title: D6_Monos_IFN_y

description: normalizedCounts.txt.gz

value: IFN-y


title: HP_w/o_5

status: Public on Oct 01 2019

type: RNA

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: biol.replicate 5

hyb_protocol: 750 ng Cy3-labelled cRNA was fragmented and hybridized following Agilents instructions. After hybridization, microarrays were washed with GE Wash Buffer (Agilent).

scan_protocol: Slides were scanned with extended dynamic range (XDR) and 5 µm resolution (4x44K) using a G2565CA high-resolution laser microarray scanner (Agilent)

data_processing: Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol

molecule: total RNA

organism: Danio rerio

source_name: total fish larvae

label_protocol: Cy3 labeled cRNA was prepared from 200ng total RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Wild type zebrafish (AB strain, https://zfin.org/action/genotype/view/ZDB-GENO-960809-7) were set up for mating overnight, in 3:2 ratios, females and males, respectively. Fertilized embryos from wildtype zebrafish AB strain were used for all experiments and kept in Embryo medium (E3, 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in an incubator at 28ºC. At 1dpf, larvae were manually dechorionated under a stereomicroscope. At 2dpf, zebrafish larvae were divided randomly into the different experimental groups, at a density of 12 larvae per well of a 12 well plate (Corning) in 1.5mL of E3.

extract_protocol: After the desired exposure to diverse ligands, larvae were euthanized with Tricaine (MS-222, 300 µg/mL) and placed in Trizol for RNA isolation. RNA was isolated according the manufacturers instruction.

treatment_protocol: Three biological replicates of 12 larvae per condition were exposed to different conditions for 4 hours at 28 ºC: DMSO; DMSO + CH223191 (5mM); 3-o-C12-L-HSL (50mM); 3-o-C12-L-HSL (50mM) + CH223191 (5 mM ); 1-hydroxyphenazine (1-HP, 5mM); 1-HP (5mM) + CH223191(5mM) and 1-HP (5mM) + 3-o-C12-L-HSL (50mM).To mention, in experiments using the Aryl hydrocarbon Receptor inhibitor CH223191, larvae were pre-exposed to 5uM of the inhibitor for 2h prior to the start of the experiment and the inhibitor was kept during the experiment.

tag: treatment

value: 1-HP stimulation

tag: additional treatment

value: w/o CH223191 inhibitor


title: non_involved_lung_tissue_patient_6 9983140008_F_Expression

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Primary microarray data were collected using BeadStudio v3 software package. Raw data were log2-transformed and normalized using the robust spline normalization method, implemented in the lumi R/Bioconductor package. Batch effects were removed using ComBat function implemented in the sva R/Bioconductor package.

label: biotin

organism: Homo sapiens

source_name: Non-involved (apparently normal) lung parenchyma

label_protocol: RNA was reverse transcribed, labeled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit (Life Technologies).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: Sex

value: F

tag: age

tag: smoking status

value: never-smoker

tag: batch


title: D6_PMNs_IL_13

type: SRA

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

country: USA

institute: New York University Langone Health

description: normalizedCounts.txt.gz

library_source: transcriptomic

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the hg38 reference genome
Uniquely mapped indices (UMI) determined by HTSeq-counts
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

molecule: polyA RNA

source_name: blood

growth_protocol: Primary human polymorphonuclear neutrophils (PMNs) and peripheral blood mononuclear cells (PBMCs) from anonymous, healthy donors (New York Blood Center) were isolated by Ficoll gradient separation as previously described. CD14+ monocytes were then isolated from the PBMC fraction by positive selection. In brief: PBMCs were resuspended in MACS buffer (PBS + 0.05% BSA + 2 mM EDTA) at a concentration of 1x108 PBMCs per 950 mL. 50 mL of CD14+ microbeads (Miltenyi Biotec) were added for every 1x108 PBMCs. Cells were incubated for 20 minutes at 4°C, washed, and filtered through a cell strainer. The cells were run on an AutoMACS Pro (Miltenyi Biotec) using the ‘Posselds’ program. Monocytes were used directly after sorting. Monocyte-derived dendritic cells (DCs), and Monocyte-derived macrophages were differentiated from CD14+ monocytes by culturing the cells for 4 days at 37°C and 5% CO2 in RPMI medium supplemented with 10% FBS, 10 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin with either 110 U/mL granulocyte-macrophage colony-stimulating factor (GM-CSF) (Leukine; Sanofi) and 282 U/mL interleukin-4 (IL-4) (Affymetrix, eBioscience) for DCs or 280 U/mL GM-CSF for macrophages. Media was replenished with fresh cytokine on day 2.

extract_protocol:
RNA for each donor was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

treatment_protocol: Differentiated cells were resuspended in clear RPMI + 10% FBS. 1x105 cells were added to each stimulation well. Stimulations comprised of buffer control (PBS + 0.01% Glycerol), 500 U/mL IFN-b1a (Carrier Free; R&D Systems), 10 ng/mL IFN-g (Carrier Free, R&D Systems), IFN-l2 (Carrier Free, R&D Systems), 1000 IU/mL IL-4 (Carrier Free, Life Technologies), 100 IU/mL IL-10 (Carrier Free, Life Technologies), and 100 IU/mL IL-13 (Carrier Free, R&D Systems). Plates were spun for 5 minutes at 1200 rpm and incubated for 4 hours at 37°C and 5% CO2. Cells were then washed with PBS. Cells were resuspended in RLT buffer (Qiagen) and vortexed for 1 minute before being placed at -80°C.

tag: donor

tag: cell type

value: PMNs

tag: stimulation


title: WT-CCL4-S6

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

data_processing:
HCS V2.2 software was used for sequencing Control
Sequenced read were trmmed for adaptor sequence and masked for low-compleity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Differentially expressed genes was analyzed using DESeq2 and the hciR package on Github to simplify the R code.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: excel file include counts and FPKM values for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
livers were flash frozen in liquid N2, and TruSeq Stranded Total RNA LT sample Prep Kit was used for library generation.
TruSeq Stranded Total RNA LT sample Prep Kit was used for library generation.
Library Protocol followed TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

tag: strain

tag: genotype

value: wild type


title: WT-Oil-S3

value: Oil


title: non_involved_lung_tissue_patient_4 9983140008_D_Expression


title: WT-CCL4-S4


title: D6_Monos_IFN_B1a

description: normalizedCounts.txt.gz

value: Monos


title: D6_PMNs_IL_10

description: normalizedCounts.txt.gz


title: HPC12LHSL_plus_4

description: biol.replicate 4

value: 1-HP + 3-o-C12-L-HSL stimulation

value: plus CH223191 inhibitor


title: HPC12LHSL_w/o_5

description: biol.replicate 5


title: DMSO_w/o_5

description: biol.replicate 5

value: DMSO stimulation


title: 6179412_ARV1

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: As per instructions for Illumina HT12v4.0 BeadArrays.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value. Values below the detection threshold (determined from the P95) value for negative control probes were floored, i.e., set to the detection threshold value. Probes were then excluded for which <25% of the samples in the dataset exceeded the detection threshold value.

label_protocol: 300 ng of total RNA was reverse-transcribed, biotinylated, and amplified by standard Eberwine labeling with the  Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Per replicate, 1 million BM-MSC were cultured in 8 mL of MEM medium, supplemented with 20% fetal bovine serum, 1X penicillin/streptomycin, and 4% pooled human platelet lysate. After 24 hr treatment with either DMSO or ARV-825 (25 nM) for 24 hours, cells were collected and washed 2X with PBS for gene expression analysis.

extract_protocol: Total RNA was isolated from harvested cells with the RNeasy Plus Mini Kit (Qiagen, catalog#:74134) with subsequent RNA quality assessment using Agilent 2100 Bioanalyzer.

value: BM-MSC

tag: agent


title: D6_PMNs_IL_4

description: normalizedCounts.txt.gz


title: 6179412_ARV2


title: WT-Oil-S1


title: HP_plus_4

description: biol.replicate 4


title: 6179412_DMSO3

value: DMSO


title: C12LHSL_plus_4

description: biol.replicate 4

value: 3-o-C12-L-HSL stimulation


title: 6179412_ARV3


title: WT-Oil-S2


title: non_involved_lung_tissue_patient_1 9983140008_A_Expression


title: S Lycopersicum rdr6, IL, rep2

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v 3.2
Supplementary_files_format_and_content: csv, raw abundances

