number

value: Medium


title: px0494-TCATTCA_deep

tag: donor

tag: markers


title: px0494-TACAGCA_deep


title: cCLP rep2


title: RDEB_1.cDNA.001.C68

tag: c1 chip size


title: px0494-TAGCTTA_deep


title: px0494-GTAGAGA_deep


title: px0494-GTCCGCA_deep


title: px0494-GTGAAAA_deep


title: Colon biopsy from UC [1B02_14072200005]

description:
SAMPLE 35
RNA from Ulcerative Colitis biopsies

tag: patient id

tag: Sex

value: Brigham and Womens

tag: secondary id


title: CLP exvivo rep4

source_name: CLP ex vivo

value: CLP (Lin-Flk2+IL7R+CD27+Ly6d-) isolated ex vivo


title: RDEB_1.cDNA.001.C63


title: RDEB_1.cDNA.001.C66


title: CLP exvivo rep3


title: Colon biopsy from UC [3G09_14072200124]

description:
SAMPLE 34
RNA from Ulcerative Colitis biopsies

tag: tissue state

value: Lesional

tag: hospital site

tag: age


title: RDEB_1.cDNA.001.C73


title: px0494-GGCTACA_deep

tag: type

value: single-cell


title: cCLP rep3


title: px0494-GTGGCCA_deep


title: RDEB_1.cDNA.001.C59


title: Colon biopsy from UC [3F05_14072200120]

description:
SAMPLE 32
RNA from Ulcerative Colitis biopsies

value: Ulcerative Colitis

tag: hybe kit

value: Intestine;Large


title: CLP exvivo rep2


title: CLP exvivo rep1


title: RDEB_1.cDNA.001.C58

tag: disease


title: px0494-GGCCTGA_deep


title: cCLP rep1


title: Colon biopsy from UC [3F03_14072200130]

description:
SAMPLE 31
RNA from Ulcerative Colitis biopsies

value: Female

value: Nugen Ovation V2

tag: tissue location

value: Intestine;Colon;Sigmoid


title: Colon biopsy from UC [3E03_14072200123]

description:
SAMPLE 30
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Transverse


title: RDEB_1.cDNA.001.C53

value: RDEB


title: Colon biopsy from UC [3F08_14072200128]

description:
SAMPLE 33
RNA from Ulcerative Colitis biopsies

value: Male


title: px0494-GGCACAA_deep


title: RDEB_1.cDNA.001.C52


title: px0494-GCCTTAA_deep


title: Colon biopsy from UC [3D09_14072200111]

description:
SAMPLE 29
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Descending


title: RDEB_1.cDNA.001.C51


title: Anagen_4

city: New York

first: Brian

last: Brown

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Each read in the fastq files was split into two 37-mers and stored in a non-redundant fasta file, keeping track of the number of occurrences of each 37 mer in the set.  The fasta files were mapped exactly to the genome (mm10) , in order to avoid ambiguous mappings, homologues etc..  The counts per gene (based on Refseq annotations of the mm10 genome) were computed based on this mapping and coverted to RPKM values using the same annotations.
The mapping software uses a custom implementation of suffix arrays and the annotations of the mapped reads are derived using custom software and methods based on Refseq and other annotations (mirBase and other non-coding datasets)
The methods methods are detailed here  (Yin et. al) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038464/
Annotations are detailed here, (Tam et. al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981145/)
Genome_build: mm10
Supplementary_files_format_and_content: excel spreadsheet containing gene annotations, raw counts, and RPKM values for all samples

source_name: Hair follicle

extract_protocol:
cells were directly isolated from the epidermis of mice and placed in Trizol for RNA extraction
Ovation RNA‑Seq System V2-Nugen Technologies

treatment_protocol: the back of the mice was shaved and fur was completely removed by using depilatory cream. Skin back was harvested, and placed in cold PBS after the underlying fat was removed. PBS was removed and replaced with 1x Trypsin-EDTA (Invitrogen) and skins were then placed at 37°C for 35 minutes and the epidermis was mechanically separated from the dermis by scrapping with a scalpel to obtain single cell suspensions. Cells were filtered using a 70μm cell strainer and stained for flow cytometry analysis. Cells were sorted based on GFP signal and as CD45 negative and DAPI negative (live cells)

tag: tissue

value: Hair follicle

tag: strain

value: C57Bl6 x B10D2


title: Anagen_3


title: Colon biopsy from UC [3D08_14072200112]

description:
SAMPLE 28
RNA from Ulcerative Colitis biopsies


title: Colon biopsy from UC [3D06_14072200119]

description:
SAMPLE 27
RNA from Ulcerative Colitis biopsies


title: px0494-GCCAATA_deep


title: Anagen_2


title: Anagen_1


title: RDEB_1.cDNA.001.C50

tag: cell type

value: Fibroblast


title: Telogen_3


title: px0494-GCACTTA_deep


title: px0494-GCAAGGA_deep


title: px0494-GATCAGA_deep


title: RDEB_1.cDNA.001.C42

tag: passage number

value: Medium


title: Telogen_2


title: Telogen_1


title: RDEB_1.cDNA.001.C35


title: RDEB_1.cDNA.001.C41


title: WT_1.cDNA.002.C24

value: wild-type control


title: Colon biopsy from UC [3C10_14072200121]

