title: PMv_right_3months_2

status: Public on Mar 31 2018

type: RNA

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505B with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The gene expression data were analyzed using GeneSpring GX 13 software (Agilent Technologies), and the signal intensity of each probe was normalized by a percentile shift in which each value was divided by the 75th percentile of all values in its array.

molecule: total RNA

organism: Macaca mulatta

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The tissue samples were homogenized using a conventional rotor-stator homogenizer, and total RNA was extracted from the samples using the RNeasy Lipid Tissue Mini Kit (Qiagen; Hilden, Germany). The RNA was treated with DNase 1 (Qiagen) and cleaned up using either the Qiagen RNeasy mini kit or Qiagen RNeasy MinElute kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed using ultraviolet spectrophotometry and the Agilent 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA, USA). All RNA samples had a 260/280 ratio between 1.7 and 1.9, a 28S:18S ratio of 1.5 or higher, and a RNA Integrity Number between 8.0 and 9.5.

tag: tissue

value: cerebral cortex

tag: tissue region

value: ventral premotor cortex (PMv)

tag: side

value: right

tag: time after lesioning

value: 3 months


title: PMv_left_2weeks_3

value: left

value: 2 weeks


title: PMv_right_3months_3


title: PMv_right_2weeks_2


title: PMv_left_3months_2


title: PMv_right_naive_3

source_name: PMv_right_naive, replicate 3

value: naïve


title: PMv_left_naive_3

source_name: PMv_left_naive, replicate 3


title: PMv_right_naive_2

source_name: PMv_right_naive, replicate 2


title: PMv_left_3months_3


title: PMv_right_naive_1

source_name: PMv_right_naive, replicate 1


title: PMv_right_3months_1


title: PMv_left_2weeks_1


title: PMv_right_2weeks_3


title: PMv_left_2weeks_2


title: PMd_right_3months_2

value: dorsal premotor cortex (PMd)


title: PMv_right_2weeks_1


title: PMd_right_3months_3


title: PMv_left_3months_1


title: PMv_left_naive_2

source_name: PMv_left_naive, replicate 2


title: PMd_right_3months_1


title: PMv_left_naive_1

source_name: PMv_left_naive, replicate 1


title: PMd_right_naive_3

source_name: PMd_right_naive, replicate 3


title: PMd_right_2weeks_2


title: PMd_right_2weeks_3


title: PMd_right_2weeks_1


title: PMd_right_naive_2

source_name: PMd_right_naive, replicate 2


title: PMd_left_2weeks_3


title: PMd_left_3months_1


title: PMd_left_naive_1

source_name: PMd_left_naive, replicate 1


title: PMd_left_naive_3

source_name: PMd_left_naive, replicate 3


title: M1_right_3months_1

value: primary motor cortex (M1)


title: PMd_left_2weeks_2


title: M1_right_3months_2


title: PMd_right_naive_1

source_name: PMd_right_naive, replicate 1


title: PMd_left_3months_2


title: M1_right_2weeks_2


title: PMd_left_naive_2

source_name: PMd_left_naive, replicate 2


title: M1_right_3months_3


title: PMd_left_3months_3


title: M1_right_naive_3

source_name: M1_right_naive, replicate 3


title: PMd_left_2weeks_1


title: M1_right_2weeks_3


title: M1_right_naive_1

source_name: M1_right_naive, replicate 1


title: M1_left_3months_2


title: M1_right_naive_2

source_name: M1_right_naive, replicate 2


title: M1_left_3months_3


title: M1_left_naive_3

source_name: M1_left_naive, replicate 3


title: M1_left_2weeks_3


title: M1_left_2weeks_2


title: M1_left_2weeks_1


title: M1_right_2weeks_1


title: M1_left_naive_2

source_name: M1_left_naive, replicate 2


title: M1_left_3months_1


title: formalin-fixed paraffin-embedded liver tissue: LC: B06.22186

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalization with Bioconductor v3.2

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using the RNeasy FFPE KIT (QIAGEN GmgH, Hilden, Germany) according to manufacturer’s instructions. Briefly, punch biopsies, 0.6 mm in diameter, were obtained from each tissue block and were placed in a tube containing 1 ml xylene. Immediately after the 100% ethanol extraction step, an additional 70% ethanol extraction was performed. Proteinase K digestions were at 55uC for 35 min followed by 80uC for 25 min. Genomic DNA was removed by centrifugation in gDNA Eliminator spin columns at 8000 x g for 1 min, after which a volume of 1400 ml ethanol was added to the flow-through fraction, resulting in three passes through the RNeasy MinElute spin column. The first Buffer RPE wash was performed at 8000 x g for 1 min and prior to the final elution the dried spin column membranes were incubated in 30 ml RNase-free water for 10 min at room temperature before centrifugation.

tag: liver group

value: LC

value: liver


title: formalin-fixed paraffin-embedded liver tissue: LC: B05.22119


title: formalin-fixed paraffin-embedded liver tissue: LC: B06.26147


title: formalin-fixed paraffin-embedded liver tissue: LC: B05.18290


title: formalin-fixed paraffin-embedded liver tissue: LC: B05.18413


title: formalin-fixed paraffin-embedded liver tissue: LC: B07.34757


title: formalin-fixed paraffin-embedded liver tissue: LC: B10.16034


title: formalin-fixed paraffin-embedded liver tissue: LC: B03.4919


title: formalin-fixed paraffin-embedded liver tissue: LC: B05.24724


title: formalin-fixed paraffin-embedded liver tissue: LC: B08.17129


title: formalin-fixed paraffin-embedded liver tissue: LC: B08.25497


title: formalin-fixed paraffin-embedded liver tissue: LC: B06.8359


title: formalin-fixed paraffin-embedded liver tissue: LC: B03.3196


title: formalin-fixed paraffin-embedded liver tissue: LC: B09.33274


title: M1_left_naive_1

source_name: M1_left_naive, replicate 1


title: formalin-fixed paraffin-embedded liver tissue: LC: B06.17686


title: formalin-fixed paraffin-embedded liver tissue: LC: B02.18232


title: formalin-fixed paraffin-embedded liver tissue: LC: B06.24584


title: formalin-fixed paraffin-embedded liver tissue: LC: B04.10782


title: formalin-fixed paraffin-embedded liver tissue: LC: B08.11141


title: formalin-fixed paraffin-embedded liver tissue: LC: B08.25781


title: formalin-fixed paraffin-embedded liver tissue: LC: B06.10258


title: formalin-fixed paraffin-embedded liver tissue: LC: B09.14870


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B10.17171

value: INCPH


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B10.17668


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B07.33564


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.28015


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B05.25728


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.13121


title: patient 19, N-MSCs, passage 5

city: LAUSANNE

first: Mathieu

last: Quinodoz

state: Vaud

address: Rue du Bugnon 27

department: DBC

country: Switzerland

institute: Université de Lausanne

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays were hybridized with 2.5mg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007)

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

data_processing: The data were analyzed with Affymetrix Expression Console version v 1.4.1 using Affymetrix default analysis settings and Robust Multi-array Average (RMA) as normalization method.

source_name: N-MSCs_passage 5

label_protocol: 100ng of total RNA were amplified using the WT Expression kit (Invitrogen). The resulting sense cDNA was fragmented using UDG and APE 1 and biotin-labeled with TdT using the GeneChip WT Terminal labeling kit (Affymetrix)

growth_protocol: T- and N-MSCs were isolated respectively from paired lung tumor tissues and normal adjacent tissues removed by surgical resection from lung carcinoma patients at Centre Universitaire Hospitalier Vaudois (CHUV) with the agreement of the Swiss ethic committee (project authorization n° 131/12). Tissues were mechanically disrupted and enzymatically dissociated in IMDM (Gibco) supplemented with Collagenase II and IV (0,5 mg/mL, Gibco) and DNAse (0,1 mg/mL, Roche). The resulting single cell bulk was cultured one night in MSC medium: IMDM+GlutaMAX (Gibco) supplemented with 10% fetal bovine serum (FBS, PAN Biotech), 1% penicillin streptomycin (PS, Gibco), 1% non essential amino acids (NEAA, Gibco) and 10 ng/mL platelet-derived growth factor (PDGF, Prospec). The next day, the whole medium was changed and only adherent cells were kept in culture in MSC medium. Upon reaching 80% confluence, cells were split 1:4 - 1:6 using trypsin-EDTA 0.25 mg/ml (Lonza, USA). At each passage, some cell aliquots were frozen in FBS-DMSO 10% and kept in liquid nitrogen.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNAs were then precipitated 2h at -20°C in isopropanol, washed in EtOH 75% and suspended in H2O.

treatment_protocol: Frozen MSC samples at culture passage 5 or 6 were thawed, washed once in ice-cold IMDM+PS1% and twice in ice-cold PBS1x. Cell pellets were then suspended in Trizol reagent (Ambion, Life Technologies)

tag: subject status

value: lung carcinoma patient

tag: subject id

value: patient 19

tag: cell type

value: mesenchymal stem cells (MSCs)

tag: cell group

value: non tumor-associated MSCs (N-MSCs)

tag: passage

value: passage 5


title: patient 20, N-MSCs, passage 5

value: patient 20


title: patient 21, T-MSCs, passage 5

source_name: T-MSCs_passage 5

value: patient 21

value: tumor-associated MSCs (T-MSCs)


title: patient 21, N-MSCs, passage 5


title: patient 12, T-MSCs, passage 6

source_name: T-MSCs_passage 6

value: patient 12

value: passage 6


title: patient 26, T-MSCs, passage 5

value: patient 26


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B07.4646


title: patient 12, N-MSCs, passage 6

source_name: N-MSCs_passage 6


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.37270


title: patient 20, T-MSCs, passage 5


title: 35S:CCA1 Replicate 2

city: GIFU

first: AYAN

last: SADHUKHAN

state: GIFU

address: 1-1 YANAGIDO

department: APPLIED BIOLOGICAL SCIENCES

institute: GIFU UNIVERSITY

description: 35S:CCA1 Replicate 2

hyb_protocol: 0.825 μg of Cy3- and Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5 per μg cRNA) were fragmented with Gene Expression Hybridization Kit (5188-5242, Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 4 Oligo Microarray (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. 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.

scan_protocol: scanned with a G2505C scanner (software version 6.5) Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature extraction software (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: 5 days-old whole seedlings

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA were prepared from 200 ng of total RNA using the Low Input Quick Amp Labeling kit (5190-2306, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: wild type and transgenic lines were grown in hydroponics in modified MGRL media (Fujiwara et al. 1992) for 5 days at 25°C under a 12-h day (with photon flux density of 40 µmol m-2 s-1) and 12-h night cycle.

extract_protocol: Total RNA extracted using Sepasol following manufacturer's instructions

tag: strain background

tag: genotype

value: wildtype

tag: age

value: day 5

value: Whole seedlings

value: 5 days

value: whole seedlings


title: patient 19, T-MSCs, passage 5


title: patient 16, N-MSCs, passage 5

value: patient 16


title: patient 16, T-MSCs, passage 5

value: lung carcinoma patient


title: 35S:CCA1 Replicate 1

description: 35S:CCA1 Replicate 1


title: patient 26, N-MSCs, passage 5


title: 35S:BBX29 Replicate 2

description: 35S:BBX29 Replicate 2


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B08.3533

value: INCPH

value: liver


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.8409


title: 35S:BBX29 Replicate 1

description: 35S:BBX29 Replicate 1


title: shEZH2 Mac1 Replicate 3

city: Beijing

first: Yi

last: Shengguo

address: No.1 Xi anmen Street

country: China

institute: the first hospital of Peking University

description: Biological replicate 3 of 3. shEZH2-treated Mac1 cells, RNA was extracted 96h post-transfection.