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light

extract_protocol:
Leaf tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using standard Illumina adapters

treatment_protocol: the RNA was not TAP treated prior to library construction

tag: genotype/variation

value: rdr6 mutant

tag: adapter

value: standard


title: 6179412_DMSO2


title: D6_PMNs_IFN_lambda2

description: normalizedCounts.txt.gz


title: DMSO_plus_4

description: biol.replicate 4


title: S Lycopersicum rdr6, IL, rep1


title: 6179412_DMSO1


title: D6_PMNs_IFN_y

description: normalizedCounts.txt.gz

value: IFN-y


title: HPC12LHSL_w/o_4

description: biol.replicate 4


title: HP_w/o_4

description: biol.replicate 4

value: 1-HP stimulation


title: S Lycopersicum rdr6, HD, rep2

value: HD


title: D6_PMNs_Buffer

description: normalizedCounts.txt.gz

value: Buffer


title: D6_PMNs_IFN_B1a

description: normalizedCounts.txt.gz


title: 9138d

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

library_source: genomic

data_processing:
RRBS adapters and reads less than 20 bases long were trimmed by Trimmomatic software (version 0.36)
Clean reads was aligned to the porcine reference genome (Sscrofa11.1/susScr11) by Bismark Bisulfite Mapper (version 0.19.0)
Read coverage and methylation percentage of detected methylated or unmethylated reads at one genomic position were produced by Bismark methylation extractor (version 0.19.0)
Genome_build: susScr11
Supplementary_files_format_and_content: cov text files include IDs for each Sample ...

molecule: genomic DNA

organism: Sus scrofa

source_name: Testis

extract_protocol:
Tissue samples were immediately immersed into the 1.5-milliliter (ml) RNAlater (QIAGEN, Hilden, Germany).
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: High boar taint (BT)

tag: breed

value: Danish Landrace


title: 2076120_ARV2


title: D5_Macs_IL_10

description: normalizedCounts.txt.gz

value: Macs


title: 7107d


title: C12LHSL_w/o_4

description: biol.replicate 4

value: w/o CH223191 inhibitor


title: D5_Macs_IL_4

description: normalizedCounts.txt.gz


title: 1306d


title: 2076120_ARV3


title: DMSO_w/o_4

description: biol.replicate 4


title: D5_Macs_IFN_lambda2

description: normalizedCounts.txt.gz


title: 2076120_DMSO1


title: 2076120_DMSO3


title: 8308d

value: Medium boar taint (BT)


title: HPC12LHSL_plus_3

description: biol.replicate 3

value: 1-HP + 3-o-C12-L-HSL stimulation


title: S Lycopersicum rdr6, HD, rep1


title: C12LHSL_plus_3

description: biol.replicate 3

value: plus CH223191 inhibitor


title: 2111b


title: D5_Macs_IL_13

description: normalizedCounts.txt.gz


title: D5_Macs_IFN_y

description: normalizedCounts.txt.gz


title: 1113


title: 2076120_DMSO2


title: HP_plus_3

description: biol.replicate 3


title: Primary AML_ARV825-2

source_name: Primary AML_ARV825-2

growth_protocol: OCI-AML3 cells and primary AML cells were cultured in triplicate or duplicate, respectively, using 5 million cells per replicate. Cells were cultured with ARV-825 (10 or 50 nM) or DMSO control for 24 hr, then harvested for gene expression analysis.

value: Primary AML


title: DMSO_plus_3

description: biol.replicate 3

value: DMSO stimulation


title: C12LHSL_w/o_3

description: biol.replicate 3


title: 9312d

value: Low boar taint (BT)


title: Primary AML_ARV825-1

source_name: Primary AML_ARV825-1


title: Primary AML_DMSO-2

source_name: Primary AML_DMSO-2

value: DMSO


title: D5_Macs_IFN_B1a

description: normalizedCounts.txt.gz


title: Primary AML_DMSO-1

source_name: Primary AML_DMSO-1


title: 2076120_ARV1

value: BM-MSC


title: D5_DCs_IL_13

description: normalizedCounts.txt.gz

value: DCs


title: HP_w/o_3

description: biol.replicate 3


title: OCI-AML3_ARV825-3


title: 1105f


title: 1137


title: D5_DCs_IL_10

description: normalizedCounts.txt.gz


title: DMSO_w/o_3

description: biol.replicate 3


title: D5_DCs_IL_4

description: normalizedCounts.txt.gz


title: HPC12LHSL_plus_2

description: biol.replicate 2


title: D5_Macs_Buffer

description: normalizedCounts.txt.gz


title: PDAC_282

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
mRNA and lncRNA annotated in GencodeV25 were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Blood extracellular vesicle

extract_protocol:
Plasma EV RNAs were extracted by exoRNeasy Serum/Plasma kit.
RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian

tag: tissue

value: plasma

tag: disease state

value: PDAC


title: PDAC_283


title: D5_DCs_IFN_lambda2

description: normalizedCounts.txt.gz


title: PDAC_284


title: OCI-AML3_ARV825-2


title: D5_DCs_IFN_y

description: normalizedCounts.txt.gz

value: IFN-y


title: OCI-AML3_DMSO-3


title: HP_plus_2

description: biol.replicate 2

tag: treatment

value: 1-HP stimulation

tag: additional treatment


title: PDAC_281


title: D5_DCs_IFN_B1a

description: normalizedCounts.txt.gz


title: HPC12LHSL_w/o_2

description: biol.replicate 2


title: PDAC_280


title: DMSO_plus_2

description: biol.replicate 2


title: D5_DCs_Buffer

description: normalizedCounts.txt.gz

value: Buffer


title: OCI-AML3_DMSO-1


title: PDAC_279


title: C12LHSL_plus_2

description: biol.replicate 2

value: 3-o-C12-L-HSL stimulation


title: HP_w/o_2

description: biol.replicate 2


title: PDAC_278


title: D5_Monos_IL_10

description: normalizedCounts.txt.gz

value: Monos


title: D5_Monos_IL_4

description: normalizedCounts.txt.gz


title: PDAC_277


title: C12LHSL_w/o_2

description: biol.replicate 2

value: w/o CH223191 inhibitor


title: PDAC_276


title: D5_Monos_IFN_lambda2

description: normalizedCounts.txt.gz


title: PDAC_275


title: D5_Monos_IL_13

description: normalizedCounts.txt.gz


title: D5_Monos_IFN_y

description: normalizedCounts.txt.gz


title: MOLP8_D6_KO_CX5461

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: MOLP8_clone D6_TP53 KO_CX-5461

label_protocol: 300 ng of total RNA was reverse-transcribed, amplified, and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: Cells were cultured in RPMI 1640 with L-glutamine containing 5% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: TP53 WT and KO cell lines were generated using sequence-specific zinc-finger nucleases (ZFNs; CompoZr® Knockout ZFNs; Sigma Aldrich, St. Louis, MO, USA) targeting either a non-specific sequence or exon 7 of the TP53 DNA binding domain, followed by isolation of unmodified (WT) or KO clones. Clones were then either treated with vehicle or 200 nM CX-5461 for 48 hours.

