title: ChIP_Rice_7days_leaf_H2A.Z


title: PDIS9061-173

status: Public on Sep 19 2019

type: SRA

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq (v2.16.0.10).
For RamDA-seq data with living cells, fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-l 36 --lowcomplex-pct 74 --homopolymer- pct 74 -k 4' for RamDA-seq and '-L 75 -l 46 -k 4 -q 30' for C1-RamDA-seq. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks -p 4 -k 5 -X 800 --sp 1000,1000'. Uniquely mapped reads were selected using the bamtools ‘filter’ command with the parameters '-isMapped true -tag NH:1' and samtools ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). The transcript-level expression levels were quantified using sailfish (version 0.9.2). The transcript-level expression levels were also calculated using Bowtie2 (version 2.2.6) with the parameters '-k 100 -X 800' and eXpress (version 1.5.1) with the parameter '--no-bias-correct'.
Genome_build: mm10
Supplementary_files_format_and_content: txt, bigWig

molecule: total RNA

organism: Homo sapiens

growth_protocol: 5G6GR mouse ES cells were used for bulk and single-cell RNA-seq. The cells were cultured in a feeder-free gelatin-coated dish in 10% fetal calf serum containing Glasgow minimal essential medium (GMEM; Sigma-Aldrich), 1000 U/mL leukemia inhibitory factor (ESGRO; Invitrogen), 100 µmol/l 2-mercaptoethanol (Nacalai Tesque), 1× non-essential amino acids (Life Technologies), 1 mmol/L sodium pyruvate (Life Technologies), 2 mmol/L L-glutamine (Nacalai Tesque), 0.5× penicillin/streptomycin (Life Technologies), 0.5 ug/ml puromycin (Sigma) and 10 µg/mL blasticidin (Life Technologies).

extract_protocol:
For single-cell RamDA-seq, single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa). The cell lysate solution was stored at -80ºC until use.
For library construction of RamDA-seq, refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs".

treatment_protocol: For the assessment of PrE differentiation, 5G6GR ES cells were cultured in differentiation medium containing 100 mmol/l dexamethasone rather than blasticidin. The cells are cultured for 72 hours.

tag: cell type

value: Neural stem cell derived from human induced pluripotent stem

tag: sample type

value: MoFlo sorted cell

tag: method subtype

value: RamDA-seq


title: PDIS9061-174


title: ChIP_Rice_7days_leaf_H3K4me1

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

country: USA

institute: University of Georgia

data_processing:
RNA-seq: analysis was performed using Tophat v2.1.1 and cufflinks v2.2.1
ChIP-seq: analysis was performed using bowtie1.1.1
ATAC-seq:analysis was performed using bowtie1.1.1, macs2
Genome_build: Arabidopsis thaliana, Eutrema salsugineum, Phaseolus vulgaris,  Glycine max, Brachypodium distachyon, Oryza sativa, Setaria viridis, Populus trichocarpa, Sorghum bicolor genomes were from JGI (phytozome version 11) ; Zea mays from maizeGDB AGP_v4; Hordeum vulgare from ensemble (version 42) ; Asparagus officinalis from Asparagus genome project (http://asparagus.uga.edu/tripal/);  Spirodela polyrhiza from Michael et al..
Supplementary_files_format_and_content: *BED file, the identified regulatory regions, tab delimited text file, see ACR_column_header.txt for column headers
Supplementary_files_format_and_content: *BIGWIG , the genome coverage of each sample

organism: Oryza sativa

source_name: DNA

growth_protocol: Arabidopsis thaliana (accession Col-0) were grown on 1/2MS plates under 25°C and continues light for 7 days. Leaves were collected for the experiments. Spirodela polyrhiza (accession 7498) were grown in liquid bases (Schenk and Hilldebrandt basak salt mixture) under 25°C and continuous light. Whole seedlings were collected 3 days after transferring to a new basis. Eutrema salsugineum (accession Shandong) and Asparagus officinalis (accession Gijnlim) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). All the young leaves were collected for the experiments. Phaseolus vulgaris (accession G19833) and Glycine max (accession William82) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). The 2nd and 3rd leaves were collected for the experiments. Brachypodium distachyon (accession Bd21), Oryza sativa (accession Nipponbare), Setaria viridis (accession A10), Sorghum bicolor, Zea mays (accession B73), and Hordeum vulgare (accession Morex) were grown in soil for ~6-7days under 25°C, 16 hours of light/8 hours of dark. The inner second leaves—which contains the third and fourth leaves sheathed inside—were used for experiments. Populus trichocarpa leaves were collected from the tree and flash-frozen with liquid N2 immediately for the following experiments.

extract_protocol: ChIP-seq: ChiP-seq was performed following the methods of Zhang et al (2007) (https://www.ncbi.nlm.nih.gov/pubmed/17439305).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.

tag: accession

value: Nipponbare

tag: tissue

value: leaf

tag: age


title: PDIS9061-185


title: BIBO_6y_genomic DNA [201530460051_R05C01]

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description:
201530460051_R05C01
sample: 277
Normal buccal epithelial cells.

hyb_protocol: gDNA was bisulphite converted using the Zymo EZ DNA methylation kit. Hybridized to the Infinium MethylationEPIC array.

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

data_processing:
GenomeStudio software V2-0-3.
Average Beta (after background-subtraction and colour-correction in GenomeStudio software according to standard Illumina protocol).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: QIAamp DNA Mini Kit.

value: buccal epithelial cells

tag: gender

value: Female

tag: age (days)


title: BIBO_6y_genomic DNA [201516320049_R04C01]

description:
201516320049_R04C01
sample: 286
Normal buccal epithelial cells.


title: ChIP_Rice_7days_leaf_H3K4me3


title: BIBO_6y_genomic DNA [201533620002_R08C01]

description:
201533620002_R08C01
sample: 285
Normal buccal epithelial cells.


title: PDIS9061-170


title: PDIS9061-169


title: PDIS9061-171


title: ChIP_Rice_7days_leaf_Input


title: PDIS9061-168


title: PDIS9061-167


title: ChIP_Rice_7days_leaf_H3K36me3


title: BIBO_6y_genomic DNA [201516320017_R05C01]

description:
201516320017_R05C01
sample: 272
Normal buccal epithelial cells.

value: Male


title: PDIS9061-166


title: ChIP_Rice_7days_leaf_H3K56ac


title: PDIS9061-164


title: BIBO_6y_genomic DNA [201533610043_R05C01]

description:
201533610043_R05C01
sample: 273
Normal buccal epithelial cells.


title: ChIP_Rice_7days_leaf_H3K27me3


title: BIBO_6y_genomic DNA [201530460051_R06C01]

description:
201530460051_R06C01
sample: 271
Normal buccal epithelial cells.


title: PDIS9061-163


title: PDIS9061-165


title: ChIP_Rice_7days_leaf_H3


title: PDIS9061-162


title: PDIS9061-161


title: PDIS9061-172


title: RNA_Rice_7days_leaf_rep2

source_name: mRNA

extract_protocol: RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol


title: BIBO_6y_genomic DNA [201516320001_R05C01]

description:
201516320001_R05C01
sample: 274
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201533610043_R04C01]

description:
201533610043_R04C01
sample: 268
Normal buccal epithelial cells.


title: PDIS9061-160


title: PDIS9061-159


title: RNA_Rice_7days_leaf_rep1


title: PDIS9061-156


title: BIBO_6y_genomic DNA [201516320018_R05C01]

description:
201516320018_R05C01
sample: 264
Normal buccal epithelial cells.


title: PDIS9061-154


title: BIBO_6y_genomic DNA [201516320012_R04C01]

description:
201516320012_R04C01
sample: 265
Normal buccal epithelial cells.


title: PDIS9061-153


title: BIBO_6y_genomic DNA [201533620002_R05C01]

description:
201533620002_R05C01
sample: 262
Normal buccal epithelial cells.


title: PDIS9061-152


title: BIBO_6y_genomic DNA [201533610043_R06C01]

description:
201533610043_R06C01
sample: 269
Normal buccal epithelial cells.


title: PDIS9061-150


title: PDIS9061-151


title: BIBO_6y_genomic DNA [201530440009_R04C01]

description:
201530440009_R04C01
sample: 260
Normal buccal epithelial cells.


title: PDIS9061-148


title: BIBO_6y_genomic DNA [201530460051_R08C01]

description:
201530460051_R08C01
sample: 259
Normal buccal epithelial cells.


title: PDIS9061-147


title: PDIS9061-145


title: BIBO_6y_genomic DNA [201516320017_R08C01]

description:
201516320017_R08C01
sample: 258
Normal buccal epithelial cells.


title: PDIS9061-146


title: PDIS9061-157


title: PDIS9061-144


title: PDIS9061-143


title: BIBO_6y_genomic DNA [201516320017_R07C01]

description:
201516320017_R07C01
sample: 257
Normal buccal epithelial cells.


title: PDIS9061-142


title: BIBO_6y_genomic DNA [201530440034_R03C01]

description:
201530440034_R03C01
sample: 254
Normal buccal epithelial cells.


title: PDIS9061-141


title: BIBO_6y_genomic DNA [201530440060_R02C01]

description:
201530440060_R02C01
sample: 359
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440009_R03C01]

description:
201530440009_R03C01
sample: 339
Normal buccal epithelial cells.


title: PDIS9061-140


title: Normoandrogenic PCOS s16

type: RNA

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

country: China

institute: China Medical University

hyb_protocol: The sample microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version13.1,Agilent Technologies)were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm.
The probes that at least 75% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

label_protocol: The sample labeling was performed based on the manufacturer’s standard protocols.

extract_protocol: When at least 1 follicle grew to 18 mm in diameter, 250 μg of recombinant hCG (Ovidrel, Merck-Serono, Switzerland) was administered, and oocyte retrieval was performed 34–36 hours later. The granulosa cell samples were centrifuged at 12,000 g for 10 minutes to remove blood, and the remaining fluid was used in subsequent studies.

treatment_protocol: Control and PCOS patient ovaries were stimulated with recombinant follicle-stimulating hormone (FSH) (Merck-Serono, Switzerland) after pretreatment with gonadotropin-releasing hormone agonist (Diphereline, Ipsen Pharma Biotech, France) .

value: ovary

value: granusola cells

tag: condition

value: Normoandrogenic PCOS


title: PDIS9061-139


title: Normal s15

value: Normal


title: Normoandrogenic PCOS s18


title: BIBO_6y_genomic DNA [201533610043_R07C01]

description:
201533610043_R07C01
sample: 253
Normal buccal epithelial cells.


title: Normal s14


title: BIBO_6y_genomic DNA [201533620002_R04C01]

description:
201533620002_R04C01
sample: 251
Normal buccal epithelial cells.


title: Normoandrogenic PCOS s17


title: PDIS9061-137


title: PDIS9061-135


title: Normal s12


title: Hyperandrogenic PCOS s10

value: Hyperandrogenic PCOS


title: Hyperandrogenic PCOS s9


title: BIBO_6y_genomic DNA [201530440034_R07C01]

description:
201530440034_R07C01
sample: 250
Normal buccal epithelial cells.


title: PDIS9061-133


title: PDIS9061-134


title: PDIS9061-132


title: BIBO_6y_genomic DNA [201530460051_R03C01]

description:
201530460051_R03C01
sample: 249
Normal buccal epithelial cells.