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R. The normalized data were analyzed according to Fold-Change(fold change(abs)>= 2.0 or 1.5 respectively) and Student's t-test(P-value<0.05) to select the differentially expressed genes. foldchange:the ratio ( not logarithm) of normalized intensities between two conditions ; Formula : foldchange=average(power(2,signal(CASE)))/average(power(2,signal(CONTROL))). foldchange (abs):the absolute ratio (not logarithm) of normalized intensities between two conditions ; Formula : if foldchange>1,foldchange(abs)=foldchange,foldchange<1,foldchange(abs)=1/foldchange.

source_name: Mac1-shEZH2 Mac1 cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Mac1 cells with transfection were cultured in RPMI 1640 medium with 10% fetal bovine(Life technology) serum

extract_protocol: Total RNA extracted using EZNA total RNA kit II(Omega)  following manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

value: tumorous T cells in peripheral blood of patients with PCALCL


title: 35S:ERF019 Replicate 2

description: 35S:ERF019 Replicate 2


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.37202


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.33797


title: 35S:ERF019 Replicate 1

description: 35S:ERF019 Replicate 1


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.23736


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B09.23342


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B02.23979


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B07.25678


title: shEZH2 Mac1 Replicate 2

description: Biological replicate 2 of 3. shEZH2-treated Mac1 cells, RNA was extracted 96h post-transfection.


title: Vehicle control Mac1 Replicate 2

description: Biological replicate 2 of 3. Vehicle control Mac1 cells, transfected with empty vector, RNA was extracted 96h post-transfection.

source_name: Mac1-vehicle control transfected Mac1 cells


title: Vehicle control Mac1 Replicate 3

description: Biological replicate 3 of 3. Vehicle control Mac1 cells, transfected with empty vector, RNA was extracted 96h post-transfection.


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B08.24688


title: formalin-fixed paraffin-embedded liver tissue: INCPH: B08.6387


title: formalin-fixed paraffin-embedded liver tissue: HNL: X28_R

value: HNL


title: formalin-fixed paraffin-embedded liver tissue: HNL: X6_R


title: formalin-fixed paraffin-embedded liver tissue: HNL: X25_R


title: formalin-fixed paraffin-embedded liver tissue: HNL: X27_R


title: formalin-fixed paraffin-embedded liver tissue: HNL: X29


title: Rat left ventricle at weeks 24 after ACF 3

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: 26 wks after ACF

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

organism: Rattus norvegicus

source_name: Rat left ventricle

label_protocol: Standard Affymetrix protocol

growth_protocol: Rat left ventricle

extract_protocol: Total RNA was isolated from the LVs at baseline and at weeks 8, 16 and 24 after creation of the ACF (n = 4 per group) using a Qiagen RNeasy Fibrous Tissue Mini kit (Qiagen, Valencia, CA). The quality and quantity of the total RNA were analyzed using a Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Adult male Sprague-Dawley rats (300- 350 g)  were performed in creation of aortocaval fistulae (ACF) operations .

value: Adult

tag: Sex

value: male

tag: strain

value: Sprague-Dawley

value: left ventricle


title: formalin-fixed paraffin-embedded liver tissue: HNL: X3_R


title: Vehicle control Mac1 Replicate 1

description: Biological replicate 1 of 3. Vehicle control Mac1 cells, transfected with empty vector, RNA was extracted 96h post-transfection.


title: formalin-fixed paraffin-embedded liver tissue: HNL: X30


title: Rat left ventricle at weeks 16 after ACF 4

description: 16 wks after ACF


title: Rat left ventricle at weeks 24 after ACF 1

description: 24 wks after ACF


title: Rat left ventricle at weeks 24 after ACF 2

description: 25 wks after ACF


title: formalin-fixed paraffin-embedded liver tissue: HNL: X26


title: Rat left ventricle at weeks 24 after ACF 4

description: 27 wks after ACF


title: formalin-fixed paraffin-embedded liver tissue: HNL: X21


title: Rat left ventricle at weeks 16 after ACF 2

description: 16 wks after ACF


title: Negative Control 3 Macs

city: Chicago

first: Afsar

last: Naqvi

state: IL

address: 801 S Paulina, Room 561B

department: Periodontics

country: USA

institute: University of Illinois at Chicago

description: Sample 31

hyb_protocol: RNA was hybridized onto miRCURY LNA microRNA (7th Gen; miRBase v19)  arrays following the procedures described by the manufacturer.

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing:
Data normalization were performed by Exiqon using Quantile normalization. The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007)  and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Initial analysis was performed by Exiqon using R/bioconductor, primarily by use of the limma package (Exiqon). Expression analysis of variance over time was performed with P values adjusted using the Benjamini-Hochberg method and identified genes subjected to the Tukey’s "honest significant difference" test.
The file "normalized_data.txt" contains the normalized Hy3 values.  This file is available on the series record.

source_name: Negative Control 3 Macs

label_protocol: Total RNA (225 ng) was labeled by use ofusing the miRCURY LNA microRNA Hi-Power Labeling Kit Hy3/Hy5  following the procedures described by the manufacturer.

growth_protocol: Human gingival keratinocytes: Primary HGEC were purchased from ScienCell Research Laboratories (Carlsbad, CA, USA). These cells were isolated from human oral mucosa and cryopreserved on passage one culture. Cells were cultured using Keratinocyte Medium (LifeLine Cell Technology, Friedrich, MD) which contains basal medium, growth supplements (hormones, growth factors and proteins) and penicillin/streptomycin. Macrophages: Monocytes were isolated from freshly prepared buffy coats collected from healthy donors (n ≥ 3, Sylvan N. Goldman Oklahoma Blood Institute, Oklahoma City, OK, USA) by density gradient  centrifugation and magnetic bead sorting as previously described (Self-Fordham et al., 2015; Naqvi et al., 2015, 2016).

extract_protocol: After 36 hours, cells were harvested for RNA isolation using miRNeasy kit according to manufacturer's protocol.  The reference RNA is a pool of total RNA from 20 different normal, human tissues. This is commercially available as FirstChoice(r) Human Total RNA Survey Panel at ThermoFisher Catalog Number AM6000.

treatment_protocol: Transient transfections of miR-H1, miR-K12-3-3p or control mimic were performed using Lipofectaine 2000 reagent (Life Technologies, San Diego, CA) according to manufacturer’s instructions.

value: Primary human Macrophages

tag: transfected with

value: control mimic

source_name: Reference RNA

tag: control type


title: Negative Control 4 Macs

description: Sample 32

source_name: Negative Control 4 Macs

value: pool of total RNA from 20 different normal, human tissues.


title: formalin-fixed paraffin-embedded liver tissue: HNL: X15

tag: tissue


title: formalin-fixed paraffin-embedded liver tissue: HNL: X16


title: UL70 2 Macs

description: Sample 26

source_name: UL70 2 Macs


title: Rat left ventricle at weeks 16 after ACF 1

description: 16 wks after ACF


title: UL70 3 Macs

description: Sample 27

source_name: UL70 3 Macs


title: Negative Control 2 Macs

description: Sample 30

source_name: Negative Control 2 Macs


title: formalin-fixed paraffin-embedded liver tissue: HNL: X5


title: formalin-fixed paraffin-embedded liver tissue: HNL: X1


title: Rat left ventricle baseline 4

description: Control


title: Rat left ventricle baseline 3

description: Control


title: UL70  1 Macs

description: Sample 25

source_name: UL70  1 Macs


title: formalin-fixed paraffin-embedded liver tissue: HNL: X4


title: Rat left ventricle baseline 1

description: Control


title: Rat left ventricle at weeks 8 after ACF 2

description: 8 wks after ACF


title: Rat left ventricle at weeks 8 after ACF 4

description: 8 wks after ACF


title: UL70 4 Macs

description: Sample 28

source_name: UL70 4 Macs


title: Rat left ventricle at weeks 16 after ACF 3

description: 16 wks after ACF


title: Rat left ventricle at weeks 8 after ACF 3

description: 8 wks after ACF


title: Rat left ventricle baseline 2

description: Control


title: Rat left ventricle at weeks 8 after ACF 1

description: 8 wks after ACF


title: K12-3p 4 Macs

description: Sample 24

source_name: K12-3p 4 Macs


title: K12-3p 3 Macs

description: Sample 23

source_name: K12-3p 3 Macs


title: K12-3p 2 Macs

description: Sample 22

source_name: K12-3p 2 Macs


title: K12-3p  1 Macs

description: Sample 21

source_name: K12-3p  1 Macs


title: miR-H1  4 Macs

description: Sample 20

source_name: miR-H1  4 Macs


title: miR-H1  3 Macs

description: Sample 19

source_name: miR-H1  3 Macs


title: miR-H1  1 Macs

description: Sample 17

source_name: miR-H1  1 Macs


title: Control mimic HEC 4

description: Sample 16

source_name: Control mimic HEC 4

value: Human Oral Keratinocytes

value: 3-5 passages


title: miR-H1  2 Macs

description: Sample 18

source_name: miR-H1  2 Macs


title: Control mimic HEC 2

description: Sample 14

source_name: Control mimic HEC 2


title: Control mimic HEC 3

description: Sample 15

source_name: Control mimic HEC 3

source_name: Reference RNA


title: T1 early carcinoma patients versus normal

type: genomic

city: Daejeon

first: Jinjong

last: Bong

address: Daehak-ro

country: South Korea

institute: NEXBIO

hyb_protocol: The labeled DNA was hybridized by Cot-1 DNA(1.0mg/ml), 10x aCGH Blocking agent and 2x HI-RPM Hybridization buffer

scan_protocol: The signal density was acquired by Agilent Scanner B and Feature extraction software

data_processing: The chromosome location and abundance of cell-free DNA was analyzed by Agilent Genomic workbench.