tag: cell line

value: Multiple myeloma cell line

tag: clone id

value: TP53 KO

tag: treated with

value: 200 nM CX-5461 for 48hrs


title: MOLP8_F7_KO_CX5461

source_name: MOLP8_clone F7_TP53 KO_CX-5461


title: HP_plus_1

description: biol.replicate 1

value: plus CH223191 inhibitor


title: C12LHSL_plus_1

description: biol.replicate 1


title: PDAC_274


title: HPC12LHSL_plus_1

description: biol.replicate 1

value: 1-HP + 3-o-C12-L-HSL stimulation


title: DMSO_w/o_2

description: biol.replicate 2

value: DMSO stimulation


title: MOLP8_G7_WT_CTRL

source_name: MOLP8_clone G7_TP53 WT_vehicle

value: TP53 WT

value: vehicle for 48hrs


title: PDAC_273


title: HPC12LHSL_w/o_3

description: biol.replicate 3


title: MOLP8_G7_WT_CX5461

source_name: MOLP8_clone G7_TP53 WT_CX-5461


title: MOLP8_F7_KO_CTRL

source_name: MOLP8_clone F7_TP53 KO_vehicle


title: MM1S_4E6_KO_CX5461_B

source_name: MM1S_clone 4E6_TP53 KO_CX-5461


title: D5_Monos_Buffer

description: normalizedCounts.txt.gz

tag: donor


title: MOLP8_D6_KO_CTRL

source_name: MOLP8_clone D6_TP53 KO_vehicle

tag: cell type


title: OCI-AML3_DMSO-2

value: DMSO


title: MM1S_4F3_KO_CX5461

source_name: MM1S_clone 4F3_TP53 KO_CX-5461


title: D5_PMNs_IL_13

description: normalizedCounts.txt.gz

source_name: blood

value: PMNs

tag: stimulation


title: MM1S_4E6_KO_CTRL_B

source_name: MM1S_clone 4E6_TP53 KO_vehicle


title: Phf21b_RNA_mESC_mDox_Replicate5

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

description:
RNA-seq in mESC
Normalized_counts_mESC.txt
mESC_mDox_Replicate5

data_processing:
For the RNA-Seq samples, sequenced reads were aligned to the mouse reference genome (mm9) with UCSC’s annotations using TopHat v2.0.8. SAMTOOLS v0.1.19 was used to convert the BAM output to SAM format and to sort the BAM file. From the aligned BAM files, the read counts per gene were calculated using the HTSeq program v0.5.4p1. Read counts from HTSeq program was normalized using DESeq program.
Genome_build: mm9
Supplementary_files_format_and_content: For the RNA-Seq samples, tab-delimited text files include DESeq normalized read counts for each Sample. For the ChIP-Seq and ATAC-Seq samples, wig files for UCSC genome browser track were provided.

growth_protocol:
For ES cell experiments, ES159 cells on feeders were splitted every 2 days onto tissue culture dishes coated with 0.2% gelatin, and the media was changed daily. All ES cell experiments were performed at feeder-free five stage. In vitro neuronal differentiation was performed as described by Bibel et al (2004, 2007) where ES cells were directly plated on PORN/Laminin-coated tissue culture dishes and cultivated for 2 days in N2 media followed by complete media for induced neuron (iTN) formation.
Murine Neuro2a cells (N2a cells)  were cultured at 37°C in 7% CO2 and 88% relative humidity in 10 ml of DMEM supplemented with 10% fetal calf serum, 1× NEAA and 2 mM L-glutamine. Neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA.  For ES cell experiments, ES159 cells on feeders were splitted every 2 days onto tissue culture dishes coated with 0.2% gelatin, and the media was changed daily. All ES cell experiments were performed at feeder-free five stage. In vitro neuronal differentiation was performed as described by Bibel et al (2004, 2007) where ES cells were directly plated on PORN/Laminin-coated tissue culture dishes and cultivated for 2 days in N2 media followed by complete media for induced neuron (iTN) formation.

extract_protocol:
Total RNA of cultured cells was prepared using TRIzol reagent (Invitrogen)
RNA libraries for inducible ES cells were prepared for sequencing using standard Illumina protocols.

treatment_protocol: (1) For ES cell ChIP and RNA seq: Transgenic A2lox ES cells harboring the murine Phf21b fused to an N-terminal HA-tag under the control of a doxycycline-inducible promoter were generated according to Iacovino et al (2011). Ectopic induction of Phf21b was achieved with 500 ng/ml doxycycline for 24 hours.2) ChIP-seq, ATAC seq and RNA seq  from  N2a day2  neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA. (3) For all siRNA-mediated knockdown experiments, cells were seeded and pre-depleted for two days by transfecting with ON-TARGETplus SMARTpool siRNAs (i.e., a mixture of 4 siRNAs provided as a single reagent from Dharmacon) every second day. For siRNA transfections, Lipofectamine RNAiMax was used according to the manufacturer's instructions. For N2a differentiation pre-depleted cells were differentiated by adding retinoic acid along with siRNAs for two days in N2a differentiation media.

value: mESC

tag: replicate

tag: developmental stage

value: Undifferentiated


title: D5_Monos_IFN_B1a

description: normalizedCounts.txt.gz


title: PDAC_271

value: plasma

value: PDAC


title: D5_PMNs_IL_10

description: normalizedCounts.txt.gz


title: D5_PMNs_IL_4

description: normalizedCounts.txt.gz


title: PDAC_270


title: D5_PMNs_IFN_lambda2

description: normalizedCounts.txt.gz


title: ZZ01

city: Beijing

first: Junling

last: Pang

address: No.12 Zhongguancun South St.,Haidian District

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequenced reads were cleaned after removing low quality sequences and adapter. Then cleaned reads were mapped to maize B73 AGPv3 reference genome using tophat2 software with the following key parameters: “-i 5 -I 60000 --library-type fr-unstranded -r 250 --mate-std-dev 60 --no-novel-juncs --microexon-search”. The insertion size (-r) and standard deviation (--mate-std-dev) of paired reads were estimated using “CollectInsertSizeMetrics.jar” plugin in picard tools (http://picard.sourceforge.net). Only reads that are uniquely mapped to the genome were retained for further analysis
Reads count of annotated genes (AGPv3.27) were calculated using R packages “GenomicFeatures” and “GenomicAlignments”. DESeq2 package were used to normalize the reads count among samples and to calculate the FPKM value of genes.
Genome_build: maize B73 (AGPv3 )
Supplementary_files_format_and_content: tab-delimited text files include reads counts or FPKM values for each Sample

organism: Zea mays

source_name: 5-DAP kernel

growth_protocol: A maize association mapping population consists of 318 inbred lines, including tropical, subtropical and temperate germplams was planted in one-row plots and incompletely randomized block design with three replicates in Hainan province of China in 2014. Eight ears in each block were self-pollinated, and 10-20 seeds from three to four ears in each block were collected at 5 DAP.

extract_protocol:
The collected seeds in three replications were mixed for total RNA preparation. Total RNA was extracted using RNAprep pure Kit For Plant (TIANGEN, Beijing, China) according to its protocol. Total mRNAs were accumulated using oligo(dT).
Library construction was following the standard protocol (Illumina, Inc.), and pair-end sequencing with 125 bp was carried out for each sample.