description:
SAMPLE 26
RNA from Ulcerative Colitis biopsies

value: Brigham and Womens


title: Colon biopsy from UC [3C09_14072200122]

description:
SAMPLE 25
RNA from Ulcerative Colitis biopsies

value: Lesional


title: px0494-GAGTGGA_deep

value: single-cell

tag: donor


title: RDEB_1.cDNA.001.C34


title: Colon biopsy from UC [3B09_14072200131]

description:
SAMPLE 22
RNA from Ulcerative Colitis biopsies

value: Ulcerative Colitis


title: RDEB_1.cDNA.001.C32


title: px0494-GACGGAA_deep

tag: markers


title: RDEB_1.cDNA.001.C33

tag: c1 chip size


title: Colon biopsy from UC [3C04_14072200129]

description:
SAMPLE 23
RNA from Ulcerative Colitis biopsies

tag: patient id


title: Colon biopsy from UC [3C06_14072200113]

description:
SAMPLE 24
RNA from Ulcerative Colitis biopsies

tag: Sex


title: px0494-GAATAAA_deep


title: px0494-GAAACCA_deep


title: RDEB_1.cDNA.001.C28


title: px0494-CTTGTAA_deep


title: RDEB_1.cDNA.001.C26


title: px0494-CTGCTGA_deep


title: Colon biopsy from UC [3B06_14072200132]

description:
SAMPLE 20
RNA from Ulcerative Colitis biopsies

tag: secondary id


title: px0494-CTCAGAA_deep


title: RDEB_1.cDNA.001.C25


title: RDEB_1.cDNA.001.C24


title: Colon biopsy from UC [2G08_14072200085]

description:
SAMPLE 19
RNA from Ulcerative Colitis biopsies

tag: tissue state


title: px0494-CGATGTA_deep


title: Colon biopsy from UC [2G07_14072200084]

description:
SAMPLE 18
RNA from Ulcerative Colitis biopsies

tag: hospital site


title: RDEB_1.cDNA.001.C23


title: Colon biopsy from UC [2F10_14072200080]

description:
SAMPLE 17
RNA from Ulcerative Colitis biopsies

tag: age


title: px0494-CGAGAAA_deep

tag: type


title: RDEB_1.cDNA.001.C19


title: RDEB_1.cDNA.001.C16


title: px0494-CCTTAGA_deep


title: px0494-CTATACA_deep


title: RDEB_1.cDNA.001.C14


title: px0494-CATGGCA_deep


title: RDEB_1.cDNA.001.C12


title: Colon biopsy from UC [3B07_14072200127]

description:
SAMPLE 21
RNA from Ulcerative Colitis biopsies

tag: hybe kit


title: Colon biopsy from UC [2D09_14072200065]

description:
SAMPLE 13
RNA from Ulcerative Colitis biopsies

tag: disease


title: Colon biopsy from UC [2E10_14072200073]

description:
SAMPLE 15
RNA from Ulcerative Colitis biopsies

tag: tissue location


title: RDEB_1.cDNA.001.C09


title: Colon biopsy from UC [2E06_14072200069]

description:
SAMPLE 14
RNA from Ulcerative Colitis biopsies

value: Intestine;Large


title: Colon biopsy from UC [2B11_14072200053]

description:
SAMPLE 11
RNA from Ulcerative Colitis biopsies


title: px0494-CACTCAA_deep


title: Colon biopsy from UC [2F08_14072200078]

description:
SAMPLE 16
RNA from Ulcerative Colitis biopsies


title: Colon biopsy from UC [2C08_14072200057]

description:
SAMPLE 12
RNA from Ulcerative Colitis biopsies

value: Female


title: Colon biopsy from UC [1F08_14072200039]

description:
SAMPLE 9
RNA from Ulcerative Colitis biopsies

value: Nugen Ovation V2


title: Colon biopsy from UC [1G03_14072200041]

description:
SAMPLE 10
RNA from Ulcerative Colitis biopsies


title: pair13 recurrent tumor

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

description:
P13b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

scan_protocol: Scanned on an Agilent microarray scanner G2565BA.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1). Rank segmentation algorithm (significance threshold: 5E-6) of Nexus Copy Number 9 was applied to analyze aCGH data. Significance threshold: 5E6

source_name: colorectal adenoma

label_protocol: Protocol Version 3.2, Oct 2010, Agilent. Sex-matched human genomic DNA (Promega) was used as reference DNA.

extract_protocol: Genomic DNA was isolated from formalin-fixed paraffin-embedded colorectal adenoma samples using Gentra Puregene Kit (handbook, June 2011) according to the manufacturer's instructions (Qiagen, Hilden, Germany). DNA quality and quantity were assessed using a Nanodrop ND1000 spectrophotometer.

tag: tissue

value: recurrent colorectal adenoma

value: female

tag: recurrence

value: yes

tag: ploidy

value: near 2N

tag: sample type

source_name: Control DNA

value: reference


title: pair12 recurrent tumor

description:
P12b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

hyb_protocol: Protocol Version 3.2, Oct 2010, Agilent.

value: male


title: pair14 recurrent tumor

description:
P14b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.