molecule: genomic DNA

source_name: gastric cancer

label_protocol: Cell-free DNAs were amplified by whole genome amplification kit. Two ug of DNA was labeled using random primer, 5x reaction buffer, 10x dNTPs, Cyanine 3-dUTP or Cyanine 5-dUTP, and Exo(-) Klenow

extract_protocol: Exosome was precipitated from patient serum. Cell-free DNA was extracted from exosome by phenol:chloroform method

tag: disease state

value: t1 early carcinoma

value: serum

tag: gender pool

value: men & women (n=27)

source_name: normal

value: normal


title: HFF-Towne 12hpi-rep3

city: Detroit

first: Philip

middle: E.

last: Pellett

state: MI

address: 540 E Canfield St

department: Biochemistry, Microbiology, and Immunology

institute: Wayne State University School of Medicine

description:
SAMPLE 3
replicate 3

hyb_protocol: Labeling, hybridization and scanning were performed off-site at the Wayne State University Advanced Genomics Technology Center (AGTC).

scan_protocol: Chips were scanned using an Illumina iScan.

data_processing: Non-normalized data are the raw expressions from the bead chip. Normalization was done using log2 transformation.

source_name: HFF-Towne 12hpi

label_protocol: Cy3 labeled.

growth_protocol: Primary human foreskin fibroblasts were cultured in DMEM supplemented with minimal non-essential amino acids and 10% FBS before and after infection.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Cells were infected with HCMV Towne at a multiplicity of 3.

value: primary human foreskin fibroblasts

tag: infected with

value: HCMV strain Towne

tag: time point

value: 12 hpi


title: HFF-Towne 96hpi-rep3

description:
SAMPLE 6
replicate 3

source_name: HFF-Towne 96hpi

value: 96 hpi


title: HFF-Towne 96hpi-rep1

description:
SAMPLE 4
replicate 1


title: T3 advanced carcinoma patients versus normal

value: t3 advanced carcinoma

value: men & women (n=20)


title: miR-UL70 HEC 4

description: Sample 12

source_name: miR-UL70 HEC 4


title: scls8-epi-A6380

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: SCLS patients were diagnosed and identified according to established criteria described previously. Written informed consent was obtained from each patient, and the study protocol (09- I-0184) conformed to the ethical guidelines of the 2008 Declaration of Helsinki as reflected in a priori approval from the Institutional Review Board of the National Institute of Allergy and Infectious Diseases of NIH.  Blood was collected into BD Vacutainer® Plus K2EDTA tubes (Becton-Dickinson, USA).

extract_protocol: Qiagen RNAeasy mini kit

treatment_protocol: Baseline blood samples were obtained by venipuncture during convalescent intervals at the NIH Clinical Center. Acute samples were drawn at outside institutions and shipped to NIH for processing. Whole blood was subjected to density gradient centrifugation using lymphocyte separation medium (LSM). Residual red blood cells were lysed using ACK lysing buffer (Lonza Walkersville) and washed with PBS. The isolated peripheral blood mononuclear cell fraction (PBMC) was stored at -80oC.

tag: diagnosis

value: Systemic Capillary Leak Syndrome

tag: subjectid

tag: disease interval

value: crisis

value: Peripheral blood mononuclear cells

value: Blood


title: scls9-epi-A6382

institute: National Institute of Allergy and Infectious Diseases

tag: cell type


title: scls9-bas-A6381

value: convalescent


title: scls6-epi-A6376


title: scls8-bas-A6379


title: shEZH2 Mac1 Replicate 1

description: Biological replicate 1 of 3. shEZH2-treated Mac1 cells, RNA was extracted 96h post-transfection.

source_name: Mac1-shEZH2 Mac1 cells

value: tumorous T cells in peripheral blood of patients with PCALCL


title: scls5-epi-A6374


title: HFF-Towne 96hpi-rep2

description:
SAMPLE 5
replicate 2


title: HFF-Towne 12hpi-rep2

description:
SAMPLE 2
replicate 2


title: miR-UL70 HEC 3

description: Sample 11

source_name: miR-UL70 HEC 3

value: Human Oral Keratinocytes

tag: passage

value: 3-5 passages

value: pool of total RNA from 20 different normal, human tissues.


title: Control mimic HEC 1

description: Sample 13

source_name: Control mimic HEC 1

value: control mimic


title: scls6-bas-A6375


title: HFF-Towne 12hpi-rep1

description:
SAMPLE 1
replicate 1


title: miR-K12-3-3 HEC 4

description: Sample 8


title: miR-UL70 HEC 2

description: Sample 10

source_name: miR-UL70 HEC 2


title: scls7-epi-A6378


title: miR-K12-3-3 HEC 3

description: Sample 7


title: miR-UL70 HEC 1

description: Sample 9

source_name: miR-UL70 HEC 1


title: miR-K12-3-3 HEC 2

description: Sample 6


title: miR-H1 HEC 4

description: Sample 4

source_name: miR-H1 HEC 4


title: scls5-bas-A6373


title: scls2-bas-A1300


title: miR-H1 HEC 1

description: Sample 1

source_name: miR-H1 HEC 1


title: scls10-bas-A6618


title: miR-K12-3-3p HEC 1

description: Sample 5

source_name: miR-K12-3-3p HEC 1


title: scls4-epi-A2302


title: miR-H1 HEC 3

description: Sample 3

source_name: miR-H1 HEC 3


title: miR-H1 HEC 2

description: Sample 2

source_name: miR-H1 HEC 2


title: scls3-epi-A2300


title: scls1-bas-A1299


title: scls11-epi-A7681


title: scls12-epi-A7683


title: scls12-bas-A7682


title: scls11-bas-A7680


title: DCM-1

city: Changzhou

first: Lichan

last: Tao

address: Juqian Road 185, Changzhou, Jiangsu province, China

department: cardiology

institute: The third affilated hospital of Soochow University

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48°C on Aligent miRNA Array. GeneChips were washed and stained in the Aligent Fluidics Station.

scan_protocol: The arrays were scanned by the Aligent.

data_processing: Agilent Feature Extraction Software (v10.7) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 75 percent of samples in any 1 condition out of 2 conditions have flags in P were chosen for further data analysis.

label: Biotin

source_name: heart, DCM, patients with dilated cardiomyopathy

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: Tissues for detection was collected from left ventricular free wall of explanted hearts from patients undergoing heart transplantation with a diagnosis of DCM, and from unmatched healthy donors.

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

tag: gender

value: female

value: DCM

value: heart


title: DCM-2


title: Normal-3

source_name: heart, control, healthy persons

value: male

value: control


title: Normal-2


title: DCM-3


title: Negative Control 1 Macs

description: Sample 29

source_name: Negative Control 1 Macs

value: Primary human Macrophages

source_name: Reference RNA


title: d10a

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

country: United Kingdom

institute: Ulster University

description: d10 replicate one

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Illumina proprietary software, GenomeStudio.
R using the lumi package and the limma package.

source_name: hTERT

label_protocol: Standard Illumina Protocol.

growth_protocol: The parental or wild type (WT) adherent hTERT1604 lung fibroblast cell line was cultured in 4.5g/l glucose DMEM  supplemented with 10% FBS and 2x NEAA. Knockdown (KD) cells (d8, d10 and d16) were maintained as for WT but media was supplemented with 150μg/ml hygromycin B, which was removed at least 48hrs before any experimental procedure.

extract_protocol:
Total RNA was extracted using the RNeasy minikit (Qiagen) as per the manufacturer’s instructions; a DNase step was included to ensure the removal of contaminating genomic DNA.
The concentration, purity and integrity of the resulting cRNA were measured by SpectroStar and bioanalyser.

treatment_protocol: The knockdown cell lines carrying an shRNA construct targeting DNMT1 were generated by transfecting the hTERT-immortalised human lung fibroblast cell line hTERT-1604 with pSilencer plasmid containing an shRNA

value: Male

value: hTERT-immortalised adult fibroblasts

tag: replicate

value: one


title: Normal-1


title: d16b

description: d16 replicate two

value: two


title: d10c

description: d10 replicate three

value: three


title: d16c

description: d16 replicate three


title: d8b

description: d8 repliciate two


title: d10b

description: d10 replicate two


title: d16a

description: d16 replicate one


title: WThTERTc

description: WThTERT replicate three

value: WThTERT


title: d8c

description: d8 replciate three


title: I53A_B_H3K27me3 rep2

type: SRA

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using the Trim Galore (v0.4.1; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) by 3 bases at the 5’ end prior to alignment, as recommended by the ChIP kit manufacturer.
The trimmed reads were then aligned to the mm10 reference genome using either the bowtie (v1.1.1, for samples of 50bp read length) or the bowtie2 (v2.2.3, for samples of 100bp read length) (Langmead et al. 2009, Langmead et al. 2012).
Only uniquely aligned reads were kept for downstream analysis, with duplicate reads removed by the software samtools (v0.1.19).  The ChIP kit has been reported to amplify biasedly poly-A+ genomic regions (Vardi et al. 2017), therefore we developed SMARTcleaner (https://github.com/dzhaobio/SMARTcleaner) to exclude reads adjacent to >= 12 As (or Ts) and exhibiting strong strand biases.
Peaks from Rybp, Bmi1 and Auts2 ChIP-seq were called using the MACS2 software (v2.1.0) with input as controls and default settings (Feng et al. 2012).
Peaks (mostly broad) in H3K27me3, H2AK119ub1, and Ring1b were called as described previously (Goldberg et al. 2010).
Genome_build: mm10
Supplementary_files_format_and_content: TDF files for IGV

organism: Mus musculus

source_name: Epidermal  progenitor cells

extract_protocol:
P0 back skins were collected and incubated for 4-6 hours in 1.26U/ml dispase at 4ºC. The epidermis was gently peeled from the underlying dermis, dissociated by 0.25% trypsin, and washed twice with 1x PBS. Cells were stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend), 1:100 α6-integrin-FITC (eBiosciences), and 1:200 EpCAM-APC (Biolegend) for 30 minutes on ice, and washed twice with 1x HBSS prior to cell sorting. Epidermal progenitor cells were sorted as EpCAM(+), Sca1(+), and α6-integrin(high).  A total of 0.4 x 10^6 cells was used for H3K27me3 ChIP, and a total of 6 x 10^6 cells was used for each Polycomb subunit per ChIP.  Prior to cell sorting, cells were stained for viability using Zombie violet (Biolegend; San Diego, CA), then cross-linked using fresh solution with a final concentration of 1% formaldehyde (Thermo Fisher Scientific; Rockford, IL) for 10 minutes at room temperature. Crosslinking was stopped by the addition of Glycine (final concentration 125mM) for 5 minutes of incubation at room temperature, followed by two washes with 1x PBS. Cells were incubated in lysis buffer 1 (50mM HEPES pH=7.5, 140mM Nacl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail (Roche)) for 10 min on ice, then incubated for 10 min with lysis buffer 2 (10mM Tris-HCl pH=7.5, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Before ChIP, cells were resuspended in lysis buffer 3 (10mM Tris-HCl pH=8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-laurylsarcosine, 1% Triton X-100) and sonicated using a Bioruptor Sonicator (Diagenode, UCD-200) according to a 25x regimen of 30 seconds of sonication followed by 90 seconds of rest at 2.7ºC.  Chromatin was incubated overnight at 4ºC with antibodies as indicated in Table S5.  Dynal protein G magnetic beads (Invitrogen) were added the next day and incubated for 4 hours. The beads were sequentially washed with low salt, high salt, LiCl, and Tris-EDTA buffers for 10 minutes each at 4ºC. Bound chromatin was eluted and crosslinking was reversed by overnight incubation at 65ºC, followed by RNase A (Sigma-Aldrich) and proteinase K (Roche Diagnostics) treatments.  Samples were purified using ChIP DNA Clean and Concentrator kit (Zymo Research; Irvine, CA).
For high-throughput ChIP sequencing, libraries were constructed from 3ng of Purified DNA using the DNA SMART ChIP-Seq Kit (Clontech; Palo Alto, CA, USA) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on the Illumina HiSeq 4000 platform

