title: MCF7 Cells treated with CPI-203 Replicate 3

description: Biological replicate 3 of 3

source_name: MCF7 cells treated with CPI-203

value: breast

value: Breast


title: MCF7 Cells treated with CPI-203 Replicate 2

status: Public on Dec 07 2017

type: RNA

city: Baltimore

first: Benjamin

last: Leadem

state: MD

address: 1650 Orleans St. Suite 541

country: USA

institute: Johns Hopkins University

description: Biological replicate 2 of 3

hyb_protocol: standard as recommended by Agilent

scan_protocol: standard as recommended by Agilent standard as recommended by Agilent

data_processing: Data were normalized using loess and aquantile methods as described in the Bioconductor limma package.

molecule: total RNA

organism: Homo sapiens

label_protocol: standard as recommended by Agilent

growth_protocol: standard as recommended by ATCC

extract_protocol: Total RNA extracted using Qiagen RNeasy following manufacturer's instructions

tag: cell line

value: MCF7 adenocarcinoma cells

tag: age

value: day 3

tag: tissue

source_name: MCF7 cells Mock Treatment

tag: strain


title: MCF7 Cells treated with DAC Replicate 2

description: Biological replicate 2 of 3

source_name: MCF7 cells treated with DAC


title: MCF7 Cells treated with CPI-203 Replicate 1

description: Biological replicate 1 of 3


title: MCF7 Cells treated with DAC Replicate 3

description: Biological replicate 3 of 3


title: STD_PROTOCOL_EOMES_KO_hESCs_d7

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description:
EOMES KO hESCs, standard cardiac induction protocol day 7
SAMPLE 16

hyb_protocol: 18 hours according to manufacturer's instructions (Illumina)

scan_protocol: Default settings on a HiScan SQ (Illumina)

data_processing: Cubic spline normalization with background subtration in GenomeStudio (Illumina)

label: biotin

source_name: differentiated cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Thermo); 14h of in-vitro transcription

growth_protocol: Undifferentiated hESCs (HuES6 background) were grown to full confluency in chemically defined FTDA medium. Differentiation was initiated after - or concomitant with - replating cells at 1 M or 500,000 cells per well in Matrigel-coated 24-well plates.

extract_protocol: Qiagen RNeasy columns with on-column DNA-digestion. Three independent experiments were carried out for each series. RNA was then pooled from these replicates to be processed for microarray sample preparation.

treatment_protocol: Series 1 and 2 (standard cardiac induction protocol): d0 cells = confluent undifferentiated WT or EOMES knockout cells before replating. Replating medium used on d0 (500,000 cells per 24-well): KO-DMEM / ITS / PenStrep / 10 µM Rock Inhibitor Y27632 / 20 ng/ml FGF2 / 1 µM CHIR99021 / 0.75 ng/ml BMP4. Day 1 medium: KO-DMEM / Transferrin-Selenium / PenStrep / 250 µM phospho-ascorbate. Day 2 and 3: Same medium + 2 µM IWP2. Day 4 onwards: Same as on day 1. Volume of medium: 2 ml per well throughout. Series 3 (TET-ON protocol): Cells replated at 1 M per 24-well in FTA medium + 10µM Rock Inhibitor Y27632. Day 0 medium: KO-DMEM / ITS / PenStrep / 0.25 µg/ml doxycycline (DOX) - no signaling factors added. Day 1 medium: KO-DMEM / Transferrin-Selenium / 250 µM phospho-ascorbate / PenStrep / 0.25 µg/ml DOX. Day 2: Same medium + 0.5 µM C59. Day 3: Same, but with C59 only (no DOX). Hence after: Plain KO-DMEM / Transferrin-Selenium / phospho-ascorbate / PenStrep.

value: Human ES cells (line HuES6)

tag: genotype/variation

tag: protocol

value: standard directed differentiation protocol

tag: time

value: day 7


title: STD_PROTOCOL_EOMES_KO_hESCs_d6

description:
EOMES KO hESCs, standard cardiac induction protocol day 6
SAMPLE 15

value: day 6


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d0

description:
undifferentiated EOMES KO / TET-ON hESCs at start of TET-ON protocol
SAMPLE 17

source_name: undifferentiated cell line

value: TET-ON protocol

value: day 0


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d3

description:
EOMES KO / TET-ON hESCs, TET-ON protocol day 3
SAMPLE 20


title: MCF7 Cells treated with CPI-455 Replicate 2

description: Biological replicate 2 of 3

source_name: MCF7 cells treated with CPI-455


title: STD_PROTOCOL_EOMES_KO_hESCs_d2

description:
EOMES KO hESCs, standard cardiac induction protocol day 2
SAMPLE 11

value: day 2


title: MCF7 Cells treated with DAC Replicate 1

description: Biological replicate 1 of 3


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d1

description:
EOMES KO / TET-ON hESCs, TET-ON protocol day 1
SAMPLE 18

value: day 1


title: STD_PROTOCOL_EOMES_KO_hESCs_d3

description:
EOMES KO hESCs, standard cardiac induction protocol day 3
SAMPLE 12


title: STD_PROTOCOL_EOMES_KO_hESCs_d4

description:
EOMES KO hESCs, standard cardiac induction protocol day 4
SAMPLE 13

value: day 4


title: MCF7 Cells treated with CPI-455 Replicate 3

description: Biological replicate 3 of 3


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d2

description:
EOMES KO / TET-ON hESCs, TET-ON protocol day 2
SAMPLE 19


title: URE-/- cells + DB2313, biological rep3

city: Bronx

first: Ileana

last: Antony-debre

address: 1300 Moris park Avenue

department: cell biology

institute: albert einstein college of medicine

description: Gene expression data from URE-/- cell line after 24h of treatment with small molecule DB2313

hyb_protocol: RNA was hybridized to Affymetrix 2.0 Mouse GeneST microarrays (Affymetrix)

scan_protocol: The scan was done using GeneChip Scanner 3000 7G system (Affymetrix)

data_processing: Raw data were normalized using Expression Console (Affymetrix).

organism: Mus musculus

source_name: URE-/- cell line 24h after treatment with pu.1 inhibitor DB2313

label_protocol: RNA was labeled with the GeneChip WT terminal labeling kit (Affymetrix)

growth_protocol: Cells were cultured in M5300 media supplemented with 10% FBS, 15% WEHI supernatant, 15% BHK supernatant and 1% P/S

extract_protocol: Extraction of total RNA was performed using RNeasy Mini Kit (Qiagen), according to manufacturer's instructions.

treatment_protocol: Small molecule DB2313 was added to the culture at the concentration of 330 nM, equivalent volume of Vehicle (water) was added in the Vehicle treated cells.

tag: cell type

value: acute myeloid leukemia (AML)

value: PU.1low URE-/-


title: URE-/- cells + DB2313, biological rep2


title: STD_PROTOCOL_EOMES_KO_hESCs_d5

description:
EOMES KO hESCs, standard cardiac induction protocol day 5
SAMPLE 14

value: day 5


title: MCF7 Cells treated with CPI-455 Replicate 1

description: Biological replicate 1 of 3


title: STD_PROTOCOL_WT_hESCs_d6

description:
WT HuES6 cells, standard cardiac induction protocol day 6
SAMPLE 7

value: WT


title: STD_PROTOCOL_WT_hESCs_d7

description:
WT HuES6 cells, standard cardiac induction protocol day 7
SAMPLE 8


title: STD_PROTOCOL_WT_hESCs_d4

description:
WT HuES6 cells, standard cardiac induction protocol day 4
SAMPLE 5


title: STD_PROTOCOL_WT_hESCs_d5

description:
WT HuES6 cells, standard cardiac induction protocol day 5
SAMPLE 6


title: STD_PROTOCOL_EOMES_KO_hESCs_d1

description:
EOMES KO hESCs, standard cardiac induction protocol day 1
SAMPLE 10


title: STD_PROTOCOL_EOMES_KO_hESCs_d0

description:
undifferentiated EOMES KO hESCs at start of standard cardiac induction protocol
SAMPLE 9


title: URE-/- cells + DB2313, biological rep1


title: URE-/- cells + vehicle, biological rep2

description: Gene expression data from URE-/- cell line after 24h of treatment with vehicle

source_name: URE-/- cell line 24h after treatment with vehicle


title: STD_PROTOCOL_WT_hESCs_d1

description:
WT HuES6 cells, standard cardiac induction protocol day 1
SAMPLE 2


title: URE-/- cells + vehicle, biological rep3


title: STD_PROTOCOL_WT_hESCs_d2

description:
WT HuES6 cells, standard cardiac induction protocol day 2
SAMPLE 3


title: URE-/- cells + vehicle, biological rep1


title: Untreated

description:
Untreated hESCs
SAMPLE 1

growth_protocol: Human ES cells (line HuES6) were grown in MEF-conditioned medium and replated as single cells into new Matrigel-coated culture wells. Next day, medium was switched to a more defined Serum Replacement-based standard hESC medium supplemented with 20 ng/ml FGF2 and 5 ng/ml Activin A. One day later, cells were used for short-term signaling factor stimulation.