tag: inbred lines

value: kernel

value: 5 day after pollination


title: ZZ03


title: ZI330


title: D5_PMNs_IFN_y

description: normalizedCounts.txt.gz

value: IFN-y


title: PDAC_267


title: PDAC_268


title: DMSO_plus_1

description: biol.replicate 1

source_name: total fish larvae


title: ZHONG69


title: C12LHSL_w/o_1

description: biol.replicate 1

value: 3-o-C12-L-HSL stimulation

value: w/o CH223191 inhibitor


title: HP_w/o_1

description: biol.replicate 1

value: 1-HP stimulation


title: DMSO_w/o_1

description: biol.replicate 1


title: PDAC_266


title: MM1S_4F3_KO_CTRL

source_name: MM1S_clone 4F3_TP53 KO_vehicle

value: Multiple myeloma cell line

tag: genotype/variation

value: TP53 KO


title: D5_PMNs_IFN_B1a

description: normalizedCounts.txt.gz


title: MM1S_4E3_WT_CTRL

source_name: MM1S_clone 4E3_TP53 WT_vehicle


title: ZHI41


title: MM1S_2E2_WT_CX5461

source_name: MM1S_clone 2E2_TP53 WT_CX-5461

value: 200 nM CX-5461 for 48hrs


title: MM1S_4E3_WT_CX5461

source_name: MM1S_clone 4E3_TP53 WT_CX-5461

value: TP53 WT


title: PDAC_269

source_name: Blood extracellular vesicle


title: MM1S_4E6_KO_CX5461_A


title: MM1S_4E6_KO_CTRL_A

value: vehicle for 48hrs


title: PDAC_265


title: ZHENG653


title: MM1S_2E2_WT_CTRL

source_name: MM1S_clone 2E2_TP53 WT_vehicle


title: ZHENG58


title: D4_Macs_IL_13

description: normalizedCounts.txt.gz

value: Macs


title: D4_Macs_IL_10

description: normalizedCounts.txt.gz


title: PDAC_263


title: ZHENG30


title: PDAC_262


title: D4_Macs_IL_4

description: normalizedCounts.txt.gz


title: D4_Macs_IFN_lambda2

description: normalizedCounts.txt.gz


title: ZHENG29


title: D4_Macs_IFN_y

description: normalizedCounts.txt.gz


title: ZHENG28


title: ZH68


title: D4_Macs_IFN_B1a

description: normalizedCounts.txt.gz


title: PDAC_260


title: PDAC_259


title: D4_Macs_Buffer

description: normalizedCounts.txt.gz

value: Buffer


title: ZB648


title: PDAC_258


title: ZAC546


title: D4_DCs_IL_13

description: normalizedCounts.txt.gz

value: DCs


title: 1nM estradiol and 500nM ICI-182,780 24h replicate 2

city: Washington

first: Henghong

last: Li

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

hyb_protocol: Labelled cRNA samples were hybridized to Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A, Agilent Microarray Design ID: 028004; Agilent Technologies, Santa Clara, CA) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: Agilent Feature Extraction version 11.5.1.1 was used to background subtraction, LOWESS normalization, and calculate the signal intensities.

source_name: MCF7 cells

label_protocol: One hundred nanograms of total RNA were converted to cDNA and then cRNA using Agilent LowInput QuickAmp Labeling Kit (Agilent).  The resulting cRNA was labeled with Cy3 and purified.  The concentration and incorporation of dye was measured using NanoDrop ND-100 spectrophotometer.

growth_protocol: The MCF-7 breast cancer cell line was maintained in improved minimal essential medium (IMEM) containing 2mM glutamine and 5% fetal bovine serum (FBS).  For estrogen free experiments, the cells were cultured in phenol red-free IMEM containing 5% charcoal stripped calf serum (CCS) for 48 hours.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The quantity of RNA was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and the quality of the RNA was analyzed using Agilent Bioanalyzer (Agilent).

treatment_protocol: The cells were treated with estradiol (1nM), arsenite (1μM), or cadmium (1μM) in the absence or presence of the antiestrogen ICI-182,780 (500nM) for 24 hours.

value: Estradiol / ICI-182,780

tag: concentration


title: 1nM estradiol and 500nM ICI-182,780 24h replicate 3


title: 1μM cadmium and 500nM ICI-182,780 24h replicate 3

value: Cadmium / ICI-182,780


title: 1nM estradiol and 500nM ICI-182,780 24h replicate 1


title: 1μM cadmium and 500nM ICI-182,780 24h replicate 1


title: PDAC_261

value: plasma

value: PDAC


title: 1μM cadmium and 500nM ICI-182,780 24h replicate 2


title: 1μM arsenite and 500nM ICI-182,780 24h replicate 3

value: Arsenite / ICI-182,780


title: PDAC_257


title: PDAC_264


title: Z2018F

value: kernel

value: 5 day after pollination


title: D4_DCs_IL_10

description: normalizedCounts.txt.gz


title: PDAC_256


title: YU374


title: 1μM arsenite and 500nM ICI-182,780 24h replicate 2


title: YE8001


title: D4_DCs_IL_4

description: normalizedCounts.txt.gz


title: PDAC_255


title: D4_DCs_IFN_lambda2

description: normalizedCounts.txt.gz


title: HPC12LHSL_w/o_1

description: biol.replicate 1

value: 1-HP + 3-o-C12-L-HSL stimulation

value: w/o CH223191 inhibitor


title: 1μM arsenite and 500nM ICI-182,780 24h replicate 1


title: PDAC_254


title: 500nM ICI-182,780 24h replicate 3


title: OCI-AML3_ARV825-1

tag: agent


title: D4_DCs_IFN_y

description: normalizedCounts.txt.gz

value: IFN-y


title: YE52106


title: YE515


title: 500nM ICI-182,780 24h replicate 2


title: PDAC_252


title: D4_DCs_Buffer

description: normalizedCounts.txt.gz


title: D4_DCs_IFN_B1a

description: normalizedCounts.txt.gz


title: YE478


title: 500nM ICI-182,780 24h replicate 1


title: Y2348


title: PDAC_253


title: PDAC_251


title: PDAC_250


title: Y1382


title: D4_Monos_IL_10

description: normalizedCounts.txt.gz

value: Monos


title: 1nM estradiol 24h replicate 4

value: Estradiol


title: 1nM estradiol 24h replicate 2


title: PDAC_249


title: 1nM estradiol 24h replicate 3


title: D4_Monos_IL_4

description: normalizedCounts.txt.gz


title: D4_Monos_IFN_lambda2

description: normalizedCounts.txt.gz


title: PDAC_248


title: PDAC_247


title: WH413


title: vehicel control 24h replicate 4

value: vehicle control


title: 1nM estradiol 24h replicate 1


title: W138


title: U8112


title: D4_Monos_IFN_y

description: normalizedCounts.txt.gz


title: D4_Monos_IL_13

description: normalizedCounts.txt.gz


title: PDAC_246


title: D4_Monos_IFN_B1a

description: normalizedCounts.txt.gz


title: vehicel control 24h replicate 3


title: D4_Monos_Buffer

description: normalizedCounts.txt.gz


title: TY-HZ4


title: WU109


title: PDAC_244


title: TY6


title: D5_PMNs_Buffer

description: normalizedCounts.txt.gz

value: PMNs


title: vehicel control 24h replicate 1


title: D4_PMNs_IL_10

description: normalizedCounts.txt.gz


title: TY5


title: PDAC_245


title: PDAC_242


title: 1μM cadmium 24h replicate 4

value: Cadmium


title: D4_PMNs_IL_4

description: normalizedCounts.txt.gz


title: 1μM cadmium 24h replicate 2


title: PDAC_241


title: D4_PMNs_IFN_lambda2

description: normalizedCounts.txt.gz


title: TY2


title: PDAC_240


title: PDAC_239


title: 1μM cadmium 24h replicate 3


title: TY1


title: D4_PMNs_IL_13

description: normalizedCounts.txt.gz


title: 1μM cadmium 24h replicate 1


title: vehicel control 24h replicate 2


title: D4_PMNs_IFN_B1a

description: normalizedCounts.txt.gz


title: 1μM arsenite 24h replicate 4

value: Arsenite


title: TY4


title: PDAC_237


title: TIAN77


title: 1μM arsenite 24h replicate 2


title: D4_PMNs_Buffer

description: normalizedCounts.txt.gz

value: Buffer


title: TY3


title: PDAC_236


title: BS-seq worker head (experiment 1)

city: Tel Aviv

first: Assaf

last: Zemach

address: Haim Levanon

department: School of Plant Sciences and Food Security

country: Israel

institute: Tel Aviv University

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold (Amel_4.5), allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads were divided in half and 50 base reads were processed as single reads. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
Identifying differential methylation between various samples was performed by Fisher Exact Test using the number of Cs (methylated cytosines) and Ts (unmethylated cytosines) of any pair of samples. A site was determined to be differentially methylated if its p-value was lower than 0.001 in both biological replicates.
Percent methylation change: This number was calculated by dividing the difference in methylation level between two samples by the level of methylation in the sample with the higher methylation level. For example, percent-methylation-change between embryo and W. larva was calculated as follows:  Embryo mCG-W.larva mCGEmbryo mCG ifEmbryo mCG>W.larva mCG  -W.larva mCG-Embryo mCGW.larva mCGifEmbryo mCG<W.larva mCG
Gene expression: Raw Illumina RNA-Seq 100 base reads were first mapped to the most recent honey bee genome assembly (Amel_4.5; (Elsik et al., 2014)) using Tophat (Trapnell et al., 2012), with the following changes to the default Tophat v2.0.1 parameters –I 100000 (maximum intron length) and --no-novel-juncs (limiting the alignment to v3.2 honey gene annotation). Gene expression abundance and changes were calculated using the Cufflinks and Cuffdiff softwares (Trapnell et al., 2012) based on the honeybee 4.5 genome, as well as the v3.2 gene annotation file and default parameters with the addition of --min-reps-for-js-test. Differential expression was considered as statistically significant when the q-value (FDR correction) was lower than 0.05 and the FPKM fold change between two samples was higher than two.
Genome_build: Amel_4.5
Genome_annotation: OGS 3.2 scaffolds
Supplementary_files_format_and_content: GFF - Annotation of methylated CG sites
Supplementary_files_format_and_content: TXT (tab-delimited table) - Table of FPKM and differential expression of genes (rows) for each or between pairs of samples (cols).