value: Epidermal  progenitor cells

value: Epidermis

tag: age

value: Postnatal day 0

tag: genotype

value: Ring1a-/- Ring1b-/I53A

tag: chip antibody


title: scls3-bas-A2299

value: Systemic Capillary Leak Syndrome

value: convalescent

value: Peripheral blood mononuclear cells

value: Blood


title: d8a

description: d8 replciate one


title: I53A_B_H3K27me3 rep1


title: I53A_A_Ring1b rep2

value: Ring1b (Cell Signaling, Cat# 5694S)


title: I53A_A_Suz12 rep2

value: Suz12 (Active Motif, Cat# 39357, RRID:AB_2614929)


title: WThTERTb

description: WThTERT replicate two


title: E50C_Cellobiose_None_0 [390156_6_Dartmouth#2_grid]

city: Oak Ridge

first: Jason

last: Whitham

address: 1 Bethel Valley Rd Bld 1505 Rm 366 MS 6038

institute: Oak Ridge National Labs

description: 5-L Twin BIOSTAT B Plus 4L Batch pH 7.0 100 rpm 55 deg C

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Microarrays were scanned with a SureScan High-Resolution DNA Microarray Scanner (5 μm) (Agilent), and the images were quantified using NimbleScan software (Roche NimbleGen, Madison, WI, USA). Raw data was log2 transformed and Loess normalized in JMP Genomics 5 (SAS Institute Inc., Cary, NC). We extracted probe data corresponding to genes while excluding probes for intergenic regions in our downstream analyses.

organism: Acetivibrio thermocellus ATCC 27405

growth_protocol: Ruminiclostridium thermocellum ATCC 27405 and adapted strains were grown at 55 deg C in the 4L volume in 5L Twin BIOSTAT B Plus Fermenter in modified MTC medium as described by Shao et al., 2011.

extract_protocol: Briefly, samples were centrifuged and total cellular RNA was extracted by the TRIzol reagent (Invitrogen, Carlsbad, CA) and bead beating. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: Duplicate fermentations using MTC medium were conducted for Clostridium thermocellum strains, ATCC 27405 wild-type; ethanol adapted strain E50A (adapted to grow in presence of up to 50 g/L ethanol on Avicel); and ethanol adapted strain E50C (adapted to grow in presence of up to 50 g/L ethanol on cellobiose). These strains have been described previously by Shao X., et al Appl Microbiol Biotechnol (2011) 92:641–652. In this study, strains ATCC 27405 and E50A were grown by temperature and pH controlled Avicel fermentations and strain E50C by temperature and pH controlled cellobiose fermentations. At mid-log phase wild-type strain ATCC 27405 was shocked with 10g/L ethanol. At mid-log phase strain E50A was shocked with either 10 or 40 g/L ethanol. At mid-log phase strain E50C was shocked with either 40g/L ethanol. Samples were harvested at 0.25, 1, 2, and 4 h for transcriptomics analysis.

tag: strain

tag: treatment

tag: substrate

value: Cellobiose 5g/L

tag: harvest time (hrs post treatment)


title: I53A_A_Input

tag: tissue


title: E50C_Cellobiose_None_0 [389237_A2_RL_FH_grid]

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: E50C_Cellobiose_None_0 [390155_11_Dartmouth#2_grid]

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: I53A_A_Ring1b rep1


title: I53A_B_Input


title: WThTERTa

description: WThTERT replicate one

value: Male


title: Control_B_H3K27me3 rep2

value: Control


title: E50C_Cellobiose_None_0 [390218_A8_RL_FH_grid]


title: Control_B_Input


title: E50C_Cellobiose_None_0 [389244_7_Dartmouth#2R_Grid]


title: I53A_A_Suz12 rep1


title: Control_A_Suz12 rep2


title: E50C_Cellobiose_Ethanol 40g/L_2PT [390155_8_Dartmouth#2_grid]

source_name: E50C_Cellobiose_Ethanol 40g/L_2PT

value: Ethanol 40g/L


title: Control_A_Suz12 rep1


title: E50C_Cellobiose_Ethanol 40g/L_4PT [389244_10_Dartmouth#2R_Grid]

source_name: E50C_Cellobiose_Ethanol 40g/L_4PT


title: E50C_Cellobiose_Ethanol 40g/L_4PT [390155_10_Dartmouth#2_grid]


title: Control_A_Ring1b rep2


title: Control_A_Ring1b rep1


title: E50C_Cellobiose_Ethanol 40g/L_1PT [389237_A8_RL_FH_grid]

source_name: E50C_Cellobiose_Ethanol 40g/L_1PT


title: E50C_Cellobiose_Ethanol 10g/L_4PT [389244_2_Dartmouth#2R_Grid]

source_name: E50C_Cellobiose_Ethanol 10g/L_4PT

value: Ethanol 10g/L


title: Control_B_H3K27me3 rep1


title: E50C_Cellobiose_Ethanol 40g/L_2PT [389244_9_Dartmouth#2R_Grid]


title: E50C_Cellobiose_Ethanol 40g/L_0.25PT [390218_A3_RL_FH_grid]

source_name: E50C_Cellobiose_Ethanol 40g/L_0.25PT


title: E50C_Cellobiose_Ethanol 40g/L_1PT [390218_A12_RL_FH_grid]


title: E50C_Cellobiose_Ethanol 10g/L_4PT [389244_11_Dartmouth#2R_Grid]


title: L3mbtl2_rep1

source_name: Epidermal progenitor cells

extract_protocol:
Basal layer epidermal progenitors were isolated from Krt14-RFP and Krt10-H2B-GFP newborn mice. Briefly, P0 back skins were collected and incubated for 4-6 hours in 1.26U/mL dispase (Invitrogen) at 4ºC. The epidermis was gently peeled from the underlying dermis, dissociated by 0.25% Trypsin with 2.21mM EDTA (Corning Cellgro; Manassas, VA, USA) and washed twice with 1x PBS. Cells were stained with 1:200 Sca1-APC ((Biolegend; San Diego, CA, USA) for 30 minutes on ice and washed twice with 1x HBSS prior to cell sorting. Epidermal progenitors were sorted as Sca1(+), Krt14-RFP(high), and Krt10-H2B-GFP(-). A total of 6 x 10^6 cells was used for each ChIP.  Prior to cell sorting, cells were stained for viability using Zombie violet (Biolegend; San Diego, CA), then cross-linked using fresh solution with a final concentration of 1% formaldehyde (Thermo Fisher Scientific; Rockford, IL) for 10 minutes at room temperature. Crosslinking was stopped by the addition of Glycine (final concentration 125mM) for 5 minutes of incubation at room temperature, followed by two washes with 1x PBS. Cells were incubated in lysis buffer 1 (50mM HEPES pH=7.5, 140mM Nacl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail (Roche)) for 10 min on ice, then incubated for 10 min with lysis buffer 2 (10mM Tris-HCl pH=7.5, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Before ChIP, cells were resuspended in lysis buffer 3 (10mM Tris-HCl pH=8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-laurylsarcosine, 1% Triton X-100) and sonicated using a Bioruptor Sonicator (Diagenode, UCD-200) according to a 25x regimen of 30 seconds of sonication followed by 90 seconds of rest at 2.7ºC.  Chromatin was incubated overnight at 4ºC with antibodies as indicated in Table S5.  Dynal protein G magnetic beads (Invitrogen) were added the next day and incubated for 4 hours. The beads were sequentially washed with low salt, high salt, LiCl, and Tris-EDTA buffers for 10 minutes each at 4ºC. Bound chromatin was eluted and crosslinking was reversed by overnight incubation at 65ºC, followed by RNase A (Sigma-Aldrich) and proteinase K (Roche Diagnostics) treatments.  Samples were purified using ChIP DNA Clean and Concentrator kit (Zymo Research; Irvine, CA).
For high-throughput ChIP sequencing, libraries were constructed from 3ng of Purified DNA using the DNA SMART ChIP-Seq Kit (Clontech; Palo Alto, CA, USA) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on the Illumina HiSeq 4000 platform

value: Epidermal progenitor cells

value: Krt14-RFP; Krt10-H2B-GFP

value: L3mbtl2 (Active Motif, Cat# 39570, RRID:AB_2615062)


title: L3mbtl2_rep2

value: Epidermis


title: Kdm2b_rep1

value: Postnatal day 0

value: Kdm2b (Abcam, Cat# ab137547)


title: Input [EP]


title: Control_A_Input

value: Epidermal  progenitor cells


title: E50C_Cellobiose_Ethanol 10g/L_4PT [390156_9_Dartmouth#2_grid]


title: E50C_Cellobiose_Ethanol 10g/L_2PT [390155_2_Dartmouth#2_grid]

source_name: E50C_Cellobiose_Ethanol 10g/L_2PT


title: E50C_Cellobiose_Ethanol 10g/L_2PT [390156_7_Dartmouth#2_grid]


title: Cbx8_rep1

value: Cbx8 (Bethyl Labs, Cat# A300-882A, RRID:AB_2071525)


title: Auts2_rep2

value: Auts2 (Sigma, Cat# HPA000390, RRID:AB_1845218)


title: E50C_Cellobiose_Ethanol 10g/L_1PT [390155_4_Dartmouth#2_grid]

source_name: E50C_Cellobiose_Ethanol 10g/L_1PT


title: E50C_Cellobiose_Ethanol 10g/L_4PT [390155_3_Dartmouth#2_grid]


title: Kdm2b_rep2


title: E50A_Avicel_None_0 [389237_A12_RL_FH_grid]