extract_protocol: Qiagen RNeasy columns with on-column DNA-digestion

treatment_protocol: At semiconfluency, cells were either kept in the above medium (untreated control), or stimulated for 4 hours with 20 ng/ml BMP4, or with 5 µM CHIR99021 (a GSK inhibitor activating canonical WNT signaling), or both.

tag: treatment

value: Untreated


title: STD_PROTOCOL_WT_hESCs_d3

description:
WT HuES6 cells, standard cardiac induction protocol day 3
SAMPLE 4


title: 4h WNT

description:
hESCs stimulated for 4h with CHIR99021
SAMPLE 3


title: 4h BMP+WNT

description:
hESCs stimulated for 4h with BMP4 and CHIR99021
SAMPLE 4

value: BMP4 and CHIR99021


title: NI TFBJ.b

city: Berlin

first: Nancy

last: Mah

address: Augustenburger Platz 1

department: Berlin-Brandenburger Centrum für Regenerative Therapien (BCRT)

institute: Charité - Universitätsmedizin Berlin

description: neuronal induction neuroprogenitor cells produced from iPS cells (episomal vector protocol; fibroblast donor)

hyb_protocol: Samples were hybridized onto Illumina human-12 BeadChips (Illumina, San Diego, CA, United States).

scan_protocol: not provided

data_processing: Microarray data were normalized using the Bioconductor package lumi as follows: non-normalized data were first background corrected [lumiB(rawdata, method = bgAdjust.affy)], variation stabilized using variance stabilization transform [lumiT(background.corrected, method=vst)], and then normalized using robust spline normalization [lumiN(transformed.data, method=rsn)].

source_name: NPCs

label_protocol: Biotin-labeled cRNA samples were produced as previously described (Prigione et al, Stem cells, 2010)

growth_protocol: All pluripotent stem cells (PSCs) were cultivated on mitotically-inactivated mouse embryonic fibroblasts (MEFs) grown on Matrigel (BD, Heidelberg, Germany)-coated plates, using KO-DMEM medium (Gibco) containing 20% knock-out serum replacement (KSR, Gibco), 8 ng/μl bFGF (Peprotech, Germany), non-essential amino acids, pen/strep, and sodium pyruvate. NPCs were were cultured in NI medium (Neurobasal:DMEM/F12 [1:1], N2 [1x], B27 [1x], hLIF [10 ng/ml], CHIR99021 [3 µM], SB431542 [2 µM], BSA [0.05 %], pen/strep, glutamine) to preserve the progenitor state

extract_protocol: Total RNA was isolated using the Qiagen isolation kit (Qiagen) and quality-checked by Nanodrop analysis (Nanodrop Technologies, Wilmington, DE, USA).

value: neuronal induction neuroprogenitor cell


title: eNPCs

description: ex-vivo neuroprogenitor cells purchased from Lonza, derived from brain of 8 yr-old boy

value: neuroprogenitor cell


title: 4h BMP

description:
hESCs stimulated for 4h with BMP4
SAMPLE 2

value: Human ES cells (line HuES6)


title: NI TDBJ5.b

description: neuronal induction neuroprogenitor cells produced from iPS cells (viral transduction protocol; fibroblast donor)


title: rNPCs_NI

description: neuroprogenitor cells produced by rosette protocol from H9 ESC


title: NI A3.a

description: neuronal induction neuroprogenitor cells produced from iPS cells (viral transduction protocol; patient A3 fibroblast donor)

tag: gender

value: female


title: STD_PROTOCOL_WT_hESCs_d0

description:
undifferentiated WT HuES6 cells at start of standard cardiac induction protocol
SAMPLE 1

value: standard directed differentiation protocol


title: NI A2.b

description: neuronal induction neuroprogenitor cells produced from iPS cells (viral transduction protocol; patient A2 fibroblast donor)


title: rNPCs_Ar

description: neuroprogenitor cells produced by rosette protocol from H9 ESC (Aruna)


title: NI A3.b


title: NI H9.b

description: neuronal induction neuroprogenitor cells produced from H9 ESCs


title: NI TDBJ5.a


title: NI H1.b

description: neuronal induction neuroprogenitor cells produced from H1 ESCs


title: NI H9.a


title: NI TFBJ.a


title: TDA3.1.b

description: viral transduction protocol iPS cells from patient A3

source_name: iPSCs

value: induced pluripotent stem cell

tag: cell derivation

value: retroviral transduction with OCT4, SOX2, KLF4, MYC (4F)


title: NI A2.a


title: TDA2.3.b

description: viral transduction protocol iPS cells from patient A2


title: TDA3.1.a


title: NI H1.a


title: TDA2.3.a


title: TFA2.a

description: episomal vector protocol iPS cells from patient A2

value: episomal nucleofection with 4F + NANOG, LIN28, SVLT


title: TDBJ5(iB5).b

description: viral transduction protocol iPS cells from BJ


title: TFA2.b


title: TFBJ.a

description: episomal vector protocol iPS cells from BJ fibroblasts


title: TFBJ.b


title: TDBJ5(iB5).a


title: H9

description: H9 ESC

source_name: hESCs

value: embryonic stem cell


title: H1.b

description: H1 ESC


title: TDHFF1(iPS2).b

description: viral transduction protocol iPS cells from HFF1


title: A2.a

description: fibroblast from patient A2, mother of patient A3

source_name: fibroblasts

value: fibroblast


title: TDHFF1(iPS2).a


title: BJ.a

description: BJ fibroblast

value: neonatal fibroblast


title: A3.a

description: fibroblast from patient A3


title: HFF1.a

description: HFF1 fibroblast


title: BMDM 1

status: Public on Dec 06 2017

city: Freiburg

first: Philipp

last: Henneke

address: Breisacher Str. 115

department: MEDICAL CENTER – UNIVERSITY OF FREIBURG

institute: Center for Chronic Immunodeficiency

hyb_protocol: 4,5 µg of SPIA cDNA was fragmented, terminally biotin-labeled and hybridized to Affymetrix Mouse Gene 2.0 ST arrays for 16 h at 45° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

label: Biotin

source_name: macrophage

label_protocol: Sample preparation for microarray hybridization was carried out as described in the NuGEN Ovation PicoSL WTA System V2 and NUGEN Encore Biotin Module manuals (NuGEN Technologies, Inc, San Carlos, CA, USA).

growth_protocol: Bone marrow cells were cultivated in M-CSF (20ng/ml) for 5days.

extract_protocol: Total RNA was extracted from sorted cells with the Rneasy Micro Kit (Qiagen) as per manufacturer's instructions.

treatment_protocol: Bone marrow-derived macrophages where scraped and plated either only in M-CSF (50ng/ml) or stimulated with FSL-1 (20ng/ml) or FSL-1 and nutlin-3a (10µM) for 6days for RNA extraction.

value: macrophage

value: M-CSF (50ng/ml)


title: A1.a

description: fibroblast from patient A1, grandmother of patient A3


title: BMDM 2


title: H1.a

description: H1 ESC


title: A2.b


title: A3.b

description: fibroblast from patient A3


title: BMDM + FSL-1 1

value: stimulated with FSL-1 (20ng/ml)


title: HFF1.b

description: HFF1 fibroblast


title: BJ.b

description: BJ fibroblast


title: BMDM + FSL-1 2


title: A1.b


title: BMDM + FSL-1 + nutlin-3a 2

value: stimulated with FSL-1 (20ng/ml) and nutlin-3a (10µM)


title: BMDM + FSL-1 + nutlin-3a 1


title: DAC+455

type: genomic

hyb_protocol: standard as recommended by Illumina

scan_protocol: standard as recommended by Illumina

data_processing: Preprocessed by Bioconductor Minfi package. Computed normalized average beta with minfi

label: Cy5 and Cy3

molecule: genomic DNA

source_name: MCF7 with DAC+455 treatment

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Promega Wizard Genomic DNA Purification Kit (#A1120)

value: Female

tag: sample type

value: MCF-7 Cell Line

tag: disease state

value: adenocarcinoma


title: RIVA_DUVELISIB_8H

status: Public on Dec 05 2017

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
The data were normalised using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

source_name: RIVA cell lines treated with DUVELISIB

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: treatment with novel dual PI3K/mTOR inhibitor  with anti-lymphoma activity as single agent and in combination