organism: Apis mellifera

source_name: Worker head

growth_protocol: European honey bees were grown in Langstroth hives at the Harry H. Laidlaw Jr. Honey Bee Research Facility at University of California Davis.

extract_protocol:
Worker heads were collected from bees newly emerged from their own growing cells. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: head

value: mature

tag: caste

value: worker


title: BS-seq drone larva (experiment 1)

source_name: Drone Larva

extract_protocol:
Drone larvae were obtained at about 3rd and 4th instar developmental stages. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

tag: tissue

value: larva

value: drone


title: CLL8_DMSO

city: Oviedo

first: Seila

last: Lorenzo-Herrero

state: Asturias

address: Julian Claveria

department: Functional Biology

country: Spain

institute: University of Oviedo

data_processing:
Sequence quality was verified with FastQC (v 0.11.2)
Transcript abundance was directly quantified with Salmon (v 0.8.1)
Transcript-level quantifications were aggregated to gene-level abundance using DESeq2 (v 1.20.0).
Gene-level differential analysis was performed with DESeq2 (v 1.20.0). Applying a multifactor design for paired samples
Genome_build: Ensembl GRCh38 transcriptome
Supplementary_files_format_and_content: Processed files in Excel format that include mean expression and fold change values

source_name: CLL cells

growth_protocol: Leukemic cells from patients with CLL were isolated and cultured in RPMI 1640 supplemented with 10% FBS, L-glutamine, sodium piruvate and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from lysates using RNeasy kit (Qiagen)
Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Isolated CLL cells were treated with 200 nM EC-7072 or vehicle (DMSO) for 6 hours

tag: subject id

value: Isolated leukemic cells from patients with CLL


title: PDAC_235

value: plasma

tag: disease state

value: PDAC


title: BS-seq worker pupa (experiment 1)

source_name: Worker pupa

extract_protocol:
Worker pupae were collected at about pink eyes developmental stage. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: pupa


title: SY1039

value: kernel

value: 5 day after pollination


title: SY1052


title: PDAC_272


title: D4_PMNs_IFN_y

description: normalizedCounts.txt.gz

value: IFN-y


title: PDAC_234


title: CLL7_7072


title: TY11


title: PDAC_238


title: PDAC_233


title: CLL7_DMSO


title: SW92E114


title: BS-seq drone sperm (experiment 1)

source_name: Drone sperm

extract_protocol:
Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: sperm


title: CLL6_7072


title: 1μM arsenite 24h replicate 3

tag: treatment


title: CLL8_7072


title: PDAC_232


title: SI273


title: Sham1_S1

city: new york

first: Lior

last: Zangi

state: New York

address: 1470 Madison av

department: cardiovascular research center

institute: Icahn School of Medicine at Mount Sinai

description: 24sample-RNA_NormalizedQuantification.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR8 (Version 2.6.1d).
Data were normalized using the Trimmed mean of M-values (TMM) method. The scaling factors are produced according to the algorithm described in Robinson et al Genome Biol. 2010

source_name: Heart left ventricle

extract_protocol:
Total RNA was isolated with the RNeasy mini kit (QIAGEN) and DNA was degraded by treatment with TURBO DNase (Invitrogen).
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Illumina protocol.

treatment_protocol: All animal procedures were performed according to protocols approved by the Icahn School of Medicine at Mount Sinai Institutional Care and Use Committee. CFW mice were used. MI was induced by permanent LAD ligation. When required, 100 mg of modRNA was injected into the border zone immediately after LAD ligation.

tag: stress

value: Sham operation

tag: time

value: 4 hours

value: No injection


title: SY1032


title: PDAC_231


title: CLL6_DMSO


title: SHEN5003


title: Luc3_48h_S3

value: Myocardial infarction

value: 48 hours

value: Luc injection


title: CLL5_7072


title: PDAC_229


title: PDAC_230


title: Luc4_48h_S4


title: RY729


title: RY713


title: CLL5_DMSO


title: PDAC_243


title: CLL4_7072


title: Luc2_48h_S2


title: Sham2_S2


title: R15


title: PDAC_227


title: PDAC_228


title: 1μM arsenite 24h replicate 1

value: Arsenite


title: Luc1_48h_S1


title: QI319


title: CLL4_DMSO


title: QI205


title: CLL3_7072


title: AC5_48h_S10

value: AC injection


title: PDAC_226


title: PDAC_225


title: AC4_48h_S9


title: CLL3_DMSO


title: CLL2_7072


title: AC2_48h_S7


title: PDAC_224


title: PDAC_223


title: CLL2_DMSO


title: 24BrLucD

value: 24 hours


title: CLL1_7072

value: Isolated leukemic cells from patients with CLL


title: 24BrLucC


title: PDAC_222

value: plasma


title: MO17


title: P138


title: P178


title: PDAC_221

value: PDAC


title: MO113


title: M97


title: PDAC_220


title: GATA1 KO H3K27ac_ChIPSeq_Rep2

city: Rochester

first: Rentian

last: Wu

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Sequence reads from RNA-seq samples were aligned to human genome hg19 and gene annotation from Refseq gene using STAR v2.5.3 (Dobin et al., 2013). DESeq2 v1.14.1 (Love et al., 2014) was used to normalize gene read counts and calculate log2 fold change, p value and false discovery rate (FDR).
Reads from ChIP-seq were aligned to the human genome (hg19) using the Bowtie2 (Langmead and Salzberg, 2012). The H3K27ac peaks were identified using MACS2 (Zhang et al., 2008) using 0.01 as the cutoff FDR value.
Genome_build: hg19
Supplementary_files_format_and_content: bed file and txt file

source_name: GATA1 KO HCT116

growth_protocol: Cells were cultured in DMEM (Dulbecco’s Modified Eagle Medium) supplemented with 10% FBS (Sigma), 2 mM Glutamate (Gibco), penicillin and streptomycin (Millipore).  All cell lines were maintained at 37 °C in a humidified incubator with an atmosphere of 5% CO2.

extract_protocol:
The total RNA was extract using QIAGEN RNeasy Mini Kit. 5x106 active growing cultured cells were harvest, suspended in 10ml PBS, and cross-linked with 1% formaldehyde (final concentration) for 10 min, and quenched with 125 mM glycine for 5 min at room temperature, and washed twice with PBS. The pellets were resuspended in 100 μl cell lysis buffer (1% Triton-X, 0.1% Sodium-Deoxycholate, proteinase inhibitor, TE) and incubated on ice for 10 min. Lysates were diluted with 900 ul TE, and sonicated for 15 min (30 sec on / 30 sec off) using Bioruptor pico (Diagenode, Inc., Denville, NJ), and centrifuged at top speed for 10 min. The supernants were collected and the chromatin content was estimated by the Qubit assay (Invitrogen). The chromatin was then incubated with 2.5 μg of rabbit polyclonal anti-H3K27ac antibody (Abcam, D5E4, 1:5000) on a rocker overnight. Protein G-magnetic beads (30 μL, Invitrogen) were added for 4 hours incubation. The bedads were entensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65 °C overnight. DNAs were purified using Min-Elute purification kit (QIAGEN, Valencia, CA) after the treatment of RNase A and proteinase K.
RNA library preparation and sequence were done through Novogene. ChIP-seq libraries were prepared from ChIP DNA using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB). The ChIP-seq libraries were sequenced to 50 base pairs on an Illumina HiSeq 4000 using pair-end mode in the Mayo Clinic Center for Individualized Medicine Medical Genome Facility.