value: Avicel PH-101 5g/L


title: Rybp_rep2

extract_protocol:
Basal layer epidermal progenitors were isolated from Krt14-RFP and Krt10-H2B-GFP newborn mice. Briefly, P0 back skins were collected and incubated for 4-6 hours in 1.26U/mL dispase (Invitrogen) at 4ºC. The epidermis was gently peeled from the underlying dermis, dissociated by 0.25% Trypsin with 2.21mM EDTA (Corning Cellgro; Manassas, VA, USA) and washed twice with 1x PBS. Cells were stained with 1:200 Sca1-APC ((Biolegend; San Diego, CA, USA) for 30 minutes on ice and washed twice with 1x HBSS prior to cell sorting. Epidermal progenitors were sorted as Sca1(+), Krt14-RFP(high), and Krt10-H2B-GFP(-). A total of 0.4 x 10^6 cells was used for each histone mark per ChIP, and a total of 6 x 10^6 cells was used for each Polycomb subunit per ChIP.  Prior to cell sorting, cells were stained for viability using Zombie violet (Biolegend; San Diego, CA), then cross-linked using fresh solution with a final concentration of 1% formaldehyde (Thermo Fisher Scientific; Rockford, IL) for 10 minutes at room temperature. Crosslinking was stopped by the addition of Glycine (final concentration 125mM) for 5 minutes of incubation at room temperature, followed by two washes with 1x PBS. Cells were incubated in lysis buffer 1 (50mM HEPES pH=7.5, 140mM Nacl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail (Roche)) for 10 min on ice, then incubated for 10 min with lysis buffer 2 (10mM Tris-HCl pH=7.5, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Before ChIP, cells were resuspended in lysis buffer 3 (10mM Tris-HCl pH=8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-laurylsarcosine, 1% Triton X-100) and sonicated using a Bioruptor Sonicator (Diagenode, UCD-200) according to a 25x regimen of 30 seconds of sonication followed by 90 seconds of rest at 2.7ºC.  Chromatin was incubated overnight at 4ºC with antibodies as indicated in Table S5.  Dynal protein G magnetic beads (Invitrogen) were added the next day and incubated for 4 hours. The beads were sequentially washed with low salt, high salt, LiCl, and Tris-EDTA buffers for 10 minutes each at 4ºC. Bound chromatin was eluted and crosslinking was reversed by overnight incubation at 65ºC, followed by RNase A (Sigma-Aldrich) and proteinase K (Roche Diagnostics) treatments.  Samples were purified using ChIP DNA Clean and Concentrator kit (Zymo Research; Irvine, CA).
For high-throughput ChIP sequencing, libraries were constructed from 3ng of Purified DNA using the DNA SMART ChIP-Seq Kit (Clontech; Palo Alto, CA, USA) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on the Illumina HiSeq 4000 platform

value: Rybp (Millipore, Cat# ab3637, RRID:AB_2285466)


title: Rybp_rep1


title: E50A_Avicel_None_0 [390218_A1_RL_FH_grid]


title: Input


title: E50C_Cellobiose_Ethanol 40g/L_0.25PT [389237_A11_RL_FH_grid]


title: Bmi1_rep2

value: Bmi1 (Cell Signaling, Cat# 5856S, RRID:AB_10838137)


title: E50A_Avicel_None_0 [389237_A6_RL_FH_grid]


title: Auts2_rep1


title: preB in KO, biological rep4

city: Cincinnati

first: Stephen

middle: Noel

last: Waggoner

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: SAMPLE 8

hyb_protocol: GeneChip Mouse Gene 2.0 arrays (Affymetrix)

scan_protocol: standard Affymetrix protocol

data_processing:
Raw data were used for analysis with GeneSpring GX software (v13.0, Agilent Technologies). We first applied standard RMA normalization and baseline transformation to all samples (n=4/group), then removed noise by applying a filter requiring a raw expression value >50. A p<0.05 and fold change >1.5 were set as benchmarks for differential gene expression between experimental groups. A hierarchical clustered heatmap of the top 20 up-regulated and top 15 down-regulated genes were made using R software (64bit, v3.2.2).
affymetrix-algorithm-name = plier-gene-full
affymetrix-algorithm-version = 2.0
program-name = Expression Console
program-version = 1.4.1.46

label: Ovation Pico WTA

source_name: preB in KO

label_protocol: Ovation Pico WTA kit (NuGen)

growth_protocol: Mice maintained specific pathogen-free barrier and used at 6 to 12 weeks of age

extract_protocol: Extraction of total cellular RNA using mirVana miRNA isolation kit (Thermo Fischer Scientific)

treatment_protocol: Bone marrow was extracted from untreated mice, cells were stained with antibodies, and then cells were soted on FACSAria II.

tag: strain background

tag: genotype/variation

value: Ddx3x KO

tag: Sex

value: male

value: Bone marrow late pre-B cells (CD3-,Ly6C-,Ter119-,CD11b-,Gr1-,B220+,CD43-,IgM-,IgD-)


title: preB in KO, biological rep2

description: SAMPLE 6


title: preB in KO, biological rep3

description: SAMPLE 7


title: E50A_Avicel_None_0 [390156_3_Dartmouth#2_grid]


title: H3K4me3_rep2

data_processing:
ChIP-seq reads were trimmed using the Trim Galore (v0.4.1; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) by 3 bases at the 5’ end prior to alignment, as recommended by the ChIP kit manufacturer.
The trimmed reads were then aligned to the mm10 reference genome using either the bowtie (v1.1.1, for samples of 50bp read length) or the bowtie2 (v2.2.3, for samples of 100bp read length) (Langmead et al. 2009, Langmead et al. 2012).
Only uniquely aligned reads were kept for downstream analysis, with duplicate reads removed by the software samtools (v0.1.19).  The ChIP kit has been reported to amplify biasedly poly-A+ genomic regions (Vardi et al. 2017), therefore we developed SMARTcleaner (https://github.com/dzhaobio/SMARTcleaner) to exclude reads adjacent to >= 12 As (or Ts) and exhibiting strong strand biases.
Peaks from Rybp, Bmi1 and Auts2 ChIP-seq were called using the MACS2 software (v2.1.0) with input as controls and default settings (Feng et al. 2012).
Peaks (mostly broad) in H3K27me3, H2AK119ub1, and Ring1b were called as described previously (Goldberg et al. 2010).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited peak calling results and TDF files for IGV

value: H3K4me3 (Abcam, Cat# ab8580, RRID:AB_306649)


title: Bmi1_rep1


title: Input_rep2


title: E50A_Avicel_Ethanol 40g/L_4PT [389244_5_Dartmouth#2R_Grid]

source_name: E50A_Avicel_Ethanol 40g/L_4PT

value: Ethanol 40g/L


title: Input_rep1

value: Epidermal progenitor cells


title: E50A_Avicel_None_0 [390218_A11_RL_FH_grid]


title: H3K4me1_rep2

value: Krt14-RFP; Krt10-H2B-GFP

value: H3K4me1 (Abcam, Cat# ab8895, RRID:AB_306847)


title: E50A_Avicel_Ethanol 40g/L_4PT [390155_9_Dartmouth#2_grid]


title: H3K4me3_rep1

value: Epidermis


title: H3K4me1_rep1

value: Postnatal day 0


title: preB in WT, biological rep4

description: SAMPLE 4

source_name: preB in WT

value: WT


title: Ring1b_rep1

value: Ring1b (Cell Signaling, Cat# 5694S)


title: preB in WT, biological rep2

description: SAMPLE 2


title: H3K27me3_rep2


title: preB in WT, biological rep3

description: SAMPLE 3


title: E50A_Avicel_Ethanol 40g/L_1PT [389237_A4_RL_FH_grid]

source_name: E50A_Avicel_Ethanol 40g/L_1PT


title: preB in KO, biological rep1

description: SAMPLE 5


title: H3K27me3_rep1


title: preB in WT, biological rep1

description: SAMPLE 1


title: H3K27ac_rep2


title: H2AK119ub_rep2

value: H2AK119ub (Cell Signaling, Cat# 8240S)


title: H3K27ac_rep1


title: Epi_Eed cKO rep3

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm10) using the Tophat (v2.0.13)
Gene models of Refgene were downloaded from the UCSC genome browser on March 13, 2017. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using the cufflinks (v2.2.1). Lowly expressed genes (mean FPKM values < 1 in both groups under comparison) were excluded from differential expression analysis.
read counts from the HTSeq (v0.6.1)
DESeq2 (v1.6.3) was used to determine differentially expressed genes
genes with >2 fold change, false discovery rate (FDR) < 0.05, and FPKM>1 were identified as significantly differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene expression values (htseq counts)

source_name: Skin epidermis

extract_protocol:
Newborn P0 back skins were collected and subjected to 0.25% collagenase digestion for 60 minutes at 37ºC with 80 rpm shaking, followed by 0.25% trypsin treatment for 15 minutes at 37ºC. The cell suspension was washed twice with 1x PBS, stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend), 1:100 α6-integrin-FITC (eBiosciences), and 1:200 EpCAM-APC (Biolegend) for 30 minutes on ice, and washed twice with 1x HBSS prior to cell sorting. Interfollicular epidermis, enriched for epidermal progenitors, was sorted as EpCAM(+), Sca1(+), and α6-integrin(high). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
10ng of total RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (Nugen). Libraries were constructed from 100ng of sonicated cDNA (Covaris) using the Ovation Ultra Low DR Multiplex system (Nugen). The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform, obtaining 100-nucleotide single reads.

value: Epiermal cells

value: Eed-/-


title: Epi_Eed cKO rep2


title: Epi_Eed cKO rep1


title: Epi_Control rep3

value: Control


title: Large luteal cells biological replicate 3

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

country: Germany

institute: Leibniz institute for farm animal biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the TAC 4.0 software (Affymetrix) and RMA method was used for normalization.

organism: Bos taurus

source_name: mature CL

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: small and large luteal cells were isolated form mature CL of holstein lactating cows

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: RNA from primary small and large luteal cells were used for the microarray

value: primary large luteal cells


title: E50A_Avicel_Ethanol 10g/L_4PT [389244_1_Dartmouth#2R_Grid]

source_name: E50A_Avicel_Ethanol 10g/L_4PT

value: Ethanol 10g/L

value: Avicel PH-101 5g/L


title: H2AK119ub_rep1


title: E50A_Avicel_Ethanol 40g/L_1PT [390218_A5_RL_FH_grid]


title: E50A_Avicel_Ethanol 40g/L_0.25PT [389237_A7_RL_FH_grid]

source_name: E50A_Avicel_Ethanol 40g/L_0.25PT


title: E50A_Avicel_Ethanol 10g/L_1PT [389244_3_Dartmouth#2R_Grid]

source_name: E50A_Avicel_Ethanol 10g/L_1PT


title: Large luteal cells biological replicate 2


title: Large luteal cells biological replicate 4


title: E50A_Avicel_Ethanol 10g/L_4PT [390156_1_Dartmouth#2_grid]


title: Large luteal cells biological replicate 1


title: Epi_Control rep2


title: E50A_Avicel_Ethanol 10g/L_1PT [390155_6_Dartmouth#2_grid]


title: Ring1b_rep2


title: Small luteal cells biological replicate 4

value: primary small luteal cells


title: E50A_Avicel_Ethanol 40g/L_0.25PT [390218_A9_RL_FH_grid]


title: Epi_Control rep1


title: HF_I53A rep2

source_name: Hair follicle

extract_protocol:
Newborn P0 back skins were collected and subjected to 0.25% collagenase digestion for 60 minutes at 37ºC with 80 rpm shaking, followed by 0.25% trypsin treatment for 15 minutes at 37ºC. The cell suspension was washed twice with 1x PBS, stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend), 1:100 α6-integrin-FITC (eBiosciences), and 1:200 EpCAM-APC (Biolegend) for 30 minutes on ice, and washed twice with 1x HBSS prior to cell sorting. Interfollicular epidermis, enriched for epidermal progenitors, was sorted as EpCAM(+), Sca1(+), and α6-integrin(high). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
10ng of total RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (Nugen). Libraries were constructed from 100ng of sonicated cDNA (Covaris) using the Ovation Ultra Low DR Multiplex system (Nugen). The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced on the Illumina HiSeq 4000 platform, obtaining 100-nucleotide single reads.