value: RIVA

value: Lymphoma

value: DUVELISIB


title: TMD8_DUVELISIB_8H

source_name: TMD8 cell lines treated with DUVELISIB


title: TMD8_IBRUTINIB_4H

source_name: TMD8 cell lines treated with IBRUTINIB

value: IBRUTINIB


title: DAC

source_name: MCF7 with DAC treatment


title: RIVA_IBRUTINIB_4H

source_name: RIVA cell lines treated with IBRUTINIB


title: TMD8_IDELALISIB_12H

source_name: TMD8 cell lines treated with IDELALISIB

value: IDELALISIB


title: RNA from MCF-10A transfected miRNA 7 mimic

city: Ilsan

first: Juyeon

last: Ham

address: 32, Dongguk-ro

country: South Korea

institute: Dongguk University

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufactur

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: MCF-10A_miRNA 7 mimic

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: RNA was extracted and purified from MCF-10A using ZR Dyet DNA/RNA kit (Zymo research) according to standard instructions

value: female

value: human mammary epithelial cell line

tag: transfected with

value: miRNA 7 mimic


title: RIVA_IBRUTINIB_8H


title: CPI-203

source_name: MCF7 with CPI-203 treatment


title: RIVA_IBRUTINIB_12H


title: TMD8_DUVELISIB_12H


title: TMD8_DUVELISIB_4H


title: RNA from MCF-10A transfected miRNA Negative control

value: miRNA Negative control


title: TMD8_IDELALISIB_8H


title: SUDHL2_IBRUTINIB_12h

source_name: SUDHL2 cell lines treated with IBRUTINIB


title: TMD8_IBRUTINIB_12H


title: Mock

source_name: MCF7 with mock treatment


title: RIVA_DUVELISIB_12H


title: TMD8_IDELALISIB_4H


title: U2932_DUVELIS_4H

source_name: U2932 cell lines treated with DUVELISIB


title: RIVA_IDELALISIB_8H

source_name: RIVA cell lines treated with IDELALISIB


title: TMD8_IBRUTINIB_8H


title: RIVA_DUVELISIB_4H


title: RIVA_IDELALISIB_4H


title: U2932_IBRUTINIB_4H

source_name: U2932 cell lines treated with IBRUTINIB


title: CPI-455

source_name: MCF7 with CPI-455 treatment


title: U2932_DUVELIS_12H


title: U2932_IDELALISIB_4H

source_name: U2932 cell lines treated with IDELALISIB


title: SUDHL2_IBRUTINIB_8h


title: SUDHL2_IBRUTINIB_4h


title: RIVA_IDELALISIB_12H


title: U2932_IDELALISIB_12H


title: SUDHL10_8H_DMSO

source_name: SUDHL10 cell lines treated with DMSO

value: DMSO


title: U2932_8H_PQR309

source_name: U2932 cell lines treated with PQR309


title: U2932_IBRUTINIB_8H


title: OCILY18_8H_PQR309

source_name: OCILY18 cell lines treated with PQR309


title: SUDHL2_DUVELISIB_4h

source_name: SUDHL2 cell lines treated with DUVELISIB


title: TMD8_8H_PQR309

source_name: TMD8 cell lines treated with PQR309


title: U2932_DUVELISIB_8H


title: SUDHL2_8H_PQR309

source_name: SUDHL2 cell lines treated with PQR309


title: DAC+203

source_name: MCF7 with DAC+203 treatment


title: U2932_IDELALISIB_8H


title: OCILY18_8H_DMSO

source_name: OCILY18 cell lines treated with DMSO


title: DOHH2_8H_DMSO

source_name: DOHH2 cell lines treated with DMSO


title: OCILY1_8H_PQR309

source_name: OCILY1 cell lines treated with PQR309


title: SUDHL2_IDELALISIB_4h

source_name: SUDHL2 cell lines treated with IDELALISIB


title: SUDHL2_DUVELISIB_8h


title: RIVA_8H_PQR309

source_name: RIVA cell lines treated with PQR309


title: SUDHL2_IDELALISIB_12h


title: 331a

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for cRNA target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

source_name: Whole blood (PAXgene RNA)

label_protocol: Ambion TotalPrep target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from primary peripheral blood samples (Tempus RNA Tubes; ThermoFisher) using the manufacturer's standard protocol & reagents.

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: bmi

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier

tag: adverb

tag: cdi

tag: alone

tag: talking

tag: wordcount

tag: wordspersentence


title: U2932_IBRUTINIB_12H

tag: cell line

tag: cell type

tag: treatment


title: 334a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: you

tag: shehe

tag: they


title: SUDHL10_8H_PQR309

source_name: SUDHL10 cell lines treated with PQR309

tag: cell line

tag: cell type

tag: treatment


title: SUDHL2_IDELALISIB_8h


title: OCILY1_8H_DMSO

source_name: OCILY1 cell lines treated with DMSO


title: 328a

tag: male

tag: africanamerican

tag: caucasian

tag: impersonal pronoun

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier

tag: adverb

tag: cdi

tag: alone

tag: talking

tag: wordcount

tag: wordspersentence


title: U2932_8H_DMSO

source_name: U2932 cell lines treated with DMSO

tag: cell line

tag: cell type

tag: treatment


title: 329a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: you

tag: shehe

tag: they


title: DOHH2_8H_PQR309

source_name: DOHH2 cell lines treated with PQR309

tag: cell line

tag: cell type

tag: treatment


title: SUDHL2_DUVELISIB_12h


title: SUDHL2_8H_DMSO

source_name: SUDHL2 cell lines treated with DMSO


title: 325a

tag: male

tag: africanamerican

tag: caucasian

tag: impersonal pronoun

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier

tag: adverb

tag: cdi

tag: alone

tag: talking

tag: wordcount

tag: wordspersentence


title: 324a

tag: asian

tag: age

tag: bmi

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: you

tag: shehe

tag: they


title: 322a

tag: male

tag: africanamerican

tag: caucasian

tag: impersonal pronoun

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier

tag: adverb

tag: cdi

tag: alone


title: 323a

tag: asian

tag: age

tag: bmi

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: talking

tag: wordcount

tag: wordspersentence


title: 321a

tag: male

tag: africanamerican

tag: caucasian

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: TMD8_8H_DMSO

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tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 164a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 166a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 183a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 154a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: 163a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier


title: 157a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 175a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 179a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 176a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 159a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: 153a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier


title: 151a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 152a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 167a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 147a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 150a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: 146a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier


title: 160a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 140a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 145a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 149a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 142a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: 138a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier


title: 137a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 134a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 136a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 133a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 132a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: 108a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier


title: 121a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 125a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 118a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 115a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 113a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: 123a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier


title: 129a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 112a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 116a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 119a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 127a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: 107a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier


title: 144a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: talking

tag: wordcount

tag: wordspersentence


title: 110a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: adverb

tag: cdi

tag: alone


title: 104a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: negation

tag: conjunction

tag: quantifier


title: 103a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: talking

tag: wordcount

tag: wordspersentence


title: 120a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone


title: AGS si-control (3)

status: Public on Dec 04 2017

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

description: Gene expression after 48 hours transfection.

hyb_protocol: Agilent Gene Expression Hybridization Kit was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agent and 20 ul of Agilent 2x GExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (US9230696) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: AGS cells, si-control

label_protocol: cDNA prepared from 10μg of total RNA were labeled with aa-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA). Alexa/CyDye was incorporated to aa-cDNA followed by column purification with Alexa/CyDye-cDNA cRNA purification (Qiagen).

growth_protocol: In 10% FBS/RPMI1640.

extract_protocol: RNA was prepared using the Genejet RNA Purification kit (Thermo Scientific) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: AGS

tag: sirna

value: si-control


title: AGS si-C1GALT1-3 (3)

source_name: AGS cells, si-C1GALT1-3


title: 102a

source_name: Whole blood (PAXgene RNA)

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier

tag: talking

tag: wordcount


title: MiaPaca-2 si-C1GALT1-3 (3)

source_name: MiaPaca-2 cells, si-C1GALT1-3

growth_protocol: In 10% FBS/DMEM (1X).

tag: cell line


title: 105a

tag: smoking

tag: stress

tag: depression

tag: anxiety

tag: loneliness

tag: i

tag: we

tag: article

tag: preposition

tag: auxilary verb

tag: adverb

tag: cdi

tag: alone

tag: wordspersentence


title: AGS si-control (1)

tag: sirna


title: 101a

tag: male

tag: africanamerican

tag: caucasian

tag: asian

tag: age

tag: bmi

tag: you

tag: shehe

tag: they

tag: impersonal pronoun

tag: negation

tag: conjunction

tag: quantifier

tag: talking

tag: wordcount


title: AGS si-control (2)

tag: cell line


title: MiaPaca-2 si-C1GALT1-3 (2)

tag: sirna


title: MiaPaca-2 si-control (3)

source_name: MiaPaca-2 cells, si-control


title: MiaPaca-2 si-C1GALT1-3 (1)


title: MM909_47_1

type: SRA

city: Lund

first: Martin

last: Lauss

address: Barngatan 2B

department: Dept of Oncology

country: Sweden

institute: Lund University

library_source: transcriptomic

data_processing:
Raw sequencing read data were demultiplexed and collated by library barcode into sample data sets.
TopHat 2.0.13 was used to align reads to the human reference genome hg38 together with 104,133 transcript annotations from the UCSC knownGenes table.
Cufflinks 2.2.1 was used to calculate FPKM.
Gene expression data were collapsed on 30,865 unique gene symbols by the sum of FPKM values of the individual transcripts.
The data were quantile-normlized using limma, an offset of 1 was added and the data were log2 transformed. Genes were reduced to 18,418 protein-coding genes as defined by HGNC.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing FPKM values, that have undergone quantile normalization, and log2(data+1).