title: 24: PBS injected fish3

city: Leiden

first: Lanpeng

last: Chen

state: South Holland

address: Einsteinweg 55, GW3.19

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: Hematopoietic tissue without cancer cells

data_processing:
All RNAseq libraries (150–750 bp inserts) were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single-end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample.
Illumina reads were aligned against the human (GRCh38.p3) and zebrafish (GRCz10.80) reference genome sequences using TopHat (version 2.0.5). Secondary alignments of reads were excluded by filtering the files using SAMtools (version 0.1.18)
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9).
To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor, library size estimates determined using the R/Bioconductor (release 2.11) package DESeq were employed
Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools.
Supplementary_files_format_and_content: tab-delimited text files include gene name, ID, reads and normalized comparision between each groups

organism: Danio rerio

source_name: PBS-injected fish

growth_protocol: PC-3M-Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200-400 PC-3M-Pro4 cells were injected into the duct of cuvier (DoC) of the zebrafish embryos using a Pneumatic Picopump and a manipulator (WPI). After transplantation, 120 well-engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.

extract_protocol:
Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area (80 fish per group randomly chosen from >100 engrafted fish) at 6dpi (8dpf) with a micro dissection scissor (WPI). The samples were immediately washed with cold PBS and stored in TRIzol (Sigma) at -80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at  -80 ˚C. RNA isolation was further performed using RNeasy mini kit (qiagen)
then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina, San Diego CA, USA).

tag: FISH strain

value: 8 days post fertilization


title: PDIS9061-129


title: PDIS9061-131


title: PDIS9061-130


title: PDIS9061-128


title: BIBO_6y_genomic DNA [201530460044_R04C01]

description:
201530460044_R04C01
sample: 244
Normal buccal epithelial cells.


title: PDIS9061-126


title: BIBO_6y_genomic DNA [201516320005_R05C01]

description:
201516320005_R05C01
sample: 242
Normal buccal epithelial cells.


title: PDIS9061-138


title: 22: PBS injected fish1

value: Hematopoietic tissue without cancer cells


title: 23: PBS injected fish2


title: PDIS9061-124


title: PDIS9061-125


title: Normal s3


title: Hyperandrogenic PCOS s5


title: Hyperandrogenic PCOS s13


title: PDIS9061-122


title: BIBO_6y_genomic DNA [201516320012_R06C01]

description:
201516320012_R06C01
sample: 245
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320049_R05C01]

description:
201516320049_R05C01
sample: 241
Normal buccal epithelial cells.


title: PDIS9061-123


title: BIBO_6y_genomic DNA [201530440001_R02C01]

description:
201530440001_R02C01
sample: 241
Normal buccal epithelial cells.


title: Normoandrogenic PCOS s1


title: PDIS9061-127


title: BIBO_6y_genomic DNA [201516320049_R01C01]

description:
201516320049_R01C01
sample: 240
Normal buccal epithelial cells.


title: PDIS9061-119


title: PDIS9061-118


title: BIBO_6y_genomic DNA [201530460007_R01C01]

description:
201530460007_R01C01
sample: 238
Normal buccal epithelial cells.


title: PDIS9061-117


title: PDIS9061-116


title: BIBO_6y_genomic DNA [201530460006_R08C01]

description:
201530460006_R08C01
sample: 237
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320017_R04C01]

description:
201516320017_R04C01
sample: 235
Normal buccal epithelial cells.


title: PDIS9061-114


title: PDIS9061-110


title: PDIS9061-112


title: NC_016

city: Siena

first: Mohsen

last: Navari

state: SI

address: Via delle Scotte 6

department: Medical Biotechnology

country: Italy

institute: University of Siena

description: Fresh Cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was processed in GeneSpring version GX 12  based on the following criteria: threshold: 1.0; logbase: 2; normalization: shift to 75 percentile; baseline transformation: median of all samples. Probes with missing values were removed.

label: Biotin

source_name: Normal T-Cell

label_protocol: The obtained RNA was  processed as for manufacturer’s instructions to produce biotinylated cDNA.

extract_protocol: For FFPE samples, RecoverAll™ Total Nucleic Acid Isolation Kit (Thermofisher, Waltham, MA, USA) was used to extract total RNA from FFPE samples. Up to five 10 μm-thick sections were processed per reaction. The samples were rehydrated using a series of xylene and ethanol washes. Next, they were subjected to a rigorous protease digestion with an incubation time tailored for recovery of total RNA. RNA was purified using a rapid glass-fibre filter methodology that includes an on-filter DNase treatment and were eluted into the low salt buffer provided. A NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA) was used to quantify RNA content and assess its purity in terms of 260/280 and 260/230 absorbance.  Extraction of RNA from normal CD4+ samples was achieved by means of TRIZOL (Thermofisher, Waltham, MA, USA) reagent, according to the manufacturer’s protocol.

tag: disease state

value: Healthy Donor

value: Normal T-Cells


title: PDIS9061-106

value: Neural stem cell derived from human induced pluripotent stem


title: NC_014

description: Fresh Cells


title: PDIS9061-120

value: MoFlo sorted cell


title: PDIS9061-103

value: RamDA-seq


title: BIBO_6y_genomic DNA [201516320055_R02C01]

description:
201516320055_R02C01
sample: 231
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320012_R05C01]

description:
201516320012_R05C01
sample: 228
Normal buccal epithelial cells.


title: PDIS9061-101


title: PDIS9061-102


title: BIBO_6y_genomic DNA [201516320012_R07C01]

description:
201516320012_R07C01
sample: 234
Normal buccal epithelial cells.


title: PDIS9061-104


title: PDIS9061-107


title: NC_012

description: Fresh Cells


title: NC_009

description: Fresh Cells


title: NC_010

description: Fresh Cells


title: PDIS9061-100


title: NC_008

description: Fresh Cells


title: BIBO_6y_genomic DNA [201516320024_R01C01]

description:
201516320024_R01C01
sample: 227
Normal buccal epithelial cells.


title: PDIS9061-115


title: PDIS9061-098


title: PDIS9061-099


title: PDIS9061-097


title: NC_005

description: Fresh Cells


title: BIBO_6y_genomic DNA [201533610043_R03C01]

description:
201533610043_R03C01
sample: 226
Normal buccal epithelial cells.


title: PDIS9061-096


title: PDIS9061-095


title: NC_006

description: Fresh Cells


title: NC_003

description: Fresh Cells


title: PDIS9061-093


title: PDIS9061-092


title: BIBO_6y_genomic DNA [201516320012_R08C01]

description:
201516320012_R08C01
sample: 226
Normal buccal epithelial cells.


title: NC_001

description: Fresh Cells


title: BIBO_6y_genomic DNA [201530440060_R06C01]

description:
201530440060_R06C01
sample: 224
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320005_R02C01]

description:
201516320005_R02C01
sample: 216
Normal buccal epithelial cells.


title: PDIS9061-086


title: PDIS9061-090


title: PDIS9061-232


title: PDIS9061-088


title: PDIS9061-085


title: PDIS9061-087


title: BIBO_6y_genomic DNA [201516320001_R07C01]

description:
201516320001_R07C01
sample: 215
Normal buccal epithelial cells.


title: PDIS9061-083


title: PTCL_080

description: Formalin-Fixed, Paraffin-Embedded

source_name: Peripheral T-Cell Lymphoma-Not Otherwise Specified

value: FFPE Tumor Sample


title: BIBO_6y_genomic DNA [201530440060_R03C01]

description:
201530440060_R03C01
sample: 227
Normal buccal epithelial cells.


title: PDIS9061-082


title: PDIS9061-084


title: BIBO_6y_genomic DNA [201516320001_R01C01]

description:
201516320001_R01C01
sample: 213
Normal buccal epithelial cells.


title: PDIS9061-081


title: PDIS9061-080


title: BIBO_6y_genomic DNA [201516320012_R02C01]

description:
201516320012_R02C01
sample: 210
Normal buccal epithelial cells.


title: PDIS9061-089


title: PTCL_076

description: Formalin-Fixed, Paraffin-Embedded

value: Peripheral T-Cell Lymphoma-Not Otherwise Specified


title: PDIS9061-079


title: PTCL_078

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-078


title: PTCL_077

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_075

description: Formalin-Fixed, Paraffin-Embedded


title: BIBO_6y_genomic DNA [201530440060_R05C01]

description:
201530440060_R05C01
sample: 209
Normal buccal epithelial cells.

value: buccal epithelial cells


title: PDIS9061-077


title: PTCL_079

description: Formalin-Fixed, Paraffin-Embedded


title: BIBO_6y_genomic DNA [201530440034_R08C01]

description:
201530440034_R08C01
sample: 207
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320055_R01C01]

description:
201516320055_R01C01
sample: 206
Normal buccal epithelial cells.

value: Female


title: PDIS9061-076


title: PDIS9061-073


title: PDIS9061-075


title: BIBO_6y_genomic DNA [201516320012_R01C01]

description:
201516320012_R01C01
sample: 205
Normal buccal epithelial cells.


title: PDIS9061-071


title: PDIS9061-070


title: PDIS9061-072


title: PTCL_071

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_072

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-069


title: BIBO_6y_genomic DNA [201530440009_R06C01]

description:
201530440009_R06C01
sample: 203
Normal buccal epithelial cells.

value: Male


title: PDIS9061-067


title: BIBO_6y_genomic DNA [201516320055_R03C01]

description:
201516320055_R03C01
sample: 220
Normal buccal epithelial cells.


title: PDIS9061-068


title: PTCL_073

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_074

description: Formalin-Fixed, Paraffin-Embedded


title: BIBO_6y_genomic DNA [201530460007_R03C01]

description:
201530460007_R03C01
sample: 202
Normal buccal epithelial cells.


title: PTCL_069

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_070

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-066


title: PDIS9061-065


title: PDIS9061-064


title: BIBO_6y_genomic DNA [201516320001_R03C01]

description:
201516320001_R03C01
sample: 201
Normal buccal epithelial cells.


title: PDIS9061-063


title: PDIS9061-062


title: PDIS9061-061


title: PDIS9061-060


title: PTCL_067

description: Formalin-Fixed, Paraffin-Embedded


title: BIBO_6y_genomic DNA [201516320001_R04C01]

description:
201516320001_R04C01
sample: 204
Normal buccal epithelial cells.


title: ATAC_Arabidopsis_7days_leaf_Input

organism: Arabidopsis thaliana

extract_protocol: ATAC-seq libraries were prepared following the ATAC-seq protocol  as previously described in (Lu et al. 2016).