value: HCT116 colon cancer cell

tag: genotype

value: GATA1 KO


title: M153

value: kernel

value: 5 day after pollination


title: GATA1 KO H3K27ac_ChIPSeq_Rep1


title: PDAC_219


title: 24BrLucA


title: PDAC_218


title: Q319-BC6


title: GATA1 WT H3K27ac_ChIPSeq_Rep2

source_name: GATA1 WT HCT116

value: GATA1 WT


title: LY042

source_name: 5-DAP kernel


title: 24BrACc


title: GATA1 WT H3K27ac_ChIPSeq_Rep1


title: AC1_48h_S6


title: PDAC_217


title: GATA1 KO H3K4me1_ChIPSeq_Rep2


title: 4hLuc4_S10


title: CLL1_DMSO


title: PDAC_216


title: GATA1 KO H3K4me1_ChIPSeq_Rep1


title: 4hLuc3_S9


title: LK11


title: GATA1 WT H3K4me1_ChIPSeq_Rep2


title: PDAC_215


title: LV28


title: 4hLuc2_S8


title: 24BrACd


title: PDAC_214


title: 4hLuc1_S7


title: LIAO5114


title: GATA1 WT H3K4me1_ChIPSeq_Rep1


title: LIAO5262


title: PDAC_213


title: 4hAC4_S6


title: 4hAC3_S5


title: 24BrACa


title: P235

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

description: Total RNA was extracted from whole blood drawn from kidney transplant recipients prior to transplantation (baseline), and mRNA sequencing was performed on an Illumina HiSeq4000 sequencer.

data_processing:
The reads with good quality were firstly aligned to human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering for reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. The read counts were log2 transformed and normalized at an equal global median value in order to compare transcription level across samples, followed by quantile normalization and batch correction
Genome_build: hg19

source_name: whole blood

extract_protocol:
total RNA wasextracted from pretransplant whole blood of kideny transplant recipeints
The library was generated standard TrueSeq mRNA library generation kit (Illumina Inc)
standard mRNA library

tag: set

tag: acr before or at 6m

tag: acr after 6m

tag: death censored graft loss

tag: follow up days


title: P234


title: LIAO159

tag: inbred lines

tag: developmental stage


title: PDAC_212


title: LX9801


title: LIAO138


title: PDAC_211


title: P233


title: 4hAC2-2_S4


title: LG001


title: PDAC_210


title: P232


title: BS-seq worker embyro (experiment 1)

source_name: Worker embryo

extract_protocol:
Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: embryo

value: worker


title: 4hAC1_S3

value: 4 hours


title: P231


title: L3180


title: ShamI_S2

description: 10sample-RNA_NormalizedQuantification.txt

value: No operation

value: No injection


title: PDAC_209


title: PDAC_208


title: P230


title: K22


title: K12


title: ShamH_S3


title: ShamD_S1


title: PDAC_207


title: PDAC_206


title: K10


title: 4hD_S4

value: Myocardial infarction


title: JIAO51


title: PDAC_204


title: 4hE_S5


title: JY01


title: PDAC_205


title: JI853


title: P229


title: P228


title: P226


title: P225


title: P227


title: PDAC_203


title: 24hH_S9


title: JI846


title: 24hG_S8


title: P224


title: P223


title: 24hD_S7


title: PDAC_200


title: JI63


title: JH96C


title: PDAC_199


title: JH59


title: 4hC_S6


title: Onc_Clone_4 (H1047Rhet_MEF)

city: Cambridge

first: Ralitsa

middle: Radostinova

last: Madsen

address: Addenbrookes Treatment Centre, Keith Day Road

department: Metabolic Research Laboratories, Clinical Biochemistry

institute: University of Cambridge

data_processing:
The raw reads were mapped to the mouse genome build GRCm38.95 using Spliced Transcripts Alignment to a Reference (STAR) v2.5.3a
Gene level counts were performed using STAR v2.5.3a with option --quantMode GeneCounts
All subsequent data analyses steps were performed in R using RStudio. Briefly, the edgeR package was used to calculate counts per million (CPM) for each gene and sample. Genes were included for further analysis if expressed at CPM > 0.3 in at least 1/3 of all samples. Sample library size was normalised by the TMM (trimmed mean of M values) method (Robinson and Oshlack, 2010 Genome Biology), followed by differential gene expression analysis with voom(), lmFit() and eBayes() according to the limma analysis pipeline described by Ritchie et al. (2015 Nucleic Acid Research).
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: Each sample is associated with 2 fastq files corresponding to read1 (_R1) and read2 (_R2) data from the paired-end sequencing experiment.

source_name: Mouse embryonic fibroblasts

growth_protocol: The derivation and growth conditions of the cells are provided in the following publication: doi: 10.1038/srep39985

extract_protocol:
RNA was extracted using Qiagen’s RNAeasy miniprep (with QIAshredder).
An Illumina TruSeq RNA Library Prep Kit v2 (# RS-930-2002) was used to prepare 100-bp-long paired-end libraries according to the manufacturer's instructions. All samples had a confirmed Agilent Bioanalyzer RIN score of 10.

treatment_protocol: All cultures were collected 48 hours after 4-OHT induction of flp recombinase mediated PIK3CA mutation.

tag: passage


title: PDAC_198


title: P221


title: PDAC_202


title: P222


title: J4112


title: P220


title: Onc_Clone_3 (H1047Rhet_MEF)


title: HZ4


title: PDAC_197


title: P219


title: PDAC_201


title: P218


title: HYS

value: HYS


title: PDAC_195


title: P217


title: Flp_Clone_4 (WT_MEF)


title: PDAC_196


title: HUA83-2


title: GY462


title: Onc_Clone_1 (H1047Rhet_MEF)


title: 24hC_S10


title: Onc_Clone_2 (H1047Rhet_MEF)


title: Flp_Clone_3 (WT_MEF)


title: GY386


title: PDAC_193


title: P215


title: PDAC_192


title: GY1007


title: Flp_Clone_2 (WT_MEF)


title: P213


title: PDAC_191


title: GL178


title: Flp_Clone_1 (WT_MEF)


title: GEMS9


title: PDAC_189


title: P212


title: PDAC_194


title: P214


title: PDAC_190


title: GEMS6


title: P211


title: P216


title: P209


title: PDAC_187


title: PDAC_188


title: GEMS65


title: PDAC_186


title: GEMS64


title: FASTED-H3K27ac_S2_ChIP-seq II

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the mm9 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Genome_build: mm9
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K9bhb, H4K12bhb and H3K27ac enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Small Intestine

growth_protocol: Male and female mice (strains: Lgr5EGFP-IRES-CreERT2/+ Strain name: B6.129P2-Lgr5tm1(cre/ERT2)Cle/J, JAX, 008875) and C57BL/6J (JAX, 000664)) were purchased, bred in house, and maintained at 72°F +/- 2 °F on a 12h light/dark cycle. Six- to twelve-week-old aged matched males and females were randomly assigned to either fed or fasted groups. Fed animals were provided ad libitium access to food (PicoLab 5053, #0007688) and water for 24h, fasted animals were completely food deprived for 24h with ad libitium access to water. Experimental mice were singly housed on aspen bedding for the duration of experiments

extract_protocol:
Chromatin immunoprecipitations were performed using a previously published protocol with modifications for SI crypts. Briefly, whole isolated crypts from 4 animals were pooled per treatment per replicate and cross linked for 10 min at 37°C with 1% formaldehyde in supplemented media and quenched with 0.125M glycine for 5 min at 37°C. Crypts were washed with PBS with 1× protease inhibitor cocktail (Sigma-Aldrich) and stored at -80°C. Pellets were thawed and then lysed for 30 min on ice with I-ChIP buffer (12mM Tris–HCl pH 8.0, 6mM EDTA pH 8.0, 0.1x PBS, 0.5% SDS) plus cOmplete mini protease inhibitors. Sonication conditions were optimized for SI crypt cells using a Bioruptor (Diagnode) to achieve shear length of 250-500bp. 10% total chromatin was reserved as an input control. Chromatin was diluted 5 fold and immunoprecipitation was performed overnight by incubation of the sonicated cell lysate with 30ul of protein G magnetic dynabeads (Invitrogen) previously coupled to target antibody for a minimum of 1h at 4°C. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). Elution and reverse cross linking was performed in 50ul direct elution buffer (10mM Tris–HCl, pH 8.0, 5mM EDTA, pH 8.0, 300mM NaCl and 0.5% SDS) with Proteinase K and RNaseA at 65°C overnight. Eluted DNA was cleaned up with solid-phase reversible immobilization (SPRI) beads (Beckman-Coulter).
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