value: Hair follicle cells

value: Skin

value: Ring1a-/- Ring1b-/I53A


title: HF_I53A rep3


title: HF_I53A rep1


title: Small luteal cells biological replicate 3


title: HF_CTL rep3


title: E50A_Avicel_Ethanol 10g/L_1PT [389237_A1_RL_FH_grid]


title: HF_CTL rep2


title: HF_CTL rep1


title: Epidermis CTL rep1


title: Epidermis I53A rep2


title: Epidermis I53A rep1


title: Epidermis CTL rep2


title: E50A_Avicel_Ethanol 10g/L_1PT [390218_A7_RL_FH_grid]


title: HF Control rep2


title: HF Control rep3


title: HF Ring1a/b 2KO rep1

value: Ring1a-/- Ring1b-/-


title: HF Ring1a/b 2KO rep3


title: HF Control rep1


title: Small luteal cells biological replicate 2


title: HF Ring1a/b 2KO rep2


title: Epidermis Ring1a/b 2KO rep2

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm10) using the Tophat (v2.0.13)
Gene models of Refgene were downloaded from the UCSC genome browser on March 13, 2017. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using the cufflinks (v2.2.1). Lowly expressed genes (mean FPKM values < 1 in both groups under comparison) were excluded from differential expression analysis.
read counts from the HTSeq (v0.6.1)
DESeq2 (v1.6.3) was used to determine differentially expressed genes
genes with >2 fold change, false discovery rate (FDR) < 0.05, and FPKM>1 were identified as significantly differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene expression values (Htseq counts)


title: Epidermis Ring1a/b 2KO rep1


title: Epidermis Ring1a/b 2KO rep3


title: E50A_Avicel_Ethanol 10g/L_0.25PT [389237_A9_RL_FH_grid]

source_name: E50A_Avicel_Ethanol 10g/L_0.25PT


title: Epidermis Control rep3


title: E50A_Avicel_Ethanol 10g/L_1PT [389244_6_Dartmouth#2R_Grid]


title: ATCC 27405_Avicel_None_0 [389237_A10_RL_FH_grid]

source_name: ATCC 27405_Avicel_None_0


title: E50A_Avicel_Ethanol 10g/L_0.25PT [390218_A4_RL_FH_grid]


title: Epidermis Control rep1


title: V6,5 (0h)_b

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

description: GATCAG | Sample 9 V6,5-1 (0h)

data_processing:
Reads from all datasets (Dusp9+/-_ESCs, WT_XX_ESCs and WT_XY_ESCs) were aligned to mouse reference genome GRCm38/mm10 using STAR (v2.5.3a) with default parameters followed with conversion to BAM sorted by coordinate.
The featureCounts function from the R Bioconductor package “Rsubread” was used to assign mapped reads to genomic features. For downstream analyses, only the genes with CPM value (count-per-milion) higher than 0.5 in at least two libraries were kept.
A read count matrix was used as an input for differential expression analysis using the edgeR quasi-likelihood pipeline in R (Chen et al. 2016). The resulting p values were corrected for multiple testing with the Benjamini–Hochberg method to control the FDR. Genes were considered significantly differentially expressed on the basis of both FDR < 0.05 and fold difference = or greater than 1.5, a criteria necessary to assess small differences in gene expression between male and female ESCs.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with matrix for all samples with CPM values normalized by the library size

source_name: Embryonic Stem Cells

growth_protocol: ESCs (Wild type female and male ESCs, two independent female Dusp9+/- ESC lines) were grown in serum/LIF condition in the absence of feeders. Samples were collected at 0h and 24h of LIF withdrawal (LIF withdrawal was performed in mouse ESC media with 10% serum and without LIF) at a cell density of 4*10ˆ4 cells/cm2. Cells were harvested at 0h and 24h of LIF withdrawal.

extract_protocol:
Total RNA was isolated using TRIzol reagent following the manufacturer’s protocol.
4 µg of total RNA was used for library preparation with the KAPA stranded mRNA Library prep kit for Illumina platform (KAPA Biosystems). Library concentrations were quantified with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Q32854), and equimolar amounts were pooled for single-end sequencing on an Illumina HiSeq 4000 instrument (Illumina) to yield ~20 million reads (range 16–23 million) of 36bp in length per sample.

value: male

tag: differentiation time

value: ESC


title: ATCC 27405_Avicel_Ethanol 10g/L_4PT [389244_4_Dartmouth#2R_Grid]

source_name: ATCC 27405_Avicel_Ethanol 10g/L_4PT


title: Epidermis Control rep2

value: Epidermis

value: Postnatal day 0


title: V6,5 (24h)

description: TTAGGC | Sample 3 V6,5-1 (24h)

value: WT


title: V6,5 (24h)_b

description: GCCAAT | Sample 11 V6,5-1 (24h)


title: V6,5 (0h)

description: ATCACG | Sample 1 V6,5-1 (0h)


title: ATCC 27405_Avicel_None_0 [390218_A6_RL_FH_grid]


title: Small luteal cells biological replicate 1


title: ATCC 27405_Avicel_Ethanol 10g/L_4PT [390156_10_Dartmouth#2_grid]


title: ATCC 27405_Avicel_Ethanol 10g/L_1PT [389237_A5_RL_FH_grid]

source_name: ATCC 27405_Avicel_Ethanol 10g/L_1PT


title: ATCC 27405_Avicel_Ethanol 10g/L_4PT [390155_5_Dartmouth#2_grid]


title: ATCC 27405_Avicel_Ethanol 10g/L_1PT [390218_A2_RL_FH_grid]


title: ATCC 27405_Avicel_Ethanol 10g/L_0.25PT [389237_A3_RL_FH_grid]

source_name: ATCC 27405_Avicel_Ethanol 10g/L_0.25PT


title: ATCC 27405_Avicel_Ethanol 10g/L_0.25PT [390155_1_Dartmouth#2_grid]


title: ATCC 27405_Avicel_Ethanol 10g/L_0.25PT [390218_A10_RL_FH_grid]


title: E50C_Cellobiose_Ethanol 10g/L_0.25PT [390156_5_Dartmouth#2_grid]

source_name: E50C_Cellobiose_Ethanol 10g/L_0.25PT

value: Cellobiose 5g/L


title: Cbx8_rep2

source_name: Epidermal progenitor cells

value: Epidermal progenitor cells

value: Krt14-RFP; Krt10-H2B-GFP

value: Cbx8 (Bethyl Labs, Cat# A300-882A, RRID:AB_2071525)


title: OCI-AML3 cells: NPM1-shRNA inducibly expressed by doxycycline for 6 days-replicate 1

city: Stanford

first: Min

last: Huang

state: CA

address: 265 Campus Drive

department: Internal Medicine

institute: Stanford Cancer Institute

hyb_protocol: 850 ug of labeled cRNA was hybridized overnight to Agilent  SurePrint G3 Human Gene Expression 8x60k slides

scan_protocol: Probe intensities were scanned on the Agilent microarray scanner

data_processing:
Data were processed into image analysis (.GE1) files using Agilent Feature Extraction Software.
Gene expression analysis was normalized and carried out using BRB-ArrayTools version 3.7.0 Mas5 developed by Dr. Richard Simon and BRB-ArrayTools Development Team.

source_name: Human NPM1 depleted OCI-AML3 cel line

label_protocol: Cy3 and/or Cy5 labeled, amplified antisense complementary RNA (cRNA) targets were prepared from 500 ng of the total RNA using the QuickAmp Labeling kit

growth_protocol: OCI-AML3 cells were cultured in MEM-alpha medium with 20% FBS and 1X penicillin and streptomycin

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were treated with or without 1 ug/ml doxycycline  for 6 days

tag: cell line

value: human leukemia cells

value: stably expressing inducible NPM1-shRNA

tag: treated with

value: 1 ug/ml doxycycline  for 6 days


title: 4427_dTGR_heart_BAY41-8543

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

institute: Bayer Pharma AG

description: gene expression data of heart left ventricle samples from dTGR [SD-Tg(hAGT)L1623xTg(hREN)L10J] hypertensive rats treated with BAY 41-8543 (3mg/kg/d)

hyb_protocol: Affymetrix Rat Gene 2.1 ST 96-array plates were hybridized with 3µg of fragmented and labeled ss cDNA and washed according to the protocol described in User Manual GeneTitan®Instrument User Guide for Expression Arrays Plates (P/N 702933 Rev.1)

scan_protocol: Scan was performed according to the protocol described in User Manual GeneTitan®Instrument User Guide for Expression Arrays Plates (P/N 702933 Rev.1) and Affymetrix® GeneChip® Command Console™ User’s Guide (P/N 702569 Rev.9) using the Affymetrix GeneTitan instrument.

data_processing: Genedata Refiner Array software was used to process the cel files. Antigenomic background probes were used for background subtraction. RMA condensation algorithm was employed to aggregate the probe sets on a meta probe set level. Resulting values were shifted to mean value of 100 and further normalized using LOWESS algorithm.

source_name: left ventricle

label_protocol: For microarray analysis, 250ng of total RNA of each sample were amplified using the Ambion WT Expression Kit (#4411974) and Affymetrix WT Terminal Labeling and Hybridization Kit (#901524) according to the protocol described in User Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays (P/N: 4425209 Rev. D)

growth_protocol: At the age of 3.5 weeks, age- and body weight-matched male dTGR and non-transgenic Sprague Dawley (SD) control rats were randomly assigned to 3 experimental groups: vehicle-treated dTGR , dTGR treated with 3 mg/kg/day BAY 41-8543 and SD controls.

extract_protocol: Heart samples were first homogenized in a Precellys24 homogenizer ((2,8 mm reinforced Keramik-Kit / 1x 60s @ 5.000rpm) and RNA was isolated using Qiagen RNeasy Mini kits.