value: leaf


title: PTCL_068

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-059


title: PDIS9061-058


title: PTCL_066

description: Formalin-Fixed, Paraffin-Embedded


title: ATAC_Arabidopsis_7days_leaf_rep1


title: ATAC_Arabidopsis_7days_leaf_rep2


title: PDIS9061-056


title: PDIS9061-057


title: PDIS9061-055


title: ChIP_Arabidopsis_7days_leaf_Input


title: ChIP_Arabidopsis_7days_leaf_H3K4me1


title: ChIP_Arabidopsis_7days_leaf_H2A.Z


title: PTCL_064

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-053


title: PDIS9061-054


title: PDIS9061-051


title: PDIS9061-050


title: PDIS9061-052


title: PTCL_065

description: Formalin-Fixed, Paraffin-Embedded


title: ChIP_Arabidopsis_7days_leaf_H3K4me3


title: ChIP_Arabidopsis_7days_leaf_H3K56ac


title: PDIS9061-048


title: PTCL_061

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-046


title: PDIS9061-045


title: PDIS9061-042


title: PTCL_062

description: Formalin-Fixed, Paraffin-Embedded


title: ChIP_Arabidopsis_7days_leaf_H3K36me3


title: PTCL_060

description: Formalin-Fixed, Paraffin-Embedded

source_name: Lennert Lymphoma

value: Lennert Lymphoma


title: PTCL_059

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_058

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-039


title: PDIS9061-040


title: PDIS9061-047


title: PTCL_063

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-049


title: PTCL_057

description: Formalin-Fixed, Paraffin-Embedded


title: ChIP_Arabidopsis_7days_leaf_H3


title: RNA_Arabidopsis_7days_leaf_rep2


title: PTCL_056

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-036


title: PDIS9061-035


title: PDIS9061-037


title: RNA_Arabidopsis_7days_leaf_rep1


title: PDIS9061-033


title: PDIS9061-034


title: Yap Taz-KD replicate 4

city: Charlottesville

first: Bernard

middle: Victor

last: Thisse

state: VA

address: 1340 Jefferson Park ave

department: Cell Biology

institute: University of Virginia

data_processing:
Sequenced read were trimmed for adaptor sequence then mapped to GRCz10 whole genome using STAR
Quantitation of reads aligning to each gene is done using featureCounts
DESeq2 Bioconductor package was used to normalize count data, estimate dispersion, and fit a negative binomial model for each gene.
The Benjamini-Hochberg False Discovery Rate procedure was used to re-estimate the adjusted p-values for Ensembl gene IDs mapping to known genes
Genome_build: GRCz10
Supplementary_files_format_and_content: the processed data files contains the normalized counts for each genes (expressed as Transcripts Per Kilobase Million - TPM)  in all 12 analyzed samples. Log2 fold change  and adjusted p value between control morpholino (WT) and Vgll4l Knockdown (KD) and between  control morpholino (WT) and YAP/TAZ  KD samples are also provided.

source_name: Dorsal Forerunner Cells

growth_protocol: embryos were injected at one cell stage with either control morpholino or morpholinos against the gene(s) of interest and raised at 29C until 90% epiboly

extract_protocol:
single dorsal forerunner cells cluster from Tg(sox17:gfp) injected embryos were dissected under fluoresence in DMEM/F12 and flash frozen in 2µl of medium in liquid nitrogen. Total RNA were extracted and purified using SMART-Seq®  v4 Ultra® Low Input RNA Kit for Sequencing from clontech. Purified RNA samples were then reverse transcribed into cDNA and amplified.
Libraries are constructed using NEB DNA Ultra library construction kit, with standard TruSeq-type adapters. Libraries size and concentration were assessed using Agilent 2,100 Bioanalyzer. Libraries were multiplexed and 50bp single-end were sequenced by BGI generating  a minimum of 20millons read per sample. Genome-wide transcriptome were produced from quadruplicate biological replicates.

tag: strain

tag: developmetal stage

value: 90% epiboly

tag: experimental condition

value: embryo injected with Yap1 and Wwtr1  morpholinos


title: PTCL_054

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-030


title: PTCL_053

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-029


title: PDIS9061-032


title: ChIP_Arabidopsis_7days_leaf_H3K27me3


title: Yap Taz-KD replicate 3


title: PDIS9061-028


title: PDIS9061-038


title: Yap Taz-KD replicate 2


title: PDIS9061-027


title: PDIS9061-026


title: PTCL_051

description: Formalin-Fixed, Paraffin-Embedded


title: Vgll4l-KD replicate 4

value: embryo injected with Vgll4l morpholino


title: Yap Taz-KD replicate 1


title: PTCL_050

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_055

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-022


title: PDIS9061-025


title: PTCL_049

description: Formalin-Fixed, Paraffin-Embedded


title: Vgll4l-KD replicate 3


title: PDIS9061-020


title: PTCL_048

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_047

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-019


title: PTCL_052

description: Formalin-Fixed, Paraffin-Embedded


title: Vgll4l-KD replicate 1


title: Control Morpholino replicate 4

value: embryo injected with control morpholino


title: Vgll4l-KD replicate 2


title: PDIS9061-014


title: PDIS9061-018


title: PTCL_046

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-023


title: PDIS9061-021


title: Control Morpholino replicate 3


title: F5E6_E12.5_Embryo

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
Gene_expression_E12.5_FPKM.txt
Allelic_gene_expression_E12.5_Readcount.txt

data_processing:
Gene expression for each replicate was quantitated using the RNA-seq quantitation pipeline in SeqMonk as RPKM over mRNA (merging isoforms)
Allelic gene expression was quantitated for each allelically mapped replicate using the RNA-seq quantitation pipeline in SeqMonk as raw read count over mRNA (merging isoforms)
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-Seq report is tab-delimited and shows annotated gene coordinates and their log2(RPKM) values as follows: col 1: <gene name>, col2: <Chromosome>, col 3:  <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.

organism: Mus musculus

source_name: Whole embryo

extract_protocol:
C57BL6/J females were superovulated and crossed with CAST/EiJ males.  Zygotes were recovered the next day and electroporated with two sgRNAs for the Gab1 RLTR15 ERVK element (200ng/μl each) (Fig S7) and CAS9 protein (500ng/μl).  Embryos were then implanted into NMRI pseudo-pregnant females.  Embryos were dissected on E12.5 and the following tissues were collected: 1) visceral yolk sac/amnion, 2) placental disc with as much decidua removed as possible, 3) embryo, and 4) tail clip for genotyping.  Tissue samples were washed in cold PBS and flash frozen in 50μL of RLT+ buffer (Qiagen).  RNA was extracted from E12.5 yolk sac, placenta and whole embryo using RNeasy Mini Kit (Qiagen) as per the manufacturers’ instructions.
RNA was treated TURBO DNase (Thermo Fisher Scientific) and quality was assessed with RNA Pico Kit (Agilent) on the Agilent 2100 Bioanalyzer (RIN>8.7 for all samples).  mRNA sequencing libraries were generated using SmartSeq v4 cDNA generation and Nextera XT library preparation, as per manufacturers’ instructions.  The quantification of all libraries was done using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification kit (KAPA).  Libraries were sequenced using 125bp paired-end on the Illumina HiSeq 2500 RapidRun, multiplexing 12 samples over two lanes.

value: Whole embryo

tag: genotype

value: Wildtype

tag: hybrid strain

value: C57BL6 x CAST/Ei


title: F5E6_E12.5_Placenta

source_name: Placenta (mat contamination)

value: Placenta (mat contamination)


title: F4E5_E12.5_Embryo

value: Mosaic Gab1 ERVK RLTR15 +/- (paternal allele deletion)


title: PDIS9061-010

value: Neural stem cell derived from human induced pluripotent stem

value: MoFlo sorted cell

value: RamDA-seq


title: Control Morpholino replicate 2


title: PDIS9061-009


title: Control Morpholino replicate 1


title: PDIS9061-016


title: PTCL_044

description: Formalin-Fixed, Paraffin-Embedded

value: Peripheral T-Cell Lymphoma-Not Otherwise Specified

value: FFPE Tumor Sample


title: PDIS9061-008


title: F4E5_E12.5_Placenta


title: PTCL_041

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_042

description: Formalin-Fixed, Paraffin-Embedded


title: PDIS9061-013


title: PTCL_043

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_040

description: Formalin-Fixed, Paraffin-Embedded


title: F4E5_E12.5_VE

source_name: Yolk sac

value: Yolk sac


title: PDIS9061-007


title: F4E3_E12.5_Embryo


title: PDIS9061-006


title: PDIS9061-011


title: F5E6_E12.5_VE


title: F4E3_E12.5_Placenta


title: WT fibroblast primary cell line [FH122]

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
FH122
3D collagen culture

hyb_protocol: cRNA were then hybridized on 8×60K high density SurePrint G3 human gene expression Agilent microarrays according to manufacturer's instructions (Agilent Technologies). Agilent : 100.0 ng at 55 degree_C during 20 hours.

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: The data were quantile normalized using the Bioconductor package limma. Means of ratios from all comparisons were calculated and the moderated t-statistic of the limma package provided the per gene P values. The Benjamini-Hochberg procedure was used to adjust the p-values for multiple gene comparisons.

source_name: WT fibroblast primary cell line 3

label_protocol: The integrity of the RNA was assessed using an Agilent BioAnalyzer 2100 (Agilent Technologies). Amplification and labeling were performed with the LowInput QuickAmp Labeling Kit (Agilent Technologies).

growth_protocol: Fibroblasts (1x10e6) were cultured in a tridimensional type I collagen matrix at a concentration of 2.5x10e5 cells/mL for 4 days. After that, the matrix was cultured 7 days in immersion and then 7 days at the air-liquid interface as described in (Bernerd, Asselineau et al. 2001).

extract_protocol: 3D-dermal cultures were frozen in liquid nitrogen, and then disrupted and solubilized in Qiazol reagent (Qiagen) using a gentleMACSTM Dissociator (Miltenyi Biotech) with M tubes and the RNA_02 program recommended by the manufacturer (Miltenyi Biotech). Total RNAs were extracted using miRNeasy Mini kit (Qiagen) (3D-dermal cultures) or mRNeasy Mini kit (Qiagen) (cells) and then purified using the RNA cleanup and concentration kit (Qiagen).

tag: genotype/variation

value: WT

value: 19 years

value: Skin fibroblasts


title: PTCL_045

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_039

description: Formalin-Fixed, Paraffin-Embedded


title: F4E3_E12.5_VE


title: PDIS9061-005

tag: cell type


title: PDIS9061-004

tag: sample type


title: F4E1_E12.5_Placenta


title: PDIS9061-003

tag: method subtype


title: PDIS9061-002


title: PTCL_037

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_038

description: Formalin-Fixed, Paraffin-Embedded


title: F4E1_E12.5_VE


title: Liver_H3K4me1_WT_ChIP

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

institute: fondazione Istituto italiano di tecnologia

library_source: genomic

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Transcription factors (YAP, TEAD, MYC, Pol2) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --mfold=7,30 -g mm -p 0.00001
Histone marks (H3K4me1, H3K4me3, H3K27Ac, H3K27me3) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --auto-bimodal --broad -g mm -p 0.00000001
the input alignment file wass randomly downsampled to the size of the ChIP sample alignment file
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.xls.gz files: bed files of transcription factors ChIP-Seq;  *_broad_peaks.bed.gz files: bed files of histone marks ChIP-Seq

source_name: Liver

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For Myc, TEAD, Histone Marks, RNAPol2 ChIP, 3T9 fibroblasts or dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate)  and 1% formaldehyde (FA).
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers

value: liver

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: SOX2_ChIP_96h_Rep2

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

description:
SOX2Peaks_RPKMTable.xlsx
SampleMapping_SOX2ChIP.xlsx

data_processing:
Sequencing read were aligned to the mouse genome (mm10) using bowtie with default parameters
Peaks for SOX2 ChIPs were called using MACS2 and IDR framework.
IDR called SOX2 peaks from different conditions were further processed using in-house pipeline. Peaks from different conditions were merged together if they were found to be overlapping. New peak summit for these merged peak was calcualted based on their relative contributions (heights) as a measure of distance. After calculating and assigning new peak summit to the merged peaks, peaks boundries were also redefined by extending them by 300 bps in both directions from the newly assigned peak summit.
These peaks were then used for downstream analysis. We calculated RPKM for these 600bp peaks. A meta table was created for these 600bp peaks with RPKM values for TFs, histone marks as well as ATAC signal.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited file with coordinates and RPKM.