treatment_protocol:
Crypt isolation followed previously published protocols with minor modifications [Guo, 2009 #5169;Tinkum, 2015 #4005]. Briefly fed or fasted mice were euthanized by CO2, the whole SI was collected, flushed with PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) to remove feces, and the mesentery was removed. The SI sample was cut longitudinally then cut transversely into 4 equal pieces. Each sample was placed on ice in PBS (Ca2+- and Mg2+-free, 100nM TSA) while the remaining samples were collected. After collection of all samples, SI were incubated in PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) for 10 min then transferred to HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA). Crypts were released through a series of vortex washes at 1,600rpm in HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) at 4°C. Supernatants from all vortex washes were filtered through 70-μm mesh and pooled into 50ml conical tubes to remove villus material and tissue fragments. Isolated crypts were pelleted at 1000rpm at 4°C. After this step, whole crypts were utilized for flow cytometry (detailed below), spheroid cell line establishment [de la Cruz Bonilla, 2018 #5161] and treatment (detailed below), or ChIP-seq (detailed below). For ChIP-seq, crypts were first suspended in ADMEM/F12 (D6421, Sigma) supplemented with 10 U/mL penicillin, 10μg/mL streptomycin, 2mM L-glutamine, 10mM HEPES, 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem), 10µM Y-27632 dihydrochloride (Sigma), 0.5mM N-acetylcysteine amide (Sigma), and 100nM TSA.
Whole crypt isolates were suspended in Matrigel™ and plated in a 24-well tissue culture dish (30 μl per well) as described [de la Cruz Bonilla, 2018 #5161]. Cultures were grown in 50% L-WRN conditioned media supplemented with 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem) and 10µM Y-27632 dihydrochloride (Sigma) added to each culture well. Media was changed every second day and spheroids were subcultured every third day. For experimental treatments of spheroid cultures, 50% L-WRN conditioned media was supplemented with either 5 or 10mM (R)-(–)-3-Hydroxybutyric acid (298360, Sigma) with 10µM TGF-β RI Kinase Inhibitor VI and 10µM Y-27632 dihydrochloride added to each treatment culture well. Standard media changes occurred for untreated control culture wells. All treatments were 24h prior to spheroid isolation from Matrigel™ for ChIP-qPCR or immunoblotting analyses.

tag: cell type

value: Small Intestine

tag: chip-antibody

value: H3K27ac Abcam ab4729


title: P208


title: GEMS66

tag: tissue


title: FASTED-Input_S2_ChIP-seq II


title: FASTED-Input_S5_ChIP-seq II


title: PDAC_185


title: P207


title: FED-Input_F1_ChIP-seq II


title: GEMS63


title: FED-H3K27ac_F4_ChIP-seq II


title: GEMS62


title: PDAC_184


title: P206


title: MEL_induced_2

city: Hangzhou

first: Caiyong

last: Chen

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using TopHat2.
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. Breifly, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: Txt file include RPKM values for all samples

source_name: mouse erythroleukemia cells

growth_protocol: MEL cells were maintained in a complete medium composed of Dulbecco’s Modified Eagle Medium (DMEM), 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (PS), 1% sodium pyruvate, 1% glutamine, and 1% non-essential amino acid (NEAA). Dimethyl sulfoxide (DMSO, 1.5%) was supplemented to the medium to induce the erythroid-like differentiation of MEL cells.

extract_protocol:
RNA was extracted using Trizol reagent. The mRNA was enriched by depleting ribosomal RNA using Epicentre Ribo-Zero removal kit (Illumina) and fragmented.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mouse erythroleukemia (MEL) cells

value: DMSO-induced


title: P210


title: GEMS60


title: GEMS61


title: FASTED-H3K27ac_S5_ChIP-seq II


title: PDAC_183

source_name: Blood extracellular vesicle

extract_protocol:
Plasma EV RNAs were extracted by exoRNeasy Serum/Plasma kit.
RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian

value: plasma

value: PDAC


title: P205


title: FED-Input_F4_ChIP-seq II


title: FED-H3K27ac_F1_ChIP-seq II


title: MEL_uninduced_2

value: uninduced


title: GEMS5

value: kernel


title: PDAC_182


title: P203


title: P204


title: PDAC_180


title: P202


title: GEMS59

value: 5 day after pollination


title: MEL_induced_1


title: GEMS58


title: P201


title: PDAC_179


title: EGFR Normal 3

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC mm10 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: EGFR Normal

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Proneural (PN) gene set-enriched gliomas


title: PDAC_177


title: PDAC_178


title: P200


title: PDAC_181


title: EGFR Normal 2


title: GEMS54


title: PDAC_176


title: EGFR Tumor 2

source_name: EGFR Tumor

value: CL/MES-gene set enriched glioma


title: GEMS55


title: PDAC_175


title: P198


title: GEMS50


title: GEMS51


title: P196


title: EGFR Tumor 1


title: P199


title: EGFR Normal 1


title: PDAC_174


title: P197


title: MEL_uninduced_1


title: TMA-ARB-10

city: Charlestown

first: Kamila

last: Naxerova

state: MA

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

description: Sample name: MAg20-10

data_processing:
Alignment and transcript quantification: Using the aligner Salmon (http://salmon.readthedocs.io/en/latest/salmon.html) under default filtering settings, sequencing reads (fastqs) were aligned to, and count estimates calculated for, GenCode- annotated mouse (mm10, vM9) transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts generated by Salmon in txt format

source_name: MCa-M3C breast tumors

growth_protocol: Mice bearing orthotopic MCa-M3C tumors were split into time- and size-matched (~100 mm^3) treatment groups

extract_protocol:
Total RNA extraction and poly-A selection with NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L, NEB).
NEBNext Ultra Directional RNA Library Prep Kit (E7420L, NEB)

treatment_protocol: 40 mg/kg valsartan in the TMA-ARB form or an equal volume of PBS intravenously (retro-orbital injection) each day for 6 days

value: MCa-M3C breast tumors

tag: cell line

tag: host mouse strain

value: FVB/N


title: P195

city: New York


title: TMA-ARB-9

description: Sample name: MAg20-9


title: PDAC_173

tag: disease state


title: PDAC_172


title: P194


title: GEMS44

extract_protocol:
The collected seeds in three replications were mixed for total RNA preparation. Total RNA was extracted using RNAprep pure Kit For Plant (TIANGEN, Beijing, China) according to its protocol. Total mRNAs were accumulated using oligo(dT).
Library construction was following the standard protocol (Illumina, Inc.), and pair-end sequencing with 125 bp was carried out for each sample.


title: GEMS48


title: PDAC_171


title: P193


title: PDAC_170


title: TMA-ARB-8

description: Sample name: MAg20-8


title: GEMS4


title: TMA-ARB-7

description: Sample name: MAg20-7


title: TMA-ARB-6

description: Sample name: MAg20-6


title: GEMS42


title: P192


title: P191


title: Control-5

description: Sample name: MAg20-5


title: PDAC_168


title: GEMS39


title: Control-4

description: Sample name: MAg20-4


title: GEMS3


title: P190


title: PDAC_166


title: GEMS40


title: P189


title: GEMS37


title: PDAC_169


title: P188


title: Control-3

description: Sample name: MAg20-3


title: PDAC_167


title: PDAC_165


title: GEMS36


title: P187


title: Control-1

description: Sample name: MAg20-1


title: PDAC_164


title: P186


title: E133

city: Taipei

first: Li-Jung

last: Juan

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
Basecalls performed using Illumina Casava1.7.
Data cleaning was performed with following steps: 1, remove of adaptor sequences, 2, remove of reads with percentage of unknown bases (N) greater than 10%, and 3, remove low quality reads.
Clean reads were mapped to UCSC mm 9 annotation using Avadis NGS software ver1.6 (Strand Scientific Intelligence).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to Mortazavi A. et al., Nat Methods. 2008, 5: 621-628. The formula used for calculation of RPKM of gene A  wasas following, RPKM=10^6C/(0.001*NL). C is number of reads that uniquely aligned to gene A, N is total number of reads that uniquely aligned to all genes, and L is number of bases of gene A.
Around 70 imprinted genes with FPKM > 0.4 were obtained. Imprinted genes with fold changes over 1.3 folds in comparison with the average RPKM of WT embryos were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Xls file with Gene symbol, Chromosome location, Expressing allele, Av. RPKM of WT embryos, RPKM of each individual relative to Av. RPKM of WT embryos