source_name: Melanoma

extract_protocol:
Tumor DNA and RNA was extracted from either snap frozen or frozen in DMSO tumor fragments using AllPrep DNA/RNA Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
RNAseq strategy encompasses the performance of paired end sequencing of 50 bp reads on an Illumina HiSeq 2000 instrument

value: Before TILs

value: pleura

value: unknown

tag: recist

value: SD


title: MM909_45_1

value: LN

value: PR


title: MiaPaca-2 si-control (1)


title: MM909_46_1

value: skin


title: MM909_43_1

value: SC

value: PD


title: MM909_42_1

value: CR


title: Doxorubicin 5 (heart)

city: Jyväskylä

first: Juha

middle: J

last: Hulmi

address: Rautpohjankatu 8a Viv

department: Biology of Physical Activity

country: Finland

institute: University of Jyväskylä

description:
Sample name: SAMPLE 10
replicate 5

hyb_protocol: Standard Illumina hybridization protocol. Conducted at the Functional Genomics Unit at Biomedicum Helsinki, University of Helsinki, Finland.

scan_protocol: Standard Illumina scanning protocol. Conducted at the Functional Genomics Unit at Biomedicum Helsinki, University of Helsinki, Finland.

data_processing: The data were normalized with quantiles normalization and data quality was assessed using Chipster software (IT Center for Science, Espoo, Finland)

source_name: heart

label_protocol: Biotinylated cRNA were  prepared with TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip®, P/N TAN07924, Lit.#269, 5/2013, EPILIT269.  Rev. A (Epicentre).

extract_protocol: Total RNA was extracted from the heart with TRIsure reagent (BIO-38032, Bioline, Luckenwalde, Germany) and further purified with NucleoSpin® RNA II columns (#740955.50, Macherey-Nagel, Germany) according to the manufacturer’s protocols.

tag: tissue

value: heart

tag: strain

tag: Sex

value: male

value: 8-10 weeks


title: Doxorubicin + sAcvR2B-Fc 1 (heart)

description:
Sample name: SAMPLE 11
replicate 1

tag: age


title: Control (PBS) 5 (heart)

description:
Sample name: SAMPLE 5
replicate 5


title: Doxorubicin + sAcvR2B-Fc 3 (heart)

description:
Sample name: SAMPLE 13
replicate 3


title: Control (PBS) 4 (heart)

description:
Sample name: SAMPLE 4
replicate 4


title: Doxorubicin 3 (heart)

description:
Sample name: SAMPLE 8
replicate 3


title: human dermal fibroblasts shCSL_rep1

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

description: HDFs infected with shRNA lentivirus against CSL

hyb_protocol: Biotin-labeled cRNA was hybridized on Affymetrix Human Genome U133A 2.0 Array Chips according to the manufacturer’s recommendation.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Raw microarray values were quantified using GeneChip Operating Software (Affymetrix).

data_processing: Raw data were analyzed using the RMA package, available within Bioconductor.

source_name: Human Dermal Fibroblasts

label_protocol: The resulting cDNAs were used for preparation of biotin-labeled antisense cRNA

extract_protocol: Poly(A)+ mRNAs (2–5 μg) from cells under various conditions were used as template for double-stranded cDNA preparations with T7-(dT)24 oligonucleotide primers for the first-strand reaction.

tag: cell type

value: fibroblasts


title: MiaPaca-2 si-control (2)


title: human dermal fibroblasts shCSL_rep2


title: Doxorubicin + sAcvR2B-Fc 2 (heart)

description:
Sample name: SAMPLE 12
replicate 2


title: human dermal fibroblasts CTRL

description: HDFs infected with control virus


title: MM909_40_1

value: IA


title: Doxorubicin 1 (heart)

description:
Sample name: SAMPLE 6
replicate 1


title: Control (PBS) 2 (heart)

description:
Sample name: SAMPLE 2
replicate 2


title: MM909_37_1


title: MM909_35_2

value: During Vemurafenib/Before TILs


title: MM909_34_2

value: mucosa


title: Control (PBS) 1 (heart)

description:
Sample name: SAMPLE 1
replicate 1


title: Control (PBS) 3 (heart)

description:
Sample name: SAMPLE 3
replicate 3


title: MM909_29_1


title: MM909_26_1

value: Before TILs

value: IM


title: MM909_17_1


title: MM909_16_1


title: MM909_14_1

value: unknown


title: MM909_36_1


title: MM909_06_1


title: MM909_11_1


title: MM909_03_1

value: SD


title: MM909_02_1

value: LN


title: MM909_31_1

value: PR


title: MM909_27_1

value: Before Vemurafenib/Before TILs

value: skin


title: MM909_22_2

value: After Ipilimumab/Before TILs


title: MM909_01_1

value: CR


title: MM909_25_1


title: PFC_120hr_treated_5

status: Public on Dec 01 2017

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description:
microRNA
Replicate 5
PFC-120hr-etoh-45

hyb_protocol: 21.5 ul of biotin-labeled miRNA was hybridized for 16 hr at 48C to the Affymetrix GeneChip 3.0 miRNA arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the FS450_0003 wash protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner and .cel files were generated from .dat files using Affymetrix AGCC v3 software.

data_processing:
Data were background subtracted (DABG algorithm) and RMA-normalize in Gene Expression Console (EC) v1.4 using mouse miRNA (hp and mature) annotations only.
Gene Expression Console (EC) v1.4 was used to identify outliers.
miRbaseTracker.org was used to identify miRbase v21 (currently accepted) microRNAs. Obsolete microRNA probesets were removed.
Data were filtered to include only mature mouse microRNAs with a detection p value <0.06 on 80% of arrays.
DABG-RMA (log2 normalized) signals in supplementary files

source_name: prefrontal cortex, ethanol vapor treated, 120 hr

label_protocol: Samples were biotin-labeled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was isolated using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion, Austin, TX) using the manufacturer supplied modification to collect both mRNAs and small RNAs. Quality control was performed with the Agilent Tape Station.

tag: gender

value: adult (10-12 weeks)

value: prefrontal cortex


title: PFC_120hr_treated_8

description:
microRNA
Replicate 8
PFC-120hr-etoh-71

value: male


title: PFC_120hr_treated_6

description:
microRNA
Replicate 6
PFC-120hr-etoh-55


title: PFC_120hr_treated_4

description:
microRNA
Replicate 4
PFC-120hr-etoh-37


title: PFC_120hr_treated_3

description:
microRNA
Replicate 3
PFC-120hr-etoh-25


title: PFC_120hr_control_5

description:
microRNA
Replicate 5
PFC-120hr-ctrl-48

source_name: prefrontal cortex, saline control, 120 hr


title: PFC_120hr_control_6

description:
microRNA
Replicate 6
PFC-120hr-ctrl-56


title: PFC_120hr_treated_2

description:
microRNA
Replicate 2
PFC-120hr-etoh-23


title: PFC_120hr_treated_1

description:
microRNA
Replicate 1
PFC-120hr-etoh-7


title: PFC_120hr_treated_7

description:
microRNA
Replicate 7
PFC-120hr-etoh-63


title: MM909_15_2


title: PFC_120hr_control_8

description:
microRNA
Replicate 8
PFC-120hr-ctrl-72


title: FOG-2 Ki-27-1

status: Public on Dec 02 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Human Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V20 was used for annotation.

source_name: proliferating FOG-2 Rb- MEF experiment-1

label_protocol: 270 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WTplus) Sense Target labelling assay kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

growth_protocol: Wt and FOG-2 Rb- MEF were grown in DMEM/F12 containing 20% Donor Bovine Serum, 2mM L-Glutamine, 1x Penicillin/Streptomycin and 0,1mM beta-mecaptoethanol

extract_protocol: Trizol extraction of total RNA coupled to RNAeasy kit (Ambion) purification was performed according to the manufacturer's instructions.