source_name: iPSC

growth_protocol: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP were maintained on CF1 mouse embryonic fibroblasts (MEFs) in KO-DMEM containing 15% fetal bovine serum (FBS), 1% penicillin/streptomycin, 1X glutaMAX supplement (Gibco), 1% nonessential amino acid, and 5 × 105 U LIF. To perform the ChIP assay, iPSCs were first changed into serum-free N2B27 medium supplemented with LIF and 2i (3 μM CHIR99021 and 1 μM PD0325901) for a minimum of 24 hours. Differentiation was induced by rinsing iPSCs thoroughly with 1X PBS and changing to N2B27 media without LIF 2i. To test colony-forming potential, differentiated cells were trypsinized to single cells and seeded at very low density (~1,300 cells/cm2) on CF1 MEFs in KO-DMEM containing 15% serum and LIF (no dox condition) or supplemented with 2 μg/ml dox (+dox condition).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells were crosslinked in 1% formaldehyde for 10 minutes at 37°C with constant stirring, followed by quenching with 125 mM glycine for 5 min at room temperature. Cells were rinsed with 1X PBS and lysed, and chromatin was sheared using a Branson sonicator until the majority of DNA was in the range of 200-1,000 base pairs. Chromatin was incubated with antibody at 4°C overnight with constant stirring. Co-immunoprecipitation of antibody-protein complexes was performed using Protein A or Protein G Dynabeads for 1h at 4°C. ChIPs were completed using previously reported methods with the following antibodies: OCT4 (Santa Cruz, sc-8628x), H3K4me2 (Millipore, 07-030),H3K27ac () .Immunoprecipitated DNA was end repaired using the End-IT DNA End-Repair Kit (Epicentre), extended using Klenow fragment (3’-5’ exo) (NEB), and ligated to sequencing adapter oligos (Illumina). Each library was PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 base pairs selected for sequencing. Libraries were sequenced on the Illumina Hiseq 2000.

treatment_protocol: Dox-treatment was performed as explained above

value: Santa Cruz (sc,07-030)

value: iPSC

tag: time


title: WT fibroblast primary cell line [FTM5]

description:
FTM5
3D collagen culture

source_name: WT fibroblast primary cell line 2

tag: age

value: 25 years


title: PDIS9061-001


title: WT fibroblast primary cell line [FTM1]

description:
FTM1
3D collagen culture

source_name: WT fibroblast primary cell line 1

value: 40 years


title: PTCL_036

description: Formalin-Fixed, Paraffin-Embedded

tag: tissue


title: PTCL_035

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_034

description: Formalin-Fixed, Paraffin-Embedded


title: SOX2_ChIP_96h_Rep1


title: XP-C fibroblast primary cell line [AS148]

description:
AS148
3D collagen culture
Xeroderma pigmentosum, complementation group C (XP-C)

source_name: XP-C fibroblast primary cell line 3

value: XP-C

value: 12 years


title: MMPT109_APY0201_500nM

city: Scottsdale

first: Cecilia

last: Bonolo de Campos

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic

data_processing:
An internally developed RNA-seq analysis workflow (MAPRSeq, v3.0.1) was used to perform comprehensive analysis of raw RNA sequencing paired-end reads (Kalari et al., 2014)
Quality control was performed with RSeQC (v3.0.0) (Wang and Wang, 2012)
Reads were aligned by a fast and splice-aware aligner (STAR, v 2.5.2b) (Dobin et al., 2013) to human genome build hg38
Gene expressions were quantified with featureCounts (Liao et al., 2014) from Subread package (http://subread.sourceforge.net/, v1.5.1)
Genome_build: hg38
Supplementary_files_format_and_content: Gene expressions were quantified with featureCounts

source_name: Primary Patient Sample

growth_protocol: Cell lines and patient samples were maintained in complete medium RPMI-1640, supplemented with penicillin and streptomycin and 5-10% of sterile fetal calf serum, and treated with the DMSO control or APY0201 at concentrations specified above for 24 hours.

extract_protocol:
AllPrep DNA/RNA Kit (Qiagen #80204)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Multiple Myeloma

value: Primary Patient Sample MMPT109

tag: treatment

tag: dose


title: F4E1_E12.5_Embryo

value: Whole embryo

value: Wildtype

value: C57BL6 x CAST/Ei


title: PTCL_032

description: Formalin-Fixed, Paraffin-Embedded

value: Peripheral T-Cell Lymphoma-Not Otherwise Specified

value: FFPE Tumor Sample


title: PTCL_033

description: Formalin-Fixed, Paraffin-Embedded


title: Myc_tumor_2_mRNAseq

city: PARIS

first: Joshua

last: Waterfall

state: Please select:

address: 26 rue d'Ulm

department: Department of Translational Research and Inserm U830

institute: Institut Curie

data_processing:
STAR v 2.5.3a aligned to mm10 genome and gencode version m13 transcriptome
raw counts for gencode transcripts were obtained with STAR
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

source_name: CNS tumor of Myc subtype

extract_protocol:
total RNA was extracted using a miRNeasy mini kit (Qiagen ref: 217004)
extracted RNA was DNAse treated and Illumina TruSeq Stranded mRNA libraries were prepared according to standard manufacturer protocols

value: SMARCB1 -/-

value: CNS tumor of Myc subtype


title: SOX2_ChIP_96h_NoDox_Rep2


title: Syngeneic_tumor_3_mRNAseq

source_name: Syngeneic graft of tumor into flank

value: Syngeneic graft of tumor into flank


title: MMPT109_Control

value: DMSO


title: MMPT109_APY0201_50nM


title: Extracranial_tumor_4_mRNAseq

source_name: Extracranial tumor

value: Extracranial tumor


title: XP-C fibroblast primary cell line [AS798]

description:
AS798
3D collagen culture
Xeroderma pigmentosum, complementation group C (XP-C)

source_name: XP-C fibroblast primary cell line 2

value: 2 years

value: Skin fibroblasts


title: MMPT108_APY0201_500nM

value: Primary Patient Sample MMPT108


title: PTCL_031

description: Formalin-Fixed, Paraffin-Embedded

source_name: Peripheral T-Cell Lymphoma-Not Otherwise Specified


title: Myc_tumor_1_mRNAseq


title: PTCL_030

description: Formalin-Fixed, Paraffin-Embedded


title: MMPT108_APY0201_50nM


title: PTCL_029

description: Formalin-Fixed, Paraffin-Embedded


title: MMPT108_Control


title: SOX2_ChIP_96h_Dox_Rep1

value: Santa Cruz (sc,07-030)

value: iPSC


title: Extracranial_tumor_1_mRNAseq


title: SOX2_ChIP_48h_Rep2


title: PTCL_028

description: Formalin-Fixed, Paraffin-Embedded


title: Extracranial_tumor_2_mRNAseq


title: SOX2_ChIP_48h_Rep1


title: SHH_tumor_2_mRNAseq

source_name: CNS tumor of SHH subtype

value: CNS tumor of SHH subtype


title: MMPT107_APY0201_50nM

value: Multiple Myeloma

value: Primary Patient Sample MMPT107


title: PTCL_027

description: Formalin-Fixed, Paraffin-Embedded


title: Extracranial_tumor_3_mRNAseq


title: MMPT107_Control


title: MMPT107_APY0201_500nM


title: SOX2_ChIP_96h_Dox_Rep2


title: Syngeneic_tumor_2_mRNAseq


title: SOX2_ChIP_48h_NoDox_Rep1


title: SOX2_ChIP_48h_Dox_Rep1


title: SOX2_ChIP_48h_Dox_Rep2


title: Syngeneic_tumor_1_mRNAseq


title: MMPT106_APY0201_50nM

value: Primary Patient Sample MMPT106


title: PTCL_025

description: Formalin-Fixed, Paraffin-Embedded


title: Myc_tumor_3_mRNAseq


title: PTCL_023

description: Formalin-Fixed, Paraffin-Embedded


title: Myc_tumor_4_mRNAseq


title: PTCL_026

description: Formalin-Fixed, Paraffin-Embedded


title: SOX2_ChIP_0h_Rep2


title: PTCL_024

description: Formalin-Fixed, Paraffin-Embedded


title: SOX2_ChIP_0h_Rep1


title: SOX2_ChIP_96h_NoDox_Rep1


title: Healthy_brain_3_mRNAseq

source_name: Healthy brain

value: WT

value: Healthy brain


title: RPMI-8226_APY0201_100nM

source_name: Cell Line

extract_protocol:
RNeasy Plus Kit (Qiagen #74134)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: MMPT106_Control

tag: disease state


title: MMPT106_APY0201_500nM


title: SHH_tumor_3_mRNAseq

tag: strain


title: EJM_APY0201_100nM

value: EJM


title: SOX2_ChIP_0h_NoDox_Rep2


title: PTCL_021

description: Formalin-Fixed, Paraffin-Embedded

value: Peripheral T-Cell Lymphoma-Not Otherwise Specified

value: FFPE Tumor Sample


title: RPMI-8226_Control


title: PTCL_022

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_020

description: Formalin-Fixed, Paraffin-Embedded

source_name: Lennert Lymphoma

value: Lennert Lymphoma


title: SOX2_ChIP_0h_NoDox_Rep1


title: PTCL_019

description: Formalin-Fixed, Paraffin-Embedded


title: SOX2_ChIP_0h_Dox_Rep1


title: SHH_tumor_1_mRNAseq

value: SMARCB1 -/-


title: L363_APY0201_100nM


title: DKO.CAST_E7.5_ExE_RNA_3

description:
Gene_expression_Epi_ExE_RPKM_N17.txt
Allelic_expression_Epi_ExE_Readcount.txt

source_name: Extra-embryonic ectoderm

extract_protocol:
Reciprocal natural timed matings were set up between C57BL6/Babr and CAST animals (denoted as B6/CAST and CAST/B6), and embryos were collected on embryonic day 7.5 (E7.5).  Natural timed matings were set up between Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 +ve B6/129 females (resulting in ablation of DNA methylation in the oocyte) and CAST males (denoted as DKO.CAST). The epiblast (Epi) and extra-embryonic ectoderm (ExE) for each embryo were manually separated.  Single E7.5 epiblast and ExE samples were individually frozen in 10µL of buffer RLT Plus (Qiagen).
Total RNA was extracted using a trizol extraction method, as previously described (Veselovska et al. 2015).  In brief, samples were homogenized in 400µL of TRIzol (Invitrogen) and phase separated by adding 80µL of chloroform:isoamyl alcohol (Sigma), mix and centrifuge at 4°C for 15 minutes.  The aqueous phase was transferred to a new tube, 1uL GlycoBlue and 300µL of ice cold isopropanol was added and mixed.  Samples were incubated for 10 minutes and then centrifuged for 10 minutes at 4°C.  The pellet was washed once with 75% ethanol, air dried and then resuspended in 5µL of RNase-free water.  20µL of lysis/binding buffer was immediately added to each RNA sample and oligo(dT)25 capture of mRNA was done using Dynabeads mRNA DIRECT kit (Life Techologies).  The protocol was implemented as per manufacturers’ instructions including the additional steps for elimination of rRNA contamination. Maxymum Recovery tubes (Axygen) were used and volumes were adapted for the low amount of starting material: 5µL of Dynabeads Oligo(dT)25 were used for each sample, mRNA capture was done in a total volume of 50µL of lysis/binding buffer, washes were done using 100µL Washing Buffer A or 50µL of Washing Buffer B, and a final elution volume of 5µL 10mM Tris-HCl.  The total volume of mRNA was then immediately advanced into the library preparation protocol, using the SMARTer Stranded RNA-seq kit (Clontech), which is optimised for as little as 100pg of RNA.  The protocol was completed as per the manufacturers’ instructions and 14 amplification cycles were used for all samples. The quantification of all libraries was done using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification kit (KAPA).  Libraries were sequenced using 50bp single-end on the Illumina HiSeq 2500 RapidRun, multiplexing 12 samples per lane.