treatment_protocol: Treatment was started at the age of 4 weeks by oral gavage once daily until the end of the study at the age of 7 weeks

value: left ventricle

value: dTGR [SD-Tg(hAGT)L1623xTg(hREN)L10J]

tag: phenotype

value: HFpEF (hypertension induced)

tag: treatment protocol


title: 4431_dTGR_heart_BAY41-8543

tag: gender


title: 4435_dTGR_heart_BAY41-8543


title: OCI-AML3 cells: NPM1-shRNA inducibly expressed by doxycycline for 6 days-replicate 2

tag: cell type


title: 4434_dTGR_heart_BAY41-8543


title: OCI-AML3 cells: Atg5-shRNA inducibly expressed by doxycycline for 6 days-replicate 1

source_name: Human Atg5-depleted OCI-AML3 cell line

value: stably expressing inducible Atg5 shRNA


title: 4403_dTGR_heart_vehicle

description: gene expression data of heart left ventricle samples from dTGR [SD-Tg(hAGT)L1623xTg(hREN)L10J] hypertensive rats treated with vehicle


title: 4430_dTGR_heart_BAY41-8543


title: Control OCI-AML3 Cell  without doxycycline Replicate 1

source_name: Human control OCI-AML3 cell line

value: stably expressing control shRNA

value: none; Dox(-)


title: 4408_dTGR_heart_vehicle

value: male


title: 4433_dTGR_heart_BAY41-8543


title: 4437_dTGR_heart_BAY41-8543


title: 4429_dTGR_heart_BAY41-8543


title: 4405_dTGR_heart_vehicle


title: 4406_dTGR_heart_vehicle


title: Control OCI-AML3 Cell  without doxycycline Replicate 2


title: 4401_dTGR_heart_vehicle


title: 4426_dTGR_heart_BAY41-8543


title: Control OCI-AML3 Cell  without doxycycline Replicate 3


title: 4413_dTGR_heart_vehicle


title: E50C_Cellobiose_Ethanol 10g/L_1PT [389244_8_Dartmouth#2R_Grid]

source_name: E50C_Cellobiose_Ethanol 10g/L_1PT

value: Ethanol 10g/L


title: OCI-AML3 cells: Atg5-shRNA inducibly expressed by doxycycline for 6 days-replicate 2


title: OCI-AML3 cells: NPM1-shRNA inducibly expressed by doxycycline for 6 days-replicate 3


title: 4436_dTGR_heart_BAY41-8543


title: 4432_dTGR_heart_BAY41-8543


title: 4404_dTGR_heart_vehicle


title: 4428_dTGR_heart_BAY41-8543


title: 4411_dTGR_heart_vehicle


title: 3917_SD_heart_no

description: gene expression data of heart left ventricle samples from wildtype sprague dawley rats without treatment

value: sprague dawley

value: wildtype

value: no treatment


title: 3916_SD_heart_no


title: 3910_SD_heart_no


title: 3914_SD_heart_no


title: 3915_SD_heart_no


title: 3911_SD_heart_no


title: 3913_SD_heart_no


title: 3912_SD_heart_no


title: Patient 19 TWG_20150910

city: ChongQing

first: YanLin

last: Yang

state: ChongQing

address: 29 Gaotanyan Main Street, Shapingba District, Chongqing, China

department: Institute for Infectious Diseases

institute: The First Affiliated Hospital, Third Military Medicale University

description: All the PBMC samples were acquired before the therapy of Peg IFN,the reposne result decided which group patients should be brought in at the point of drug discontinuance.The viral load and HBsAg is low in order to decrease the influence of virial factors.

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.  a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were firstdenatured for 2 min at 95°C, incubated on ice for 2 min  b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA)  c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating  normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: non-HBsAg loss_PBMC

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C.  b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C  c, Terminated by incubation for 15 min at 65°C

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer   (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: PBMCs were stored n the liquid nitrogen until being tested.

tag: age

value: 52 years

tag: group

value: non-HBsAg loss

tag: baseline hbsag

tag: alt

value: 19 IU/ml

value: peripheral blood mononuclear cell (PBMC)


title: Patient 18 WYL_20150907

value: female

value: 49 years

value: 34 IU/ml


title: Patient 20 ZZM_20151015

value: 59 years

value: 31 IU/ml


title: Nipponbare_MOCK_24hpi_rep3

city: Montpellier

first: Alvaro

middle: Luis

last: Pérez-Quintero

state: Montpellier

address: 911 Avenue Agropolis

department: RBP

country: France

institute: IRD

description: Oryza sativa cv. Nipponbare

data_processing:
Libraries were sequenced in a HiSeq2000 machine (Illumina) at the INRA Unité de Recherche en Génomique Végétale (Evry, France).
Library quality was verified using FastQC v0.10.1.
Reads were mapped against the rice genome (Nipponbare v. MSU7) using the Tuxedo suite v2.1.1.
Transcripts obtained with Tophat (v2.1.1) were merged with annotated transcripts using Cuffmerge (v2.1.1).
Gene counts were obtained using HTSeq.
Genome_build: Oryza sativa Nippponbare v. MSU7
Supplementary_files_format_and_content: *txt: Tab-delimited text files include counts for each sample.

organism: Oryza sativa Japonica Group

source_name: Leaves

growth_protocol: X. oryzae strains grown at 28°C in PSA medium (10 g l-1 peptone, 10 g l-1 sucrose, 1 g l-1 glutamic acid, 16 g l-1 agar). Experiments were performed under glasshouse conditions under cycles of 12 hours of light at 28-30°C and 80% relative humidity (RH), and 12 hours of dark at 25°C and 70% RH.

extract_protocol:
At 1 dpi, leaf segments from three plants were ground into a fine powder using the Qiagen Tissue-Lyser system (30 rps for 30 s). Total RNA was isolated from rice leaves using the RNeasy kit (Qiagen).
Paired-end strand specific TruSeq Illumina.

treatment_protocol: Leaves of 3-week-old rice plants were infiltrated with water or Xo strains using an OD600 of 0.5. In each experiment, at least three leaves from three individuals were inoculated with a syringe. 3 independent experiments were made for each treatment.

tag: cultivar

value: Nipponbare

value: 3 weeks

value: Leaves

tag: treatment

value: H2O control

tag: time point


title: Patient 12 HXL_20140324

value: male

value: 44 years

value: 47 IU/ml


title: Nipponbare_MOCK_24hpi_rep2

description: Oryza sativa cv. Nipponbare

tag: tissue


title: Patient 14 MSY_20150423

value: 39 years

value: 35 IU/ml


title: Patient 17 XYL_20150831

value: 38 years

value: non-HBsAg loss

value: 28 IU/ml


title: Nipponbare_MOCK_24hpi_rep1

description: Oryza sativa cv. Nipponbare


title: Patient 16 MSB_20150907

value: 46 years

value: peripheral blood mononuclear cell (PBMC)


title: Patient 11 ML_20131226

value: female

value: 21 IU/ml


title: Patient 10 YL_20160107

source_name: HBsAg loss_PBMC

value: 18 years

value: HBsAg loss

value: 27 IU/ml


title: Patient 13 LYH_20140526

value: 50 years

value: 19 IU/ml


title: Patient 8 ZHJ_20151105

value: male

value: 28 years

value: 52 IU/ml


title: Patient 15 LKQ_20150702

value: 49 years

value: 45 IU/ml


title: Patient 9 YB_20151105

value: 34 years

value: 25 IU/ml


title: Patient 6 ZYP_20140821

value: 39 years


title: Patient 7 ZKD_20151026

value: 43 years

value: 31 IU/ml


title: Nipponbare_MAI1_24hpi_rep3

description: Oryza sativa cv. Nipponbare

value: Nipponbare

value: 3 weeks

value: Leaves

value: Xanthomonas oryzae pv. Oryzae MAI1 inoculated


title: Nipponbare_MAI1_24hpi_rep2

description: Oryza sativa cv. Nipponbare


title: Patient 4 HGY_20140303

value: 37 years

value: HBsAg loss

value: 36 IU/ml

value: peripheral blood mononuclear cell (PBMC)


title: Nipponbare_MAI1_24hpi_rep1

description: Oryza sativa cv. Nipponbare


title: Patient 5 SMY_20140714

value: male

value: 18 years

value: 69 IU/ml


title: Patient 3 YZW_20140220

value: female

value: 22 years

value: 12 IU/ml


title: Sample 1

city: Bremen

first: Ping-Wei

last: Ho

address: College Ring 3

institute: Jacobs University Bremen GmbH

data_processing:
For quality control of the generated reads, we applied FastQC developed by Andrews, 2010: Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
The reads were mapped to the yeast genome as provided by the Saccharomyces Genome Database (sacCer3 assembly) using Bowtie (version 2.1.0) (Langmead et al., Genome Biology, 2009).
To obtain expression values for genes, Cufflinks (version 2.1.1) (Trapnell et al.,  Nature Biotechnology, 2010.) was applied using the annotation provided for the sacCer3 assembly of the yeast genome.
Genome_build: sacCer3 assembly (Saccharomyces Genome Database)
Supplementary_files_format_and_content: Excel file includes FPKM values for each gene of Sample 1.

organism: Saccharomyces cerevisiae

source_name: strain CEN.PK113-7D GUT1JL1 UBR2JL1 in synthetic glycerol medium

growth_protocol: The strain CEN.PK113-7D GUT1JL1 UBR2JL1 was cultivated in synthetic glycerol medium until exponential growth phase was reached. The pH of the medium was controlled at 5.0 and the temperature was maintained at 30°C and a stirring rate of 800 rpm throughout the cultivations.

extract_protocol:
Approximately 6 x 10^7 cells was pelleted at 3000 rpm for 5 mins and re-suspended in 1 mL RNAlater™ (Thermo Fisher Scientific, Waltham, MA, USA) for the isolation of total RNA using the RiboPure-Yeast Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: CEN.PK113-7D GUT1JL1 UBR2JL1

tag: genotype

value: gut1::GUT1JL1 ubr2::UBR2JL1

tag: medium

value: synthetic glycerol

tag: growth phase

value: exponential


title: Patient 2 LQ_20131125

value: 24 years

value: 59 IU/ml


title: Patient 1 WJ_20131021

value: 27 years

value: 28 IU/ml


title: Baseline  [151]

city: Aarhus C

first: Anders

middle: Riegels

last: Knudsen

address: Nørrebrogade 44, building 1c, LVN-research

department: Department of Surgery, Section for upper GI surgery

country: Denmark

institute: Aarhus University Hospital

description: Sample name: 151

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip Rat Gene 2.0 ST Array (Thermo Fischer Scientific, Waltham, MA, USA) at 45C and 60 rpm for 16 hours.

scan_protocol: Affymetrix GeneChip® Scanner 3000 7 G.

data_processing: Quality control of the array data was performed in Expression Console software (Affymetrix) with default RMA Gene analysis settings. Secondary analysis was performed in GeneSpring 13.0.