treatment_protocol: Growing Wt and FOG-2  Rb- MEF were trypsinized and one million of cell pellet were washed with PBS before RNA extraction

tag: genotype

value: FOG-2 Rb-

value: embryonic fibroblast

tag: developmental stage


title: FOG-2 Wt-18-2

source_name: proliferating Wt MEF experiment-2

value: wildtype


title: PFC_120hr_control_4

description:
microRNA
Replicate 4
PFC-120hr-ctrl-32


title: FOG-2 Ki-27-2

source_name: proliferating FOG-2 Rb- MEF experiment-2


title: PFC_120hr_control_7

description:
microRNA
Replicate 7
PFC-120hr-ctrl-64


title: FOG-2 Wt-18-1

source_name: proliferating Wt MEF experiment-1


title: PFC_120hr_control_2

description:
microRNA
Replicate 2
PFC-120hr-ctrl-16


title: PFC_120hr_control_1

description:
microRNA
Replicate 1
PFC-120hr-ctrl-8


title: PFC_120hr_control_3

description:
microRNA
Replicate 3
PFC-120hr-ctrl-24


title: FOG-2 Ki-27-3

source_name: proliferating FOG-2 Rb- MEF experiment-3


title: PFC_8hr_treated_8

description:
microRNA
Replicate 8
PFC-8hr-etoh-67

source_name: prefrontal cortex, ethanol vapor treated, 8 hr


title: PFC_8hr_treated_6

description:
microRNA
Replicate 6
PFC-8hr-etoh-49


title: PFC_8hr_treated_7

description:
microRNA
Replicate 7
PFC-8hr-etoh-59


title: PFC_8hr_treated_5

description:
microRNA
Replicate 5
PFC-8hr-etoh-41


title: FOG-2 Wt-18-3

source_name: proliferating Wt MEF experiment-3


title: PFC_8hr_treated_4

description:
microRNA
Replicate 4
PFC-8hr-etoh-33


title: PFC_8hr_treated_2

description:
microRNA
Replicate 2
PFC-8hr-etoh-11


title: PFC_8hr_treated_3

description:
microRNA
Replicate 3
PFC-8hr-etoh-19


title: AGS si-C1GALT1-3 (2)

value: AGS


title: AGS si-C1GALT1-3 (1)


title: PFC_8hr_control_3

description:
microRNA
Replicate 3
PFC-8hr-ctrl-28

source_name: prefrontal cortex, saline control, 8 hr


title: PFC_0hr_treated_7

description:
microRNA
Replicate 7
PFC-0hr-etoh-57

source_name: prefrontal cortex, ethanol vapor treated, 0 hr


title: PFC_0hr_treated_8

description:
microRNA
Replicate 8
PFC-0hr-etoh-65


title: PFC_8hr_control_6

description:
microRNA
Replicate 6
PFC-8hr-ctrl-52


title: PFC_8hr_control_7

description:
microRNA
Replicate 7
PFC-8hr-ctrl-60


title: PFC_8hr_control_4

description:
microRNA
Replicate 4
PFC-8hr-ctrl-36


title: PFC_8hr_treated_1

description:
microRNA
Replicate 1
PFC-8hr-etoh-3


title: PFC_8hr_control_5

description:
microRNA
Replicate 5
PFC-8hr-ctrl-44


title: PFC_8hr_control_2

description:
microRNA
Replicate 2
PFC-8hr-ctrl-12


title: PFC_0hr_treated_5

description:
microRNA
Replicate 5
PFC-0hr-etoh-39


title: PFC_0hr_treated_4

description:
microRNA
Replicate 4
PFC-0hr-etoh-31


title: PFC_8hr_control_1

description:
microRNA
Replicate 1
PFC-8hr-ctrl-10


title: PFC_0hr_treated_3

description:
microRNA
Replicate 3
PFC-0hr-etoh-15


title: PFC_0hr_treated_1

description:
microRNA
Replicate 1
PFC-0hr-etoh-1


title: PFC_0hr_treated_2

description:
microRNA
Replicate 2
PFC-0hr-etoh-9


title: PFC_0hr_control_5

description:
microRNA
Replicate 5
PFC-0hr-ctrl-42

source_name: prefrontal cortex, saline control, 0 hr


title: PFC_0hr_control_7

description:
microRNA
Replicate 7
PFC-0hr-ctrl-58


title: PFC_0hr_control_8

description:
microRNA
Replicate 8
PFC-0hr-ctrl-66


title: PFC_8hr_control_8

description:
microRNA
Replicate 8
PFC-8hr-ctrl-68


title: PFC_0hr_control_3

description:
microRNA
Replicate 3
PFC-0hr-ctrl-26


title: PFC_0hr_control_2

description:
microRNA
Replicate 2
PFC-0hr-ctrl-20


title: PFC_0hr_treated_6

description:
microRNA
Replicate 6
PFC-0hr-etoh-47


title: NAC_120hr_treated_5

description:
microRNA
Replicate 5
Nac-120hr-etoh-45

source_name: nucleus accumbens, ethanol vapor treated, 120 hr

value: nucleus accumbens


title: NAC_120hr_treated_7

description:
microRNA
Replicate 7
Nac-120hr-etoh-63


title: PFC_0hr_control_1

description:
microRNA
Replicate 1
PFC-0hr-ctrl-18


title: NAC_120hr_treated_4

description:
microRNA
Replicate 4
Nac-120hr-etoh-37


title: NAC_120hr_treated_3

description:
microRNA
Replicate 3
Nac-120hr-etoh-25


title: NAC_120hr_treated_1

description:
microRNA
Replicate 1
Nac-120hr-etoh-7


title: NAC_120hr_treated_2

description:
microRNA
Replicate 2
Nac-120hr-etoh-23


title: NAC_120hr_treated_6

description:
microRNA
Replicate 6
Nac-120hr-etoh-55


title: NAC_120hr_control_8

description:
microRNA
Replicate 8
Nac-120hr-ctrl-72

source_name: nucleus accumbens, saline control, 120 hr


title: NAC_120hr_control_3

description:
microRNA
Replicate 3
Nac-120hr-ctrl-24


title: NAC_120hr_control_4

description:
microRNA
Replicate 4
Nac-120hr-ctrl-32


title: NAC_120hr_control_6

description:
microRNA
Replicate 6
Nac-120hr-ctrl-56


title: NAC_120hr_control_5

description:
microRNA
Replicate 5
Nac-120hr-ctrl-48


title: NAC_120hr_control_1

description:
microRNA
Replicate 1
Nac-120hr-ctrl-8


title: NAC_120hr_control_2

description:
microRNA
Replicate 2
Nac-120hr-ctrl-16


title: NAC_8hr_treated_8

description:
microRNA
Replicate 8
Nac-8hr-etoh-67

source_name: nucleus accumbens, ethanol vapor treated, 8 hr


title: NAC_8hr_treated_6

description:
microRNA
Replicate 6
Nac-8hr-etoh-49


title: NAC_8hr_treated_7

description:
microRNA
Replicate 7
Nac-8hr-etoh-59


title: PFC_0hr_control_4

description:
microRNA
Replicate 4
PFC-0hr-ctrl-34


title: NAC_8hr_treated_5

description:
microRNA
Replicate 5
Nac-8hr-etoh-41


title: NAC_8hr_treated_2

description:
microRNA
Replicate 2
Nac-8hr-etoh-11


title: NAC_120hr_treated_8

description:
microRNA
Replicate 8
Nac-120hr-etoh-71


title: NAC_8hr_treated_3

description:
microRNA
Replicate 3
Nac-8hr-etoh-19


title: Doxorubicin 4 (heart)

description:
Sample name: SAMPLE 9
replicate 4

source_name: heart

value: heart

value: 8-10 weeks


title: NAC_8hr_treated_4

description:
microRNA
Replicate 4
Nac-8hr-etoh-33


title: NAC_8hr_treated_1

description:
microRNA
Replicate 1
Nac-8hr-etoh-3


title: NAC_8hr_control_6

description:
microRNA
Replicate 6
Nac-8hr-ctrl-52

source_name: nucleus accumbens, saline control, 8 hr


title: NAC_8hr_control_4

description:
microRNA
Replicate 4
Nac-8hr-ctrl-36


title: Doxorubicin 2 (heart)