value: Extra-embryonic ectoderm

value: Dnmt3a -/+, Dnmt3b -/+ (maternal inheritance)

value: C57BL6/Babr/129 x CAST/Ei


title: XP-C fibroblast primary cell line [AS433]

description:
AS433
3D collagen culture
Xeroderma pigmentosum, complementation group C (XP-C)

source_name: XP-C fibroblast primary cell line 1

value: XP-C

value: 2 months

value: Skin fibroblasts


title: sRNA_CAD_WT_d4_3

first: Jennifer

middle: M

last: Cherone

state: Ma

address: 400 Main Street, 68-259

department: Biology

institute: Massachusetts Institute of Technology

description: small RNA-seq

data_processing:
For the RNA-seq, reads were aligned to the mm9 genome using STAR (Dobin et al., 2013), expression levels were quantified, and differentially expressed genes were assessed using DESeq2 (Love et al., 2014).
Adapter sequences were trimmed from reads using cutadapt, and then reads with identical 4 bp barcodes on the 5' and 3' ends (8 bp total with a constrained distance in between) were collapsed to single reads, yielding 4-7 M unique reads remaining per replicate. Barcode sequences were trimmed from each end using cutadapt, and reads were mapped to the miRBase genome annotations using bwa with the following options: -n 1 -o 0 -e 0 -k 1, resulting in 50-66% of reads mapped per replicate. The miRNAs were filtered, requiring a minimum of 5 counts in at least one of the samples. Differential expression was assessed using DESeq (Anders and Huber, 2010). Size factors used for normalization were calculated from two spike-in miRNAs from different species: dme-miR-14-5p (Drosophila) and xtr-miR-427 (Xenopus).
Genome_build: mm9, miRbase_v21
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene within each sample.

source_name: neuroblastoma cells

growth_protocol: All CAD cells (WT and knockout lines) were grown in DMEM/F12 (Gibco) supplemented with 10% fetal bovine serum (FBS) and differentiated in DMEM/F12 with no FBS added.

extract_protocol:
For RNA-seq, total RNA was collected with a Qiagen RNeasy Mini kit. For the small RNA-seq, total RNA was harvested from CAD cells in serum or 4 days after serum withdrawal using the miRVana kit (Thermo Fisher).
For the WT and mir-138 DKO CAD cells in serum or 24-96 h without serum, strand-specific, polyA-selected libraries were constructed using the dUTP incorporation method and sequenced on an Illumina NextSeq sequencer with paired-end 75-bp reads. Samples were prepared and sequenced in duplicate or triplicate (WT 0 and 96 h without serum), yielding approximately 30-45 million read pairs per replicate. For the mir-138 DKO CAD cells transfected with either a miR-138 mimic, miR-137 mimic, or pUC19 DNA, strand-specific, polyA-selected libraries were constructed in duplicate with the Illumina’s TruSeq Stranded mRNA Library Prep Kit for Neoprep and sequenced on an Illumina NextSeq sequencer with 50 bp single-end reads, yielding 18-36 M reads per replicate. For small RNA-seq, 1000 ng of total RNA was used with the Bioo Scientific NEXTflex Small RNA Sequencing Kit v2 and libraries were sequenced on an Illumina HighSeq Sequencer in triplicate, yielding 9-18 M reads per replicate.
RNA-seq (Samples 7-34) and small RNA-seq (Samples 1-6)

treatment_protocol: (Samples 1-20): For sequencing WT and miR-138 DKO cell lines before and after serum withdrawal, cells were plated in a 6-well plate. For wells intended to differentiate, the media was replaced with serum-free media after 24 h. (Samples 21-34): mir-138 DKO cells were plated at 0.6e5 cells/well in a poly-l-lysine coated 12-well dish. miR-138 or miR-137 mirVana miRNA mimics were transfected at a concentration of 3 nM with the Lipofectamine RNAiMAX reagent. Media was changed to serum-free media 48 h later. Total RNA was collected at 0 and 2 days after serum withdrawal using the Qiagen RNeasy kit.

value: CAD cells

value: wild type

tag: days post serum withdrawal

value: 4 days


title: PTCL_017

description: Formalin-Fixed, Paraffin-Embedded


title: L363_Control

value: Multiple Myeloma

value: DMSO


title: DKO.CAST_E7.5_ExE_RNA_2


title: JJN3_APY0201_100nM


title: sRNA_CAD_WT_d4_2

description: small RNA-seq


title: sRNA_CAD_WT_d4_1

description: small RNA-seq


title: Healthy_brain_1_mRNAseq

value: WT

value: Healthy brain


title: DKO.CAST_E7.5_ExE_RNA_1


title: PTCL_015

description: Formalin-Fixed, Paraffin-Embedded


title: JJN3_Control


title: Healthy_brain_2_mRNAseq


title: sRNA_CAD_WT_serum_3

description: small RNA-seq

value: 0 days


title: SOX2_ChIP_0h_Dox_Rep2

source_name: iPSC

value: Santa Cruz (sc,07-030)

value: iPSC


title: EJM_Control

value: EJM


title: PTCL_014

description: Formalin-Fixed, Paraffin-Embedded

value: Peripheral T-Cell Lymphoma-Not Otherwise Specified

value: FFPE Tumor Sample


title: PTCL_018

description: Formalin-Fixed, Paraffin-Embedded

value: Lennert Lymphoma


title: sRNA_CAD_WT_serum_2

description: small RNA-seq


title: KMS26_APY0201_100nM


title: DKO.CAST_E7.5_Epi_RNA_2

source_name: Epiblast

value: Epiblast

value: Dnmt3a -/+, Dnmt3b -/+ (maternal inheritance)

value: C57BL6/Babr/129 x CAST/Ei


title: PTCL_013

description: Formalin-Fixed, Paraffin-Embedded


title: KMS26_Control


title: DKO.CAST_E7.5_Epi_RNA_1


title: sRNA_CAD_WT_serum_1

description: small RNA-seq

value: CAD cells


title: PTCL_012

description: Formalin-Fixed, Paraffin-Embedded


title: CAST.B6_E7.5_ExE_RNA_3

value: Extra-embryonic ectoderm

value: Wildtype

value: CAST/Ei x C57BL6/Babr


title: CAST.B6_E7.5_ExE_RNA_2


title: WCE

description:
RPKM_Table_ChIP_ATAC.xlsx
SampleMapping_ChIP_ATAC.xlsx

data_processing:
Sequencing read were aligned to the mouse genome (mm10) using bowtie with default parameters
Peaks for OCT4 ChIPs were called using MACS2 and IDR framework.
IDR called OCT4 peaks from different conditions were further processed using in-house pipeline. Peaks from different conditions were merged together if they were found to be overlapping. New peak summit for these merged peak was calcualted based on their relative contributions (heights) as a measure of distance. After calculating and assigning new peak summit to the merged peaks, peaks boundries were also redefined by extending them by 300 bps in both directions from the newly assigned peak summit.
These peaks were then used for downstream analysis. We calculated RPKM for these 600bp peaks. A meta table was created for these 600bp peaks with RPKM values for TFs, histone marks as well as ATAC signal.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with coordinates and RPKM.

growth_protocol: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP were maintained on CF1 mouse embryonic fibroblasts (MEFs) in KO-DMEM containing 15% fetal bovine serum (FBS), 1% penicillin/streptomycin, 1X glutaMAX supplement (Gibco), 1% nonessential amino acid, and 5 × 10^5 U LIF. To perform the ChIP assay, iPSCs were first changed into serum-free N2B27 medium supplemented with LIF and 2i (3 μM CHIR99021 and 1 μM PD0325901) for a minimum of 24 hours. Differentiation was induced by rinsing iPSCs thoroughly with 1X PBS and changing to N2B27 media without LIF 2i. To test colony-forming potential, differentiated cells were trypsinized to single cells and seeded at very low density (~1,300 cells/cm2) on CF1 MEFs in KO-DMEM containing 15% serum and LIF (no dox condition) or supplemented with 2 μg/ml dox (+dox condition).


title: vhCO

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description:
Gene expression in vhCO
single-cell RNA-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Cellranger (v2.1.0).
All libraries were merged by aggr function of Cellranger.
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format.

source_name: Vascularized cortical organoid

growth_protocol: Cortical organoid were cultured in each established condition (Xiang et al., 2017).

extract_protocol: Chromium™ Single Cell 3’ Reagent Kits

treatment_protocol: Vascularization was established with ETV2 induction (Lee et al., 2017)

value: Vascularized cortical organoid

tag: status

value: Cortex

tag: vascularization

value: Yes


title: PTCL_016

description: Formalin-Fixed, Paraffin-Embedded


title: hCO

description:
Gene expression in hCO
single-cell RNA-seq

source_name: Non-vascularized cortical organoid

value: Non-vascularized cortical organoid

value: No


title: RNA_96h_Dox_rep2

data_processing:
RNA seq reads were mapped to the mouse genome (mm10) using TopHat v2.0.14 with the flags: “--no-coverage-search --GTF gencode.vM4.annotation.gtf” where gencode.vM4.annotation.gtf is the Gencode vM4 reference transcriptome available at gencodegenes.org. Cufflinks v2.2.1 (Ref 44) was used to quantify gene expression and assess the significance of differential expression. Briefly, Cuffquant was used to quantify mapped reads against Gencode vM4 transcripts of at least 200bp with biotypes: protein_coding, lincRNA, antisense, processed_transript, sense_intronic, sense_overlapping. Cuffdiff was run on the resulting Cuffquant .cxb files, with a contrast file specifying comparisons between all pairs of differentiation time points, and all time-matched +dox/-dox pairs. Genes were deemed to be “dynamic” if they showed a statistically significant change in expression between any two differentiation time points, with a minimum fold change of 2 and a minimum expression of 1 FPKM in that comparison. Expression level, fold change and statistical significance were all assessed by Cuffdiff. Genes were deemed to be “OSKM responsive” at each of four time points by applying the same criteria to the corresponding +dox/-dox conditions. Dynamic genes were grouped into three broad expression dynamics via k-means clustering of gene expression levels across the differentiation time course. k=3 was chosen by varying k from 2 to 20 and looking for maximum cluster separation as assessed by the silhouette score.
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs

growth_protocol: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP were maintained on CF1 mouse embryonic fibroblasts (MEFs) in KO-DMEM containing 15% fetal bovine serum (FBS), 1% penicillin/streptomycin, 1X glutaMAX supplement (Gibco), 1% nonessential amino acid, and 5 × 10^5 U LIF.

extract_protocol:
PolyA using Oligo dT beads (Invitrogen)
Polyadenylated RNA was selected using Oligo dT beads (Invitrogen) and fragmented to 200-600 base pairs, then ligated to RNA adaptors using T4 RNA ligase. Libraries were sequenced on the Illumina Hiseq 2000.