source_name: Liver, no operation

label_protocol: Ambion® WT Expression Kit (Thermo Fischer Scientific, Waltham, MA, USA) was used for labelling 100 ng isolated RNA. Samples were hybridized to the Affymetrix GeneChip® Rat Gene 2.0 ST Array (Thermo Fischer Scientific, Waltham, MA, USA) at 45 °C and 60 rpm for 16 hours.

growth_protocol: Liver tissue removed 24 hours liver resection.

extract_protocol: Each cryopreserved liver tissue was cut in a 2 x 2 mm piece and immediately transferred into 5 mL polypropylene tubes (BD, Franklin Lakes, New Jersey, USA) containing 200 μL chilled homogenization solution and 4 μL lysis buffer (Maxwell 16 LEV simply RNA; Promega, Fitchburg, MA, USA). While kept on ice, each tube was thoroughly mixed using a homogenizer before adding 200 μL lysis buffer (Maxwell 16 LEV simply RNA; Promega, Fitchburg, MA, USA) and vortexed at a maximum speed for 15 seconds, before further processing according to the manufacturer's protocol. The isolated RNA was stored at 80°C.

treatment_protocol: Liver tissue was snap frozen in liquid nitrogen and stored at -80 Celsius until analysis.

tag: strain/background

value: Wistar

tag: genotype/variation

value: Wildtype

value: Liver


title: Baseline  [150]

description: Sample name: 150


title: F-RCM and stressed with 100µM phenanthroline vs F-RCM

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

description: Gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: B. breve UCC2003 grown in filtered RCM supplemented with 100µM phenanthroline until OD.600 of 0.6

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 was grown in filtered reinforced clostridial medium (RCM; Oxoid Ltd.) resuspended in deminerilised water. The RCM media was filtered to remove the agarose to allow cells to be collected by centrifugation this filtration was carried out with the aid of Watt man paper.  Iron limtiation was imposed by supplementing the medium with 85µM ciclopirox olamine or 100µM phenanthroline or 275µM Dipyridyl.   Bifidobacterial cultures were incubated at 37°C, anaerobically in a modular, atmosphere-controlled system (Davidson and Hardy, Belfast, Ireland) to an optical density OD600 of 0.6.

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Cells were collected by centrifugation at 10,000rpm for 2 minutes at room temperature prior to storage in the -80 degree freezer.

value: wild type

tag: growth condition

source_name: B. breve UCC2003 grown in filtered RCM until OD.600 of 0.6

value: filtered RCM until OD.600 of 0.6


title: Baseline  [148]

description: Sample name: 148


title: Baseline  [152]

description: Sample name: 152


title: SHAM [45]

description: Sample name: 45

source_name: Liver, sham operation

value: sham operation


title: Arid1a-deficient IPMN1

city: Kyoto

first: Yoshito

last: Kimura

state: Kyoto

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

department: Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized   on GeneSpring GX 14.5 (Agilent). Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: epithelium of mouse IPMN

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ug Total RNA using the Pico WTA System(Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) 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).

value: Ptf1a-Cre; KrasG12D; Arid1af/f


title: F-RCM v. F-RCM and stressed with 85µM ciclopirox olamine

description: Gene expression array

source_name: B. breve UCC2003 grown in filtered RCM supplemented with 85µM ciclopirox olamine until OD.600 of 0.6


title: F-RCM v. F-RCM and stressed with 100µM phenanthroline

description: Gene expression array

value: filtered RCM supplemented with 100µM phenanthroline until OD.600 of 0.6


title: SHAM [143]

description: Sample name: 143


title: Brg1-deficient IPMN1

value: Ptf1a-Cre; KrasG12D; Brg1f/f


title: Baseline  [147]

description: Sample name: 147


title: SHAM [112]

description: Sample name: 112


title: Baseline  [145]

description: Sample name: 145


title: Brg1-deficient IPMN2


title: F-RCM and stressed with 85µM ciclopirox olamine vs F-RCM

description: Gene expression array

value: filtered RCM supplemented with 85µM ciclopirox olamine until OD.600 of 0.6


title: hMSCs nSi 2

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

description: rpkm.txt

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all samples

source_name: Mesenchymal stem cells

growth_protocol: hMSCs were cultured under normal media conditions consisting of α-minimal essential media (alpha-MEM, Hyclone, GE Sciences) with 16.5% fetal bovine serum (Atlanta Biologicals, USA) and 1% penicillin/streptomycin (100 U/100 µg/mL, Gibco). After every 2-3 days, half of culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching confluency of ~70% and seeded at ~2500 cells/cm2. All experiments were completed with cell populations under P5.

extract_protocol:
RNA was isolated and collected via a Roche, High Purity RNA Isolation kit following the manufacturer’s protocol. Illumina TruSeq RNA Sample Prep Kit was used with 1.5-2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured until 65% confluent and were subjected to two different media compositions for one week. One subset of cells maintained normal media conditions as a negative control (2 replicates); another group was treated with nanosilicates (Laponite XLG®, Na+0.7[(Mg5.5Li0.3Si8O20(OH)4]-0.7) (50 µg/mL) for 48 hours (2 replicates), after which the media was replaced with normal media for the remaining five days. Excess nanosilicates were removed as they are expected to be cleared within 48 hours.

value: Bone marrow derived mesenchymal stem cells

value: Nanosilicate


title: SHAM [114]

description: Sample name: 114


title: hMSCs 2

description: rpkm.txt

value: Control


title: hMSCs nSi 1

description: rpkm.txt


title: Brg1-deficient IPMN3


title: hMSCs 1

description: rpkm.txt


title: Arid1a-deficient IPMN2


title: d16R3

description: d16 replicate three

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

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

data_processing:
BeadStudio software v3.2 and RnBeads through R.
Unmethylated and methylated signal intensities

source_name: hTERT

label_protocol: Standard Illumina Protocol

growth_protocol: The parental or wild type (WT) adherent  hTERT1604 lung fibroblast cell line was cultured in 4.5g/l glucose DMEM  supplemented with 10% FBS and 2x NEAA. Knockdown (KD) cells (d8, d10 and d16) were maintained as for WT but media was supplemented with 150μg/ml hygromycin B, which was removed at least 48hrs before any experimental procedure.

extract_protocol:
Genomic DNA was harvested from cells in log phase of growth. Samples were incubated overnight at 55°C in lysis buffer (50 mM Tris pH 8, 0.1 M EDTA, 0.5% SDS, 0.2 mg/ml proteinase K ), with rotation, and DNA was subsequently isolated using the standard phenol:chloroform:isoamyl alcohol (25:24:1 pH8) extraction method. DNA quality was verified using gel electrophoresis and UV absorbance measurements at 260/280nm and 260/230nm using a Nanodrop UV spectrophotometer.
The genomic DNA isolated was assessed for purity and integrity prior to quantification using the Picogreen fluorescent assay.

tag: gender

value: Male

value: hTERT-immortalised adult fibroblasts

tag: timepoint

tag: replicate

value: three


title: SHAM [41]

description: Sample name: 41


title: d8R1

description: d8 replicate one

tag: cell type

value: one


title: 0.9 [43]

description: Sample name: 43

source_name: Liver, 90% partial hepatectomy

value: Wistar

value: 90% partial hepatectomy


title: 0.9 [111]

description: Sample name: 111

value: Wildtype

value: Liver


title: d16R2

description: d16 replicate two

value: two


title: d10R2

description: d10 replicate two


title: d8R2

description: d8 replicate two


title: d10R3

description: d10 replicate three


title: Gfi1bfl/fl MxCretg NUP98/HOXD13_2

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

institute: University Hospital Of Essen

description: Gene expression data from Gfi1b deficient bone marrow cells from NUP98/HOXD13 transgenic mice

hyb_protocol: Hybridization protocol not provided.

scan_protocol: The arrays were washed and stained according to the manufacturer's recommendation and finally scanned in a GeneChip scanner 3000 (Affymetrix) with G7 update.

data_processing: Signal summarization (RMA algorithm) and statistical analysis by ANOVA  was performed with AltAnalyze version 2.0.9 software (http://www.altanalyze.org/) applying quantile normalization, EnsMart72 database and default parameters.

source_name: leukemic bone marrow cells

label_protocol: For microarray analyses, we used the Affymetrix GeneChip platform employing the Express Kit protocol for sample preparation and microarray hybridization.  Total RNA (200 ng) was converted into biotinylated cRNA, purified, fragmented and hybridized MG-430_2.0 microarrays (Affymetrix).

growth_protocol: bone marrow cells were isolated from leukemic mice

extract_protocol: RNA extraction protocol not provided.

value: bone marrow

value: Gfi1b KO


title: d10R1

description: d10 replicate one


title: d16R1

description: d16 replicate one


title: d8R3

description: d8 replicate three


title: 0.9 [106]

description: Sample name: 106


title: WT 3 (control)

description: WThTERT replicate three

value: WThTERT


title: 0.9 [61]

description: Sample name: 61


title: SHAM [141]

description: Sample name: 141

value: sham operation


title: 0.9 [87]

description: Sample name: 87


title: Gfi1b wt MxCretg NUP98/HOXD13_1

description: Gene expression data from Gfi1b wild-type bone marrow cells from NUP98/HOXD13 transgenic mice

value: Gfi1b wildtype


title: Gfi1bfl/fl MxCretg NUP98/HOXD13_3


title: WT 2 (control)

description: WThTERT replicate two


title: 0.7 [136]

description: Sample name: 136

source_name: Liver, 70% partial hepatectomy

value: 70% partial hepatectomy


title: 0.3 [95]

description: Sample name: 95

source_name: Liver, 30% partial hepatectomy

value: 30% partial hepatectomy


title: Patient 13

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: 2565 miRNAs were spotted on each array.

hyb_protocol: Hybridized onto a human miRNA Oligo chip, version 21 (Toray, Tokyo).

scan_protocol: 3D-Gene 3000 Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by quantile normalization (Bolstad BM, et al. Bioinformatics 2003; 19: 185-193). In short, the raw data of each spot was processed by substitution with a mean+2SD of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Any miRNAs which showed values equal to 0 or less than 0 after the substitution above were deleted, where 2555 miRNAs were narrowed down to 758 miRNAs. The quantile normalization was performed further on the data according to the literature above written by Bolstad, et al.

source_name: serum

label_protocol: Extracted total RNA was labeled with Hy3 using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy Serum/Plasma kit (Qiagen).

tag: diagnosis

value: HBeAg negative chronic hepatitis B

value: serum

tag: peg-ifn dose (μg/week)

tag: weeks of peg-ifn treatment


title: Patient 14

description: 2565 miRNAs were spotted on each array.


title: Patient 12

description: 2565 miRNAs were spotted on each array.


title: Patient 15

description: 2565 miRNAs were spotted on each array.


title: Gfi1b wt MxCretg NUP98/HOXD13_2