description:
Sample name: SAMPLE 7
replicate 2


title: NAC_8hr_control_5

description:
microRNA
Replicate 5
Nac-8hr-ctrl-44


title: NAC_8hr_control_8

description:
microRNA
Replicate 8
Nac-8hr-ctrl-68


title: NAC_120hr_control_7

description:
microRNA
Replicate 7
Nac-120hr-ctrl-64


title: NAC_8hr_control_3

description:
microRNA
Replicate 3
Nac-8hr-ctrl-28


title: NAC_0hr_control_8

description:
microRNA
Replicate 8
Nac-0hr-ctrl-66

source_name: nucleus accumbens, saline control, 0 hr


title: NAC_0hr_control_7

description:
microRNA
Replicate 7
Nac-0hr-ctrl-58


title: NAC_0hr_treated_1

description:
microRNA
Replicate 1
Nac-0hr-etoh-1

source_name: nucleus accumbens, ethanol vapor treated, 0 hr


title: NAC_0hr_treated_3

description:
microRNA
Replicate 3
Nac-0hr-etoh-15


title: NAC_8hr_control_7

description:
microRNA
Replicate 7
Nac-8hr-ctrl-60


title: NAC_0hr_treated_7

description:
microRNA
Replicate 7
Nac-0hr-etoh-57


title: NAC_0hr_treated_8

description:
microRNA
Replicate 8
Nac-0hr-etoh-65


title: NAC_0hr_treated_6

description:
microRNA
Replicate 6
Nac-0hr-etoh-47


title: NAC_0hr_treated_5

description:
microRNA
Replicate 5
Nac-0hr-etoh-39


title: NAC_0hr_control_6

description:
microRNA
Replicate 6
Nac-0hr-ctrl-50


title: NAC_0hr_control_5

description:
microRNA
Replicate 5
Nac-0hr-ctrl-42


title: NAC_0hr_control_3

description:
microRNA
Replicate 3
Nac-0hr-ctrl-26


title: AMY_120hr_treated_6

description:
microRNA
Replicate 6
Amy-120hr-etoh-55

source_name: amygdala, ethanol vapor treated, 120 hr

value: amygdala


title: AMY_120hr_treated_7

description:
microRNA
Replicate 7
Amy-120hr-etoh-63


title: NAC_0hr_control_4

description:
microRNA
Replicate 4
Nac-0hr-ctrl-34


title: AMY_120hr_treated_8

description:
microRNA
Replicate 8
Amy-120hr-etoh-71


title: NAC_0hr_control_1

description:
microRNA
Replicate 1
Nac-0hr-ctrl-18


title: NAC_0hr_control_2

description:
microRNA
Replicate 2
Nac-0hr-ctrl-20


title: AMY_120hr_treated_5

description:
microRNA
Replicate 5
Amy-120hr-etoh-45


title: AMY_120hr_treated_2

description:
microRNA
Replicate 2
Amy-120hr-etoh-23


title: AMY_120hr_treated_3

description:
microRNA
Replicate 3
Amy-120hr-etoh-25


title: NAC_0hr_treated_4

description:
microRNA
Replicate 4
Nac-0hr-etoh-31


title: AMY_120hr_control_8

description:
microRNA
Replicate 8
Amy-120hr-ctrl-72

source_name: amygdala, saline control, 120 hr


title: AMY_120hr_control_4

description:
microRNA
Replicate 4
Amy-120hr-ctrl-32


title: AMY_120hr_control_6

description:
microRNA
Replicate 6
Amy-120hr-ctrl-56


title: AMY_120hr_control_2

description:
microRNA
Replicate 2
Amy-120hr-ctrl-16


title: AMY_120hr_control_5

description:
microRNA
Replicate 5
Amy-120hr-ctrl-48


title: AMY_120hr_control_3

description:
microRNA
Replicate 3
Amy-120hr-ctrl-24


title: AMY_120hr_control_1

description:
microRNA
Replicate 1
Amy-120hr-ctrl-8


title: AMY_8hr_treated_7

description:
microRNA
Replicate 7
Amy-8hr-etoh-59

source_name: amygdala, ethanol vapor treated, 8 hr


title: AMY_8hr_treated_5

description:
microRNA
Replicate 5
Amy-8hr-etoh-41


title: AMY_8hr_treated_3

description:
microRNA
Replicate 3
Amy-8hr-etoh-19


title: AMY_8hr_treated_4

description:
microRNA
Replicate 4
Amy-8hr-etoh-33


title: AMY_8hr_treated_8

description:
microRNA
Replicate 8
Amy-8hr-etoh-67


title: AMY_8hr_treated_6

description:
microRNA
Replicate 6
Amy-8hr-etoh-49


title: AMY_8hr_treated_1

description:
microRNA
Replicate 1
Amy-8hr-etoh-3


title: AMY_8hr_control_5

description:
microRNA
Replicate 5
Amy-8hr-ctrl-44

source_name: amygdala, saline control, 8 hr


title: AMY_120hr_treated_4

description:
microRNA
Replicate 4
Amy-120hr-etoh-37


title: AMY_120hr_treated_1

description:
microRNA
Replicate 1
Amy-120hr-etoh-7


title: AMY_8hr_control_3

description:
microRNA
Replicate 3
Amy-8hr-ctrl-28


title: AMY_8hr_treated_2

description:
microRNA
Replicate 2
Amy-8hr-etoh-11


title: AMY_8hr_control_2

description:
microRNA
Replicate 2
Amy-8hr-ctrl-12


title: AMY_8hr_control_1

description:
microRNA
Replicate 1
Amy-8hr-ctrl-10


title: AMY_8hr_control_4

description:
microRNA
Replicate 4
Amy-8hr-ctrl-36


title: AMY_8hr_control_6

description:
microRNA
Replicate 6
Amy-8hr-ctrl-52


title: AMY_8hr_control_7

description:
microRNA
Replicate 7
Amy-8hr-ctrl-60


title: AMY_0hr_treated_8

description:
microRNA
Replicate 8
Amy-0hr-etoh-65

source_name: amygdala, ethanol vapor treated, 0 hr


title: AMY_8hr_control_8

description:
microRNA
Replicate 8
Amy-8hr-ctrl-68


title: AMY_0hr_treated_7

description:
microRNA
Replicate 7
Amy-0hr-etoh-57


title: AMY_0hr_treated_5

description:
microRNA
Replicate 5
Amy-0hr-etoh-39


title: AMY_0hr_treated_6

description:
microRNA
Replicate 6
Amy-0hr-etoh-47


title: AMY_0hr_treated_4

description:
microRNA
Replicate 4
Amy-0hr-etoh-31


title: AMY_0hr_treated_2

description:
microRNA
Replicate 2
Amy-0hr-etoh-9


title: AMY_0hr_treated_1

description:
microRNA
Replicate 1
Amy-0hr-etoh-1


title: AMY_0hr_control_7

description:
microRNA
Replicate 7
Amy-0hr-ctrl-58

source_name: amygdala, saline control, 0 hr


title: AMY_0hr_control_8

description:
microRNA
Replicate 8
Amy-0hr-ctrl-66


title: AMY_0hr_control_4

description:
microRNA
Replicate 4
Amy-0hr-ctrl-34


title: AMY_0hr_control_6

description:
microRNA
Replicate 6
Amy-0hr-ctrl-50


title: AMY_0hr_control_3

description:
microRNA
Replicate 3
Amy-0hr-ctrl-26


title: AMY_0hr_control_2

description:
microRNA
Replicate 2
Amy-0hr-ctrl-20


title: AMY_0hr_control_1

description:
microRNA
Replicate 1
Amy-0hr-ctrl-18


title: AMY_0hr_treated_3

description:
microRNA
Replicate 3
Amy-0hr-etoh-15


title: AMY_0hr_control_5

description:
microRNA
Replicate 5
Amy-0hr-ctrl-42


title: CSCC_CTpnz-TNFAIP3_W39-1-1-O.03

city: Seattle

first: Ralph

middle: B.

last: Puchalski

state: WA

address: 550 17th Ave., Suite 570

institute: Swedish Neuroscience Institute

description:
Perinecrotic zone sampled by high expression of gene TNFAIP3
304703657