value: Dox


title: PTCL_011

description: Formalin-Fixed, Paraffin-Embedded


title: DKO.CAST_E7.5_Epi_RNA_3

tag: genotype

tag: hybrid strain


title: RNA_96h_Dox_rep1

tag: cell type

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP


title: ATAC_Maize_7days_leaf_Input1

organism: Zea mays

source_name: DNA

tag: accession

value: leaf


title: CAST.B6_E7.5_ExE_RNA_1


title: CAST.B6_E7.5_Epi_RNA_3


title: PTCL_009

description: Formalin-Fixed, Paraffin-Embedded

value: Peripheral T-Cell Lymphoma-Not Otherwise Specified

value: FFPE Tumor Sample


title: ATAC_Maize_7days_leaf_rep2


title: PTCL_008

description: Formalin-Fixed, Paraffin-Embedded


title: RNA_96h_NoDox_rep2

value: NoDox


title: PTCL_010

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_007

description: Formalin-Fixed, Paraffin-Embedded


title: CAST.B6_E7.5_Epi_RNA_1

value: Epiblast


title: ATAC_Maize_7days_leaf_rep1


title: CAST.B6_E7.5_Epi_RNA_2


title: RNA_96h_NoDox_rep1


title: ATAC_Maize_7days_leaf_Input2


title: ChIP_Maize_7days_leaf_Input

extract_protocol: ChIP-seq: ChiP-seq was performed following the methods of Zhang et al (2007) (https://www.ncbi.nlm.nih.gov/pubmed/17439305).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.


title: PTCL_006

description: Formalin-Fixed, Paraffin-Embedded


title: RNA_48h_Dox_rep1


title: B6.CAST_E7.5_ExE_RNA_2

value: C57BL6/Babr x CAST/Ei


title: ChIP_Maize_7days_leaf_H2A.Z


title: PTCL_004

description: Formalin-Fixed, Paraffin-Embedded


title: PTCL_005

description: Formalin-Fixed, Paraffin-Embedded

value: Lennert Lymphoma


title: B6.CAST_E7.5_Epi_RNA_3


title: ChIP_Maize_7days_leaf_H3K4me1


title: RNA_24h_Dox_rep2


title: ChIP_Maize_7days_leaf_H3K4me3


title: RNA_48h_NoDox_rep2


title: B6.CAST_E7.5_Epi_RNA_2


title: PTCL_003

description: Formalin-Fixed, Paraffin-Embedded


title: B6.CAST_E7.5_Epi_RNA_1


title: RNA_48h_NoDox_rep1


title: RNA_24h_Dox_rep1


title: ChIP_Maize_7days_leaf_H3K56ac


title: ChIP_Maize_7days_leaf_H3K36me3


title: RNA_48h_Dox_rep2


title: RNA_24h_NoDox_rep2


title: PTCL_002

description: Formalin-Fixed, Paraffin-Embedded


title: ChIP_Maize_7days_leaf_H3K27me3


title: RNA_24h_NoDox_rep1


title: PTCL_001

description: Formalin-Fixed, Paraffin-Embedded


title: ChIP_Maize_7days_leaf_H3


title: RNA_0h_Dox_rep2


title: RNA_Maize_7days_leaf_rep2

source_name: mRNA

extract_protocol: RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol


title: RNA_0h_Dox_rep1


title: RNA_Maize_7days_leaf_rep1


title: HiC maize Leaf-HiC rep2

description: processed_data_file: HiC_B73_leaf_merged_loops.txt

data_processing:
MethylC-seq: analysis was performed by Methylpy 1.3
RNA-seq: analysis was performed by hisat2 v2.0.5 and StringTie v1.3.3b
ChIP-seq: analysis was performed by bowtie1.1.1
DAP-seq:  analysis was performed by bowtie2.2.8 and GEM v2.5
ATAC-seq: analysis was performed by bowtie1.1.1
HiC-seq: analysis was performed by HiC-pro v2.8.0 and Juicertools v0.7.0
Genome_build: Zea mays assembly AGP.v4 reference genome
Supplementary_files_format_and_content: methylome tab delimited text file, see "allc_column_header_descriptions.txt for column headers
Supplementary_files_format_and_content: RNA tab delimited text file, see "RNA_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ChIP bed file, see "ChIP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: DAP bed file, see "DAP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ATAC tbed file, see "ATAC_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: HiC tab delimited text file, see "HiC_column_header_descriptions.txt" for column headers

source_name: B73 leaf

growth_protocol:
There are two separate growth protocols—one for the second leaf and one for the ear primordia.  For both samples, plants were grown from seed collected from field-grown ears grown during the summer of 2017 in Athens, Georgia.
Second leaf protocol: kernels were sown in Sungro Horticulture professional growing mix (Sungro Horticulture Canada Ltd., 52130 RR 65, P.O. Box 189, Seba Beach, AB T0E 2B0 Canada) approximately 0.5 inches below the soil surface.  Soil was saturated with tap water and placed under a 50/50 mixture of 4100K (Sylvania Supersaver Cool White Delux F34CWX/SS, 34W) and 3000K (GE Ecolux w/ starcoat, F40CX30ECO, 40W) light.  The photoperiod was 16 hours of light, eight hours of dark.  The temperature was approximately 25°C during light hours. The relative humidity was approximately 54%.  Seedlings were grown for approximately six days and harvested from four to six hours after photoperiod dawn.  Seedlings were harvested when the V1 leaf had emerged two to three centimeters above the apical tip of the coleoptile. The seedlings were cut approximately three millimeters above the coleoptile-mesocotyl boundary, excluding the shoot apical meristem, and the V2 leaf was removed from within the sheath of the V1 leaf.  Only the inner V2 leaves were used for experiments.
Ear primordia protocol: Plants were grown in greenhouse or field conditions.  Plants were harvested approximately one month after sowing and ear primordia were dissected from shoots. Ear primordia were harvested from any node of the shoot if they were within the desired size range: between 3 to 8 millimeters from the base to the apical tip of the ear.

extract_protocol:
MethylC-seq: prepared as previously described in (Urich et al. 2015).
RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol.
ChIP-seq: ChiP-seq was performed following the methods of (Zhang et al. 2007).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.
DAP-seq: DAP-seq experiments involving maize ARF samples were processed according to (Galli et al. 2018). All other TFs were processed according to (Bartlett et al. 2017) with the exception that 1ug of pIX-HALO-TF plasmid DNA was used for protein expression and 1ug of adapter ligated library prepared from B73 ear genomic DNA was used for DNA binding.
ATAC-seq libraries were prepared following the ATAC-seq protocol  as previously described in (Lu et al. 2016).
Hi-C libraries were prepared following the HiChIP protocol described in (Mumbach et al. 2016) with modifications described in the text.

tag: line

value: 7-day-old 2nd leaf


title: WT-Hypoxia vs WT-Normoxia - Replicat 2

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

institute: Universite de Montreal

description: Arrays are organized in 48 sub-arrays spotted with 6459 70-mer oligonucleotides.

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater. Total RNA was eluted, assessed for integrity on an Agilent 2100 Bioanalyzer prior to cDNA labeling, microarray hybridization and analysis .

treatment_protocol: Overnight cultures of snf5 mutant and WT strains were diluted to an OD600 of 0.1 in 100 ml of fresh YPS-uridine medium, grown at 30°C to an OD600 of 0.4. Cells were harvested by centrifugation at 3,000 x g for 5 min, and the pellet was washed with PBS and resuspended in 400 µl of YPS medium. Half of the C. albicans cell suspension was used to inoculate aerated flasks containing fresh YPS medium (normoxia), and the second half was added to bottles containing fresh YPS flushed with nitrogen to remove oxygen (hypoxia). Candida cells were then incubated at 30°C under agitation at 220 rpm for 1 hour. Cells were then centrifuged for 2 min at 3,500 rpm, the supernatants were removed, and the samples were quick-frozen and stored at -80 °C.

tag: input sample

value: WT grown in YP-Sucrose yeast at 30oC under normoxia (21% O2)

tag: strains

tag: sample-test

value: WT grown in YP-Sucrose yeast at 30oC under hypoxia (5% O2)


title: HiC maize Leaf-HiC rep1

tag: tissue


title: RNA_72h_rep2

tag: time


title: RNA_96h_rep1


title: WT-Hypoxia vs WT-Normoxia - Replicat 1

source_name: WT grown in YP-Sucrose yeast at 30oC under hypoxia

source_name: WT grown in YP-Sucrose yeast at 30oC under normoxia


title: snf5-Hypoxia vs snf5-Normoxia - Replicat 2

value: snf5 grown in YP-Sucrose yeast at 30oC under hypoxia (5% O2)

value: snf5 (DH2)

value: snf5 grown in YP-Sucrose yeast at 30oC under normoxia (21% O2)


title: RNA_96h_rep2


title: snf5-Hypoxia vs snf5-Normoxia - Replicat 1

source_name: snf5 grown in YP-Sucrose yeast at 30oC under normoxia

source_name: snf5 grown in YP-Sucrose yeast at 30oC under hypoxia


title: RNA_0h_NoDox_rep1

tag: treatment


title: RNA_0h_NoDox_rep2


title: RNA_72h_rep1


title: ATAC-seq maize B73Ear rep1

description: processed_data_file: ATAC_B73_ear.filtered_ACR.bed.gz

source_name: B73 ear

value: 0.5-1cm ear


title: ATAC-seq maize B73input rep2

source_name: B73 seedling

value: 7-day old seedling


title: RNA_60h_rep2


title: ATAC-seq maize B73Leaf rep1

description: processed_data_file: ATAC_B73_leaf.filtered_ACR.bed.gz


title: ATAC-seq maize B73input rep1


title: DAP-seq maize SBP8_UB2

description: processed_data_file: Peak_DAP_SBP8_UB2.dap.bed.gz

data_processing:
Library strategy: DAP-seq
MethylC-seq: analysis was performed by Methylpy 1.3
RNA-seq: analysis was performed by hisat2 v2.0.5 and StringTie v1.3.3b
ChIP-seq: analysis was performed by bowtie1.1.1
DAP-seq:  analysis was performed by bowtie2.2.8 and GEM v2.5
ATAC-seq: analysis was performed by bowtie1.1.1
HiC-seq: analysis was performed by HiC-pro v2.8.0 and Juicertools v0.7.0
Genome_build: Zea mays assembly AGP.v4 reference genome
Supplementary_files_format_and_content: methylome tab delimited text file, see "allc_column_header_descriptions.txt for column headers
Supplementary_files_format_and_content: RNA tab delimited text file, see "RNA_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ChIP bed file, see "ChIP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: DAP bed file, see "DAP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ATAC tbed file, see "ATAC_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: HiC tab delimited text file, see "HiC_column_header_descriptions.txt" for column headers

value: 7-day old leaf


title: RNA_60h_rep1

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP


title: DAP-seq maize LBD38

description: processed_data_file: Peak_DAP_LBD38.dap.bed.gz


title: B6.CAST_E7.5_ExE_RNA_3

value: Extra-embryonic ectoderm

tag: age

value: Wildtype


title: Input_HCI-013_VEH

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Patient derived xenograft, breast cancer

growth_protocol: 1 mm3 tumor fragments were implanted under the mammary fat pad. Once the tumors reach 100-200 mm3, the animals were randomized and treated with vehicle or enobosarm (10 mg/kg orally). After 30 days of treatment, the animals were sacrificed and the tumors were excised and flash frozen.