data_processing:
(RNA-Seq Data Alignment) The data generation, collection, alignment, and normalization is described in detail online at glioblastoma.alleninstitute.org  in the Documentation tab.  Raw read (fastq) files were aligned to the hg19 human genome sequence (Meyer et al., 2013) with the RefSeq transcriptome version 54 (downloaded 8/25/2012 and updated by removing duplicate gene entries from the gtf reference file for consistency with the LIMS). For alignment, Illumina sequencing adapters were clipped from the reads using the fastqMCF program (Aronesty, 2011).
After clipping, the paired-end reads were mapped using RNA-Seq by Expectation-Maximization (RSEM) (Li et al., 2010) using default settings except for two mismatch parameters: bowtie-e (set to 500) and bowtie-m (set to 100). RSEM aligns reads to known isoforms and then calculates gene expression as the sum of isoform expression for a given gene, assigning ambiguous reads to multiple isoforms using a maximum likelihood statistical model. Reads that did not map to the transcriptome were then aligned to the hg19 genome sequence using Bowtie with default settings (Langmead et al., 2009). Reads that mapped to neither the transcriptome with RSEM nor to the genome with Bowtie were mapped against the ERCC sequences (in this project as a negative control).
The final results files included quantification of the mapped reads (raw read counts, FPKM, and TPM values for the transcriptome-mapped reads, chromosome-wide counts for the genomic-mapped reads), BAM files including both transcriptome and genome-mapped reads, and fastq files for the unmapped reads. Anonymized BAM files (where sequence-level information has been removed) and gene-level quantification (TPM, FPKM, and number of reads) are available as part of the resource (see Download tab).  Resulting FPKM values (normalized for gene length and sequencing depth) used for the analyses of this paper were further adjusted for the total transcript count using TbT normalization as described below.
(RNA-Seq Data Normalization) In the Allen Human Brain Atlas, analysis of the RNA-Seq data showed minimal process batch effects but improvements in variability after normalization could be made (Miller et al., 2014), and therefore a comparable post-hoc data normalization strategy was used for this project. Gene expression values were summarized as transcripts per million (TPM) and fragments per kilobase per million (FPKM), as described above, both of which normalize read counts by gene length and for the total number of reads in slightly different ways.
In the manuscript (as well as for the heatmaps shown on the website), the FPKM data matrix was further adjusted for the total transcript count using TbT normalization (Kadota et al., 2012), which scales each sample based on the summed expression of all genes that are not differentially expressed. FPKM values were TbT normalized in linear space, with the differential expression vector defined as TRUE if a sample was from cellular tumor and FALSE otherwise.
Sample data was then scaled such that the total log2(FPKM) across the entire data set remained unchanged after normalization. The result of this step was that expression levels for all genes in a particular sample were multiplied by a scalar value close to 1 (in most cases between 0.7-1.3).
Genome_build: GRCh37.p5
Supplementary_files_format_and_content: fpkm_table.csv contains the (row, column) matrix of fpkm values obtained for each (gene, sample).  The first row contains the sample unique identifiers (rna_well_id).  The first column contains the gene unique identifiers (gene_id).
Supplementary_files_format_and_content: columns-samples.csv  contains information about the samples profiled with RNA sequencing:  (1) tumor_id, block_id, specimen_id and corresponding names:  Specimen from which the sample was dissected and the specimen's parent block and tumor.  (2) rna_well_id:  Unique identifier of the sample.  (3) polygon_id:  Unique identifier of an avg_graphic_object that outlines where the sample was cut from.  (4) structure_id, structure_abbreviation, structure_color, structure_name:  Label that groups samples obtained from laser micro-dissected anatomic structures or putative cancer stem cell clusters.
Supplementary_files_format_and_content: rows-genes.csv contains information about the genes for which fpkm values were calculated. (1) gene_id:  Unique identifier for the gene. (2) chromosome:  Chromosome associated with the gene.  (3) gene_entrez_id, gene_symbol, gene_name:  entrez_id, NCBI symbol, and name of the gene.

source_name: glioblastoma

extract_protocol:
(Laser Microdissection)  In preparation for laser microdissection, PEN slides were removed from -80°C and quickly processed through cresyl violet and Eosin to lightly stain the tissue. Sections were fixed in ice-cold 70% ethanol for 30 seconds, washed for 15 seconds in nuclease-free water, stained with 0.7% cresyl violet in 0.05% NaOAc, pH 3.4 for 4 minutes, rinsed in nuclease-free water for 10 seconds, 15 seconds in 70% ethanol, followed by 2 dips in 0.25% Eosin, and 20 seconds each in 95%, 100%, and 100% ethanol rinses. Slides were air-dried for 2 minutes and desiccated by vacuum for 1 hour at room temperature, then frozen at -80°C until microdissection. For both RNA-Seq studies, cresyl violet/Eosin-stained sections mounted on PEN membranes were microdissected while visually referring to H&E-stained sections that had been curated to identify matched target regions. For the Cancer Stem Cells RNA-Seq study, ISH reference gene expression patterns informed the curation of the H&E-stained sections. A Leica LMD6000 (Leica Microsystems, Inc., Bannockburn, IL) was used for microdissection, and the system included an upright research microscope fitted with a diode laser and a CCD camera to acquire live images of slides. The scope and laser were controlled via a dedicated computer running Leica LMD software (v.6.6.2.3552).  (RNA Isolation and RNA Integrity)  Microdissected tissue was collected directly into RLT buffer from the RNeasy Micro PLUS kit (Qiagen Inc., Valencia, CA) with 1:100 beta-mercaptoethanol diluation, per manufacturer’s instructions. Samples were volume-adjusted with water to 75μl, vortexed, centrifuged, and frozen at -80°C. RNA samples, after following the manufacturer’s directions, were eluted in 14μl, and 1μl was run on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) using the Pico assay. Due to low sample volume and incompatibility of the eluent with the Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE), samples were quantitated using the Bioanalyzer concentration output. This was done by running a 1ng/μl RNA standard on the same Pico chip and then dividing the sample concentration output by the output of the standard concentration. The average RNA Integrity Number (RIN) of all passed samples was 7.1. Samples were failed when the Bioanalyzer traces showed degraded 18S and 28S bands, with RINs typically lower than 4.5 failing.
In most cases, 5ng of total RNA was used as the input amount for the library prep.  5ng total RNA was used as input into CloneTech SMARTer Ultra Low Input RNA Kit for Illumina Sequencing-HV (# 634820). 12 PCR cycles were used for amplification as suggested in the manufacturer’s instructions (ClonTech SMARTer Kit Manual 120213). The Modified Nextera DNA sample preparation was used after step V.B of the CloneTech SMARTer kit, instead of Covaris shearing and instead of step VI in the CloneTech SMARTer kit. RNA Sequencing was done on Illumina HiSeq 2000, producing approximately 30M 50bp paired-end clusters per sample. In most cases, 5 samples per lane were run.  RNA-Seq libraries were assessed for quality by yield and visual inspection of the presence, quality, and size of cDNA product on a Bioanalyzer.  Initially, 11 samples failed (7 for no product and 4 for majority of product <500bp) the quality control criteria.  However, upon a second attempt at synthesis, all 275 samples passed.  One of the 275 samples was failed for low inter-array-correlation (IAC) and was excluded from the data set.  The average concentration of samples that passed the criteria was 1582 pM.

tag: study

value: cancer stem cell clusters

tag: structure acronym

tag: rin

tag: gene-level raw fpkm profile  file_download_link


title: CSCC_CTpnz-TNFAIP3_W36-1-1-E.03

description:
Perinecrotic zone sampled by high expression of gene TNFAIP3
303748344


title: CSCC_CTpnz-TNFAIP3_W4-1-1-C.2.03

description:
Perinecrotic zone sampled by high expression of gene TNFAIP3
304357601


title: CSCC_CTpnz-PROM1_W29-1-1-F.03

description:
Perinecrotic zone sampled by high expression of gene PROM1
304477579


title: CSCC_CTpnz-PI3_W6-1-1-C.2.06

description:
Perinecrotic zone sampled by high expression of gene PI3
305273042


title: CSCC_CT-POSTN_W20-2-1-L.03

description:
Cellular Tumor sampled by high expression of gene POSTN
304950407

value: CT-POSTN


title: CSCC_CTpnz-PROM1_W10-1-1-E.2.03

description:
Perinecrotic zone sampled by high expression of gene PROM1
306124456


title: CSCC_CTpnz-PROM1_W54-1-1-F.03

description:
Perinecrotic zone sampled by high expression of gene PROM1
305461072


title: CSCC_CTpnz-TNFAIP3_W10-1-1-E.2.03

description:
Perinecrotic zone sampled by high expression of gene TNFAIP3
306124458


title: CSCC_CT-POSTN_W34-1-1-G.03

description:
Cellular Tumor sampled by high expression of gene POSTN
305272794


title: CSCC_CT-POSTN_W43-1-1-J.03

description:
Cellular Tumor sampled by high expression of gene POSTN
304950259


title: CSCC_CTpnz-PROM1_W38-1-1-I.03

description:
Perinecrotic zone sampled by high expression of gene PROM1
306124482


title: wildtype mouse c antrum at 4 weeks old

city: Chapel Hill

first: Di

last: Wu

state: North Carolina

address: 385 S. Columbia Street, CB#7455

institute: University of North Carolina

description: miRNA expression before tumor initiation

hyb_protocol: Affymetrix miRNA 2.0. follow the manufacturer's instructions.

data_processing:
The Affymetrix miRNA 2.0 microarray contains perfect match probes (PM) only.
RMA probe set summarized value.  The normalized data is from robust Normexp-by-control background correction, cyclic loess normalization (using 220 spike.in probes as control) and RMA summarization. The version R version 3.2.3 was used. The raw CEL microarray files were read using the ReadAffy function in the Affy package

source_name: mouse antrum, WT

growth_protocol: no

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

treatment_protocol: no

value: WT

value: mixed

value: 4 weeks old

value: antrum


title: wildtype mouse d antrum at 4 weeks old

scan_protocol: Affymetrix miRNA 2.0. follow the manufacturer's instructions.


title: gp130F/F mouse a antrum at 4 weeks old

source_name: mouse antrum, gp130F/F

label_protocol: Affymetrix miRNA 2.0. follow the manufacturer's instructions.

value: FF


title: gp130F/F mouse b antrum at 4 weeks old


title: CD49d+PMN3

city: Milwaukee

first: Dorothy

last: Cheung

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: Gene expression data from CD49d expressing neutrophils in BAL of SeV infected mice

hyb_protocol: The Affymetrix GeneChip Mouse Genome 430 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor.

source_name: Neutrophils from BAL on day 3 post-inoculation with SeV

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

treatment_protocol: Cells from BAL of mice inoculated with SeV were pelleted, washed, and stained with mAb to Gr-1 and CD49d.  Cells were than flow-sorted into either Gr-1+/CD49d+ or Gr-1+/CD49d- fractions.

tag: cd49d expression

value: Positive

value: neutrophil

tag: cell source

value: Bronchial alveolar lavage


title: gp130F/F mouse d antrum at 4 weeks old


title: wildtype mouse e antrum at 4 weeks old


title: gp130F/F mouse e antrum at 4 weeks old


title: wildtype mouse a antrum at 4 weeks old


title: CD49d+PMN1


title: CD49d+PMN2


title: CD49d-PMN2

description: Gene expression data from CD49d non-expressing neutrophils in BAL of SeV infected mice

value: Negative


title: CD49d-PMN1


title: CD49d-PMN3


title: CSCC_CTpnz-PI3_W4-1-1-A.1.03

description:
Perinecrotic zone sampled by high expression of gene PI3
305952556


title: CSCC_CTpnz-PI3_W43-1-1-J.03

description:
Perinecrotic zone sampled by high expression of gene PI3
304950415


title: CSCC_CTpnz-PI3_W34-1-1-D.03

description:
Perinecrotic zone sampled by high expression of gene PI3
305273036


title: CSCC_CTpnz-PI3_W22-2-1-A.03

description:
Perinecrotic zone sampled by high expression of gene PI3
305461117


title: CSCC_CTpnz-PI3_W21-1-1-B.06

description:
Perinecrotic zone sampled by high expression of gene PI3
305461105


title: CSCC_CTpnz-PI3_W12-1-1-D.2.05

description:
Perinecrotic zone sampled by high expression of gene PI3
304357522


title: CSCC_CTpnz-PDPN_W22-2-1-A.03

description:
Perinecrotic zone sampled by high expression of gene PDPN
305461078

value: CTpnz-PDPN


title: CSCC_CTpnz-PDPN_W3-1-1-E.1.04

description:
Perinecrotic zone sampled by high expression of gene PDPN
306124420


title: CSCC_CTpnz-ID1_W33-1-1-F.03

description:
Perinecrotic zone sampled by high expression of gene ID1
305952568


title: CSCC_CTpnz-DANCR_W43-1-1-I.03

description:
Perinecrotic zone sampled by high expression of gene DANCR
305405300

value: CTpnz-DANCR


title: CSCC_CTpnz-PDPN_W1-1-2-E.1.03

description:
Perinecrotic zone sampled by high expression of gene PDPN
304950322


title: CSCC_CTpnz-PI3_W22-1-1-H.03

description:
Perinecrotic zone sampled by high expression of gene PI3
305272998


title: CSCC_CTpnz-ID1_W48-1-1-M.03

description:
Perinecrotic zone sampled by high expression of gene ID1
304950328


title: CSCC_CTpnz-IGFBP2_W10-1-1-I.2.03

description:
Perinecrotic zone sampled by high expression of gene IGFBP2
305952562


title: CSCC_CTpnz-CD44_W29-1-1-G.03

description:
Perinecrotic zone sampled by high expression of gene CD44
305405294


title: CSCC_CTpan-TNFAIP3_W11-1-1-E.2.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene TNFAIP3
303748266


title: CSCC_CTpan-TNFAIP3_W34-1-1-D.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene TNFAIP3
305273038


title: CSCC_CT-PI3_W10-1-1-I.2.03

description:
Cellular Tumor sampled by high expression of gene PI3
305952564


title: CSCC_CT-PDGFRA_W20-2-1-H.03

description:
Cellular Tumor sampled by high expression of gene PDGFRA
304950372

value: CT-PDGFRA


title: CSCC_CTpan-TNFAIP3_W3-1-1-B.2.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene TNFAIP3
303748254


title: CSCC_CT-PDPN_W40-1-1-I.03

description:
Cellular Tumor sampled by high expression of gene PDPN
304357563

value: CT-PDPN


title: CSCC_CTpan-PDPN_W7-1-1-A.2.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene PDPN
304950265

value: CTpan-PDPN


title: CSCC_CTpan-PROM1_W9-1-1-C.2.04

description:
Pseudopalisading cells around necrosis sampled by high expression of gene PROM1
306124450


title: CSCC_CTpan-PROM1_W20-2-1-I.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene PROM1
304950376


title: CSCC_CT-PI3_W12-1-1-D.2.05

description:
Cellular Tumor sampled by high expression of gene PI3
305461109


title: CSCC_CTpan-PI3_W16-1-1-B.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene PI3
303748332


title: CSCC_CTpan-PDPN_W27-2-1-I.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene PDPN
305461113


title: CSCC_CTpan-MYC_W27-2-1-D.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene MYC
305272808

value: CTpan-MYC


title: CSCC_CTpnz-PDPN_W42-1-1-J.03

description:
Perinecrotic zone sampled by high expression of gene PDPN
305272800

value: cancer stem cell clusters


title: CSCC_CTpan-PI3_W42-1-1-J.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene PI3
305272802


title: CSCC_CTpan-MYC_W22-1-1-H.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene MYC
305272996


title: CSCC_CTpan-ID2_W53-1-1-B.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene ID2
304357514


title: CSCC_CTpan-ID2_W32-1-1-E.04

description:
Pseudopalisading cells around necrosis sampled by high expression of gene ID2
306124412


title: CSCC_CTpan-ID2_W8-1-1-A.1.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene ID2
303748262


title: CSCC_CTpan-ID2_W12-1-1-D.2.05

description:
Pseudopalisading cells around necrosis sampled by high expression of gene ID2
304357520


title: CSCC_CTpan-PDPN_W2-1-1-K.2.03

description:
Pseudopalisading cells around necrosis sampled by high expression of gene PDPN
304357593


title: CSCC_CTmvp-TGFBR2_W31-1-1-E.03

description:
Microvascular proliferation sampled by high expression of gene TGFBR2
305273030


title: CSCC_CT-NOS2_W53-1-1-C.03

description:
Cellular Tumor sampled by high expression of gene NOS2
305405306


title: CSCC_CT-NOS2_W34-1-1-D.03

description:
Cellular Tumor sampled by high expression of gene NOS2
305273034


title: CSCC_CTmvp-ITGA6_W16-1-1-D.03

description:
Microvascular proliferation sampled by high expression of gene ITGA6
304477571


title: CSCC_CT-MET_W53-1-1-B.03

description:
Cellular Tumor sampled by high expression of gene MET
304357516

value: CT-MET


title: CSCC_CTmvp-TGFBR2_W29-1-1-B.03

description:
Microvascular proliferation sampled by high expression of gene TGFBR2
304357587


title: CSCC_CT-MET_W53-1-1-A.03

description:
Cellular Tumor sampled by high expression of gene MET
304357569


title: CSCC_CT-IGFBP2_W21-1-1-E.03

description:
Cellular Tumor sampled by high expression of gene IGFBP2
303748340


title: CSCC_CTpnz-MYC_W29-1-1-G.03

description:
Perinecrotic zone sampled by high expression of gene MYC
305405296

value: CTpnz-MYC


title: CSCC_CT-IGFBP2_W31-1-1-E.03

description:
Cellular Tumor sampled by high expression of gene IGFBP2
305273028


title: CSCC_CT-ID1_W28-1-1-A.03

description:
Cellular Tumor sampled by high expression of gene ID1
304477575


title: CSCC_CT-HIF1A_W28-1-1-N.03

description:
Cellular Tumor sampled by high expression of gene HIF1A
306124408


title: CSCC_CT-ID1_W7-1-1-A.2.03

description:
Cellular Tumor sampled by high expression of gene ID1
304950263


title: CSCC_CT-HIF1A_W27-2-1-I.03

description:
Cellular Tumor sampled by high expression of gene HIF1A
305461111


title: CSCC_CThbv-TGFBR2_W48-1-1-M.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
304950330


title: CSCC_CThbv-TGFBR2_W53-1-1-A.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
304357571


title: CSCC_CThbv-TGFBR2_W34-1-1-G.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
305272796