extract_protocol:
Tumors were harvested, flash frozen and sectioned. Chromatin was extracted using an SDS based sonication protocol and immunoprecipitated.
DNA libraries were prepared using Swift Accel-NGS 2S Plus kit in an automated platform

treatment_protocol: Vehicle (DMSO+PEG-300 15:85): Enobosarm (10 mg/kg): Oral treatment

value: tumor tissue

tag: chip antibody

value: input


title: S440_2187_VEH_ER

value: ER

tag: chip antibody vendor

value: Santa Cruz Biotechnology, Thermo

tag: chip antibody cat.#

tag: chip antibody lot/batch#


title: DAP-seq maize SBP30_UB3

description: processed_data_file: Peak_DAP_SBP30_UB3.dap.bed.gz


title: S186_ENOB_ER


title: DAP-seq maize LBD5

description: processed_data_file: Peak_DAP_LBD5.dap.bed.gz


title: RNA_36h_rep2


title: RNA_48h_rep1


title: Input_HCI-009_VEH


title: DAP-seq maize SBP6

description: processed_data_file: Peak_DAP_SBP6.dap.bed.gz


title: RNA_36h_rep1


title: DAP-seq maize LBD19_IG1

description: processed_data_file: Peak_DAP_LBD19_IG1.dap.bed.gz


title: RNA_48h_rep2


title: S181_ENOB_ER


title: Tuscany98

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2.0 with GT module 2.0.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: blood

tag: geographical region

value: Tuscany


title: RNA_24h_rep2


title: Tuscany65


title: DAP-seq maize LBD16_RA2

first: Robert

last: Schmitz

address: B416 Davison Life Sciences

institute: University of Georgia

description: processed_data_file: Peak_DAP_LBD16_RA2.dap.bed.gz


title: DAP-seq maize EREB29

description: processed_data_file: Peak_DAP_EREB29.dap.bed.gz


title: RNA_24h_rep1


title: SS182_ENOB_ER


title: S440_2190_ENOB_ER


title: RNA_0h_rep1


title: DAP-seq maize EREB71 rep1

description: processed_data_file: Peak_DAP_EREB71.dap.bed.gz


title: RNA_0h_rep2


title: provance4409

value: Provance


title: Tuscany54


title: S176_VEH_ER


title: DAP-seq maize EREB24_BBM rep1

description: processed_data_file: Peak_DAP_EREB24_BBM.dap.bed.gz


title: K4me2_ChIP_96h_Dox_Rep1

description:
RPKM_Table_ChIP_ATAC.xlsx
SampleMapping_ChIP_ATAC.xlsx

value: K4me2 (Millipore, 07-030)

value: Dox


title: Tuscany93


title: FOXA1_HCI013_VEH_2860

value: abcam,abcam


title: DAP-seq maize BZIP96

description: processed_data_file: Peak_DAP_BZIP96.dap.bed.gz


title: Tuscany74


title: Portugal7

value: Portugal


title: DAP-seq maize EREB138

description: processed_data_file: Peak_DAP_EREB138.dap.bed.gz


title: Portugal9


title: provance4109


title: S179_VEH_ER


title: Tuscany38


title: K4me2_ChIP_96h_Dox_Rep2


title: Tuscany27


title: DAP-seq maize EREB127

description: processed_data_file: Peak_DAP_EREB127.dap.bed.gz


title: provance2708


title: K4me2_ChIP_96h_NoDox_Rep2

value: NoDox


title: K4me2_ChIP_96h_Rep2


title: DAP-seq maize BZIP57_FEA4 rep1

description: processed_data_file: Peak_DAP_BZIP57_FEA4.dap.bed.gz


title: K4me2_ChIP_96h_NoDox_Rep1


title: Portugal6


title: provance2508


title: FOXA1_HCI013_VEH_2858_2861


title: DAP-seq maize BZIP54

description: processed_data_file: Peak_DAP_BZIP54.dap.bed.gz


title: DAP-seq maize BZIP72

description: processed_data_file: Peak_DAP_BZIP72.dap.bed.gz


title: FOXA1_HCI013_ENOB_2854


title: K4me2_ChIP_96h_Rep1


title: FOXA1_HCI013_VEH_2856


title: Portugal2


title: K4me2_ChIP_48h_Dox_Rep1


title: FOXA1_HCI013_VEH_131_132


title: FOXA1_HCI013_ENOB_2852_2859


title: DAP-seq maize BZIP25

description: processed_data_file: Peak_DAP_BZIP25.dap.bed.gz


title: K4me2_ChIP_48h_NoDox_Rep2


title: S177_VEH_ER


title: FOXA1_HCI013_ENOB_2849_2850


title: K4me2_ChIP_48h_NoDox_Rep1


title: Portugal3


title: K4me2_ChIP_48h_Dox_Rep2


title: DAP-seq maize ARF7

description:
Raw data previously accessioned as: SRR6830292
processed_data_file: Peak_DAP_ARF7.dap.bed.gz

value: 1-3cm ear


title: AR_HCI013_VEH_2860

value: AR

value: Spring Bioscience


title: K4me2_ChIP_48h_Rep2

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP


title: FOXA1_HCI013_ENOB_2848


title: K4me2_ChIP_48h_Rep1


title: DAP-seq maize BAD1

description: processed_data_file: Peak_DAP_BAD1.dap.bed.gz

value: 7-day old leaf


title: DAP-seq maize ARF4

description:
Raw data previously accessioned as: SRR6830284
processed_data_file: Peak_DAP_ARF4.dap.bed.gz


title: AR_HCI013_VEH_2858_2861

value: tumor tissue


title: K4me2_ChIP_0h_Dox_Rep2


title: DAP-seq maize ARF36

description:
Raw data previously accessioned as: SRR6830291
processed_data_file: Peak_DAP_ARF36.dap.bed.gz


title: AR_HCI013_VEH_131_132


title: Portugal12

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).


title: AR_VEH_440_2187


title: DAP-seq maize ARF35

description:
Raw data previously accessioned as: SRR6830282
processed_data_file: Peak_DAP_ARF35.dap.bed.gz


title: Portugal1


title: AR_S182_ENOB


title: K4me2_ChIP_0h_Dox_Rep1


title: DAP-seq maize ARF34

description:
Raw data previously accessioned as: SRR6830279
processed_data_file: Peak_DAP_ARF34.dap.bed.gz


title: DAP-seq maize control

description: Raw data previously accessioned as: SRR6830293


title: Portugal11


title: provance4509


title: K4me2_ChIP_0h_NoDox_Rep2


title: Piedmont154

value: Piedmont


title: AR_HCI013_ENOB_2854


title: K4me2_ChIP_0h_NoDox_Rep1


title: Portugal13


title: AR_HCI013_ENOB_2852_2859


title: DAP-seq maize ARF29

description:
Raw data previously accessioned as: SRR6830285
processed_data_file: Peak_DAP_ARF29.dap.bed.gz


title: Piedmont61


title: AR_HCI009_VEH_994_2003_2013


title: DAP-seq maize ARF27

description:
Raw data previously accessioned as: SRR6830283
processed_data_file: Peak_DAP_ARF27.dap.bed.gz


title: K4me2_ChIP_0h_Rep1

description:
RPKM_Table_ChIP_ATAC.xlsx
SampleMapping_ChIP_ATAC.xlsx


title: DAP-seq maize ARF25

description:
Raw data previously accessioned as: SRR6830289
processed_data_file: Peak_DAP_ARF25.dap.bed.gz


title: AR_HCI009_ENOB_995_2004_2008


title: K27ac_ChIP_96h_Dox_Rep1

value: K27ac (Diagenode, C15410196)


title: DAP-seq maize ARF18

description:
Raw data previously accessioned as: SRR6830281
processed_data_file: Peak_DAP_ARF18.dap.bed.gz


title: Portugal10


title: K27ac_ChIP_96h_NoDox_Rep2


title: Fibroblasts-R77C-alpha-SGmCh-MG132 1µM n3

city: Corbeil-Essonnes

first: MARGOT

last: JARRIGE

address: 28, Rue Henri Desbruères

institute: I-Stem/INSERM U861

description:
IonXpress_015_R_2018_02_14_19_04_03_NGS#41-libamp_261-Fibroblasts_lenti_R77C_mCherry_MG132_1_ｵM_n3
MG132 1µM

data_processing:
Torrent Suite Software was used for basecalling, trimming of adaptator sequence, quality check and to generated FASTQ file
FastQ files were exported to PartekFlow software (v6 Partek Inc) for alignement and quantification step. Briefly sequence were mapped to hg19 reference genome using TOPHAT2 (v2.0.8).  and bowtie 2 (v2.1.0) following the WT Pipeline for Ion Torrent. Mapped reads were annotated on Refseq release 84 and quantified with Partek E/M algorithm , normalised on total count and differential gene were identified using Partek Gene Specific Algorithm (GSA)
Genome_build: hg19
Supplementary_files_format_and_content: one tab-delimited text files include RPM (read per million)

source_name: Fibroblast

growth_protocol: Fibroblasts were cultured in Dulbecco’s modified Eagle’s medium+GlutaMAX (Invitrogen) supplemented with 10% fetal bovine serum (research grade, Sigma) and 1% Penicillin-Streptomycin (Invitrogen). Cells were seeded on plates coated with 50µg/ml of collagen I and maintained in a humidified atmosphere of 5% CO2 at 37◦C.

extract_protocol:
Medium was remove and 350µl RLTplus were add. Sample were extracted on QIACUBE following the Rneasy Plus Mini kit protocole (Qiagen)
The Ion Ampliseq Transcriptome Human Gene expression kit was used with 50ng of mRNA for the construction of sequencing libraries following the manufacturer protcol.
Ampliseq Transcriptome Human gene expression kit (Termofisher Scientific)

treatment_protocol: Twenty-four hours after seeding, cells were treated with 3 µM of thiostrepton (Sigma-Aldrich), 30 nM of bortezomib (Selleckchem), 1 µM of MG132 (Selleckchem) or the carrier 0.1% dimethyl sulfoxide (DMSO, VWR). Cells were analyzed after 24 hours of treatment. For overexpression of the mutated alpha-SG, immortalized fibroblasts were transduced with a lentiviral vector expressing human  R77C-alpha-SG-mCh with a multiplicity of infection (MOI) of 20 in the presence of 4 µg/ml of polybrene (Sigma-Aldrich).

tag: cell line

tag: lentivirus

value: MG132 1microM


title: K27ac_ChIP_96h_NoDox_Rep1

tag: cell type


title: Fibroblasts-R77C-alpha-SGmCh-MG132 1µM n2

description:
IonXpress_014_R_2018_02_14_19_04_03_NGS#41-libamp_260-Fibroblasts_lenti_R77C_mCherry_MG132_1_ｵM_n2
MG132 1µM


title: K27ac_ChIP_96h_Rep2


title: Fibroblasts-R77C-alpha-SGmCh-MG132 1µM n1

description:
IonXpress_013_R_2018_02_14_19_04_03_NGS#41-libamp_259-Fibroblasts_lenti_R77C_mCherry_MG132_1_ｵM_n1
MG132 1µM


title: DAP-seq maize ARF16

description:
Raw data previously accessioned as: SRR6830280
processed_data_file: Peak_DAP_ARF16.dap.bed.gz


title: DAP-seq maize ARF13

description:
Raw data previously accessioned as: SRR6830287
processed_data_file: Peak_DAP_ARF13.dap.bed.gz


title: K4me2_ChIP_0h_Rep2


title: K27ac_ChIP_96h_Rep1


title: Fibroblasts-R77C-alpha-SGmCh-Thsp 3µM n3

description:
IonXpress_009_R_2018_02_14_19_04_03_S#41-libamp_255-Fibroblasts_lenti_R77C_mCherry_Thsp_3_ｵM_n3
Thiostrepton 3µM

value: Thiostrepton 3microM


title: DAP-seq maize ARF39

description:
Raw data previously accessioned as: SRR6830290
processed_data_file: Peak_DAP_ARF39.dap.bed.gz


title: K27ac_ChIP_48h_Dox_Rep2


title: ItalyPiedmont98

value: blood

value: Italy, Piedmont


title: DAP-seq maize ARF10

description:
Raw data previously accessioned as: SRR6830286
processed_data_file: Peak_DAP_ARF10.dap.bed.gz


title: ItalyPiedmont63

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).


title: ItalyPiedmont145


title: Fibroblasts-R77C-alpha-SGmCh-Thsp 3µM n2

description:
IonXpress_008_R_2018_02_14_19_04_03_NGS#41-libamp_254-Fibroblasts_lenti_R77C_mCherry_Thsp_3_ｵM_n2
Thiostrepton 3µM


title: Fibroblasts-R77C-alpha-SGmCh-BTZ 30nM n3

description:
IonXpress_006_R_2018_02_14_19_04_03_NGS#41-libamp_252-Fibroblasts_lenti_R77C_mCherry_Btz_30_nM_n3
bortezomib 30nM

value: bortezomib 30nM


title: K27ac_ChIP_48h_Dox_Rep1

value: Dox


title: Fibroblasts-R77C-alpha-SGmCh-Thsp 3µM n1

description:
IonXpress_007_R_2018_02_09_13_50_28_NGS#41-libamp_253-Fibroblasts_lenti_R77C_mCherry_Thsp_3_ｵM_n1
Thiostrepton 3µM


title: ItalyPiedmont52


title: K27ac_ChIP_48h_NoDox_Rep1


title: Chip B73 ear H3K56ac rep2

description: processed_data_file: mapped_chip_B73_ear_H3K56ac_rep2.bed.gz

value: 0.5-1cm ear


title: Fibroblasts-R77C-alpha-SGmCh 30nM n2

description:
IonXpress_005_R_2018_02_09_13_50_28_NGS#41-libamp_251-Fibroblasts_lenti_R77C_mCherry_Btz_30_nM_n2
bortezomib 30nM


title: Chip B73 ear input rep1

description: processed_data_file: mapped_chip_B73_ear_input_rep1.bed.gz


title: Chip B73 ear H3K56ac rep1

description: processed_data_file: mapped_chip_B73_ear_H3K56ac_rep1.bed.gz


title: K27ac_ChIP_48h_Rep2

description:
RPKM_Table_ChIP_ATAC.xlsx
SampleMapping_ChIP_ATAC.xlsx


title: Chip B73 ear H3 rep1

description: processed_data_file: mapped_chip_B73_ear_H3_rep1.bed.gz


title: Fibroblasts-R77C-alpha-SGmCh-BTZ 30nM n1

description:
IonXpress_004_R_2018_02_09_13_50_28_NGS#41-libamp_250-Fibroblasts_lenti_R77C_mCherry_Btz_30_nM_n1
bortezomib 30nM


title: DAP-seq maize ARF14

description:
Raw data previously accessioned as: SRR6830288
processed_data_file: Peak_DAP_ARF14.dap.bed.gz


title: ItalyPiedmont43


title: Chip B73 ear H3K4me3 rep2

description: processed_data_file: mapped_chip_B73_ear_H3K4me3_rep2.bed.gz


title: Fibroblasts-R77C-alpha-SGmCh-DMSO 0,1% n3

description:
IonXpress_003_R_2018_02_14_19_04_03_NGS#41-libamp_249-Fibroblasts_lenti_R77C_mCherry_DMSO_n3
DMSO 0,1%

value: DMSO 0.1 percent


title: CorsicaS15608

value: Corsica


title: K27ac_ChIP_48h_NoDox_Rep2

value: NoDox


title: K27ac_ChIP_48h_Rep1


title: K27ac_ChIP_0h_Dox_Rep2


title: Fibroblasts-R77C-alpha-SGmCh-DMSO 0,1% n2

description:
IonXpress_002_R_2018_02_09_13_50_28_NGS#41-libamp_248-Fibroblasts_lenti_R77C_mCherry_DMSO_n2
DMSO 0,1%


title: Chip B73 ear H3K4me3 rep1

description: processed_data_file: mapped_chip_B73_ear_H3K4me3_rep1.bed.gz


title: Chip B73 ear H3K36me3 rep2

description: processed_data_file: mapped_chip_B73_ear_H3K36me3_rep2.bed.gz


title: NASH+ISO2: NASH treated with isorhamnetin

city: Tsukuba

first: Munkhzul

last: Ganbold

state: Ibaraki Prefecture

address: 1 Chome-1-1 Tennodai

institute: AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL)

description: Gene expression data from NASH-induced treated with isorhamnetin mouse liver

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome Array (MS-430 PM). GeneChip was washed and stained in the Gene Atlas Fluidics Station

scan_protocol: GeneChip was scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).

label: biotin

source_name: NASH-induced treated with isorhamnetin, technical rep-2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: Six-week-old male C57BL/6J mice (Charles River Laboratories JAPAN Inc., Kanagawa, Japan) were maintained at room temperature in a 12h light/dark cycle. After one week of acclimatization with standard chow diet and tap water ad libitum, all animals were randomly assigned (Day 0) into three experimental groups (n = 8 / group): Control (CTL), NASH, and NASH treated with isorhamnetin (NASH+ISO). All animal procedures were approved by the Animal Study Committee of University of Tsukuba (No.17-312) and were handled according to the Guiding Principles for the Care and Use of Animals in the Field of Physiological Sciences approved by The Physiological Society of Japan.

extract_protocol: Total RNA was extracted from liver tissue stocked at -80°C using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The total RNA was resuspended in Tris-EDTA and stocked at -80°C until use.

treatment_protocol: CTL group mice were fed with laboratory chow diet and received vehicles. NASH and NASH+ISO groups were subjected to high fat diet (60% cal from fat, D12492, Research Diets Inc., New Brunswick, NJ, USA) from Day 0-24. Rodents received intraperitoneal injections of CCl4 at 0.1ml/kg of body weight 4 times (Day 14, 17, 21, and 24), and T0901317 at 2.5ml/kg of body weight 5 times (Day 20-24) to induce NASH. Corn oil and dimethyl sulfoxide (DMSO) were used as vehicle for CCl4 and T0901317 injections respectively. NASH+ISO group was treated with daily oral administration of isorhamnetin at 50 mg/kg of body weight (vehicle for CTL and NASH group) for last two weeks (Day 11-24).

value: Liver


title: ItalyPiedmont127

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).


title: NASH2: NASH

description: Gene expression data from NASH-induced mouse liver

source_name: NASH-induced, technical rep-2


title: NASH+ISO1: NASH treated with isorhamnetin

source_name: NASH-induced treated with isorhamnetin, technical rep-1


title: Chip B73 ear H3K27me3 rep2

city: Athens

description: processed_data_file: mapped_chip_B73_ear_H3K27me3_rep2.bed.gz


title: CorsicaS13308


title: Fibroblasts-R77C-alpha-SGmCh-DMSO 0,1% n1

description:
IonXpress_001_R_2018_02_09_13_50_28_NGS#41-libamp_247-Fibroblasts_lenti_R77C_mCherry_DMSO_n1
DMSO 0,1%


title: CTL2: Healthy control

description: Gene expression data from untreated healthy mouse liver

source_name: Healthy control, technical rep-2


title: ItalyPiedmont149


title: Chip B73 ear H3K36me3 rep1

description: processed_data_file: mapped_chip_B73_ear_H3K36me3_rep1.bed.gz


title: CorsicaS10208


title: CorsicaS00708


title: CorsicaS04208


title: NASH1: NASH

source_name: NASH-induced, technical rep-1


title: Chip B73 ear H3K27me3 rep1

description: processed_data_file: mapped_chip_B73_ear_H3K27me3_rep1.bed.gz


title: K27ac_ChIP_0h_Dox_Rep1

description:
RPKM_Table_ChIP_ATAC.xlsx
SampleMapping_ChIP_ATAC.xlsx


title: K27ac_ChIP_0h_NoDox_Rep2


title: K27ac_ChIP_0h_NoDox_Rep1


title: corsica29008


title: Chip B73 leaf input rep2

description: processed_data_file: mapped_chip_B73_leaf_input_rep2.bed.gz

value: 7-day-old 2nd leaf


title: TP- stimulated macrophages_48h_rap3

city: nanjing

first: Wenlong

last: Hu

address: Jiangwangmiao Street

department: Institute of Dermatology

institute: Chinese Academy of Medical Science & Peking Union Medical College

description: Macrophage culture supernatants with T. pallidum inoculation at a multiplicity of infection (MOI) of 30 (12 h), washed in PBS twice and further grown in fresh medium for 48 h to collect exosomes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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.

source_name: TP- stimulated, macrophages, 48h, replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

growth_protocol: THP-1 cell were cultured in RPMI 1640 containing 10% FBS and 1% penicillin/streptomycin. Macrophages were derived by stimulating THP-1 cells with 100 ng/ml PMA and cultured in RPMI-1640 containing 10% FBS

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: A total of 2×106 macrophages grown in RPMI-1640 containing 10% exosome-free FBS. Exosomes were acquired from macrophage culture supernatants with or without T. pallidum inoculation at a multiplicity of infection (MOI) of 30 (12 h). Briefly, macrophages were washed in PBS twice and further grown in fresh medium for 12 h, 24 h and 48 h to collect exosomes

tag: agent

value: Treponema pallidum

tag: time point


title: K27ac_ChIP_0h_Rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells were crosslinked in 1% formaldehyde for 10 minutes at 37°C with constant stirring, followed by quenching with 125 mM glycine for 5 min at room temperature. Cells were rinsed with 1X PBS and lysed, and chromatin was sheared using a Branson sonicator until the majority of DNA was in the range of 200-1,000 base pairs. Chromatin was incubated with antibody at 4°C overnight with constant stirring. Co-immunoprecipitation of antibody-protein complexes was performed using Protein A or Protein G Dynabeads for 1h at 4°C. ChIPs were completed using previously reported methods with the following antibodies: OCT4 (Santa Cruz, sc-8628x), H3K4me2 (Millipore, 07-030),H3K27ac () .Immunoprecipitated DNA was end repaired using the End-IT DNA End-Repair Kit (Epicentre), extended using Klenow fragment (3’-5’ exo) (NEB), and ligated to sequencing adapter oligos (Illumina). Each library was PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 base pairs selected for sequencing. Libraries were sequenced on the Illumina Hiseq 2000.

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP


title: CorsicaS13808


title: Chip B73 leaf input rep1

description: processed_data_file: mapped_chip_B73_leaf_input_rep1.bed.gz

tag: line


title: OCT4_ChIP_96h_Dox_Rep2

value: OCT4 (Santa Cruz, sc-8628x)