growth_protocol: Embryos were harvested from Naa10-/X female mice crossed with Naa10X/Y male at 10.5 days post copulation

extract_protocol:
Total RNAs were purified from mouse embryos at 10.5 dpc using RNeasy® Plus Mini Kit (Qiagen).
Total RNAs purified from mouse embryos at 10.5 dpc using RNeasy® Plus Mini Kit (Qiagen) were treated with DNase I to remove residual genomic DNA, enriched by oligo-dT magnetic beads, and sonicated (Bioruptor1 ®, Diagenode) into roughly 200 bp fragments. cDNAs were synthesized with random hexamer-primers, purified by silicon-coated magnetic beads, blunted in the ends, added with a single adenine at 3'-end, ligated with sequencing adaptors and PCR-amplified. The quality and quantity of the resulting library were determined by Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, respectively. The library products were sequenced by Illumina HiSeqTM 2000.

tag: strain background

tag: genotype/variation

value: Naa10-/Y; Naa10-KO

value: whole embryo

tag: molecule subtype

value: poly-dT enriched RNA


title: GEMS33


title: E132


title: P185

tag: set


title: PDAC_163


title: E131

source_name: littermate WT embryo

value: Naa10X/Y; WT


title: P184

tag: acr before or at 6m


title: GEMS31


title: GEMS32


title: P183

tag: acr after 6m


title: Control-2

description: Sample name: MAg20-2


title: PDAC_160


title: PDAC_159


title: P181

tag: death censored graft loss


title: P182

tag: follow up days


title: GEMS28

tag: inbred lines


title: PDAC_158


title: P180

value: Borderline


title: GEMS35

tag: developmental stage


title: PDAC_157


title: PDAC_162


title: GEMS25


title: P179


title: PDAC_161


title: P178


title: cKO pDC_rep4

city: St. Louis

first: Kenneth

last: Murphy

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology

institute: Washington University School of Medicine

description: pDC from Bcl6 cKO mice

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: pDC from Bcl6 cKO mice

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: Spleens were minced and digested with stirring for 30 min at 37ºC in 5ml of IMDM plus 10% FBS with 30U/ml DNaseI (Sigma-Aldrich) and 250ug/ml collagenase B (Roche). For removal of debris, cells were passed through a 70-µm filter before red blood cells were lysed with ammonium chloride–potassium bicarbonate lysis buffer.

value: pDC

value: spleen

tag: genotype

value: Bcl6 cKO


title: PDAC_156

first: Shenglin

last: Huang

address: 270 Dongan

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
mRNA and lncRNA annotated in GencodeV25 were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

value: plasma


title: cKO pDC_rep5

description: pDC from Bcl6 cKO mice

tag: cell type


title: PDAC_155

value: PDAC


title: GEMS2


title: GEMS21


title: P177


title: GEMS29


title: E130


title: PDAC_154


title: cKO pDC_rep2

description: pDC from Bcl6 cKO mice


title: GEMS20


title: cKO pDC_rep3

description: pDC from Bcl6 cKO mice


title: GEMS1


title: P175


title: PDAC_152


title: P176


title: GEMS19


title: P174


title: PDAC_151


title: GEMS23


title: cKO pDC_rep1

description: pDC from Bcl6 cKO mice


title: P173


title: WT pDC_rep2

description: pDC from WT mice

source_name: pDC from WT mice

value: WT


title: GEMS18

value: kernel


title: WT pDC_rep3

description: pDC from WT mice


title: GEMS17

value: 5 day after pollination


title: N_116

value: healthy


title: P172


title: GEMS16


title: PDAC_153


title: P171


title: N_115


title: WT pDC_rep1

description: pDC from WT mice


title: GEMS15


title: P170


title: N_114


title: cKO cDC2_rep4

description: cDC2 from Bcl6 cKO mice

source_name: cDC2 from Bcl6 cKO mice


title: cKO cDC2_rep5

description: cDC2 from Bcl6 cKO mice


title: cKO cDC2_rep3

description: cDC2 from Bcl6 cKO mice


title: GEMS14


title: P169


title: N_113


title: GEMS13


title: cKO cDC2_rep2

description: cDC2 from Bcl6 cKO mice


title: N_117


title: P167


title: N_112


title: P168


title: FCD0602


title: GEMS11


title: N_111


title: cKO cDC2_rep1

description: cDC2 from Bcl6 cKO mice


title: N_110


title: ES40


title: WT cDC2_rep3

description: cDC2 from WT mice

source_name: cDC2 from WT mice


title: P165


title: EN25


title: P164


title: WT cDC2_rep2

description: cDC2 from WT mice


title: WT cDC2_rep1

description: cDC2 from WT mice


title: N_108


title: P163


title: DONG46


title: cKO cDC1_rep3

description: cDC1 from Bcl6 cKO mice

source_name: cDC1 from Bcl6 cKO mice


title: N_107


title: P162


title: N_106


title: cKO cDC1_rep4

description: cDC1 from Bcl6 cKO mice


title: P166


title: P161


title: DH3732


title: cKO cDC1_rep2

description: cDC1 from Bcl6 cKO mice


title: DAN599


title: N_109


title: N_104


title: P160

value: ACR


title: DAN4245


title: cKO cDC1_rep1

description: cDC1 from Bcl6 cKO mice


title: DMT7

type: genomic

city: Münster

first: Christian

last: Thomas

address: Pottkamp 2

institute: Institute of Neuropathology Münster, Germany

description:
desmoplastic myxoid tumor
203545190036_R08C01

hyb_protocol: bisulphite converted DNA was hybridised to either the Illumina HumanMethylation450 BeadChip array or the MethylationEPIC BeadChip array.

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

data_processing:
R environment (version 3.6.0)
Samples were normalized using the MNPpreprocessIllumina R function (https://github.com/mwsill/mnp_training)
Unmethylated and methylated signal intensities

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from formalin-fixed paraffin-embedded tumor samples using the Maxwell 16 FFPE Tissue LEV DNA Purification Kit (Promega).

tag: gender

value: male

tag: sample type

value: cancer tissue


title: P159


title: WT cDC1_rep3

description: cDC1 from WT mice

source_name: cDC1 from WT mice

tag: tissue


title: N_103


title: DAN360

source_name: 5-DAP kernel


title: P158

source_name: whole blood


title: DMT5

description:
desmoplastic myxoid tumor
200930770010_R03C01

value: female


title: DONG237


title: DAN340


title: P157


title: DMT3

description:
desmoplastic myxoid tumor
203068760186_R08C01


title: N_101


title: DAN3130


title: DMT2

description:
desmoplastic myxoid tumor
202081120046_R03C01


title: N_105


title: N_100


title: N_102


title: P155


title: D863F


title: N_099


title: P154


title: CML69


title: CML496


title: P156


title: P153


title: N_097


title: WT cDC1_rep1

description: cDC1 from WT mice


title: N_098


title: CML493


title: WT cDC1_rep2

description: cDC1 from WT mice


title: N_096


title: P152


title: P151


title: N_095


title: CML486


title: CML479


title: P150


title: P149


title: N_094


title: N_093


title: CML433


title: CML454


title: P148


title: CML426


title: N_092


title: P147


title: P146


title: N_090


title: CML423


title: CML415


title: N_091


title: N_088


title: SAMPLE 16: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_8

city: Tsu

first: Akihiro

last: Ikuno

state: Mie

address: 1577 Kurimamachiyacho

department: Bioresources

country: Japan

institute: Mie University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip array. The primer hybridized to the DNA was extended and labeled using labeled nucleotides.

scan_protocol: After fluorescent staining of labeled primer,  the arrays were scanned using Illumina iScan® System. All these processes were performed according to the standard Illumina protocol.

data_processing:
Raw IDAT files were processed using Methylation module (Version 1.90) in GenomeStudio software (V2011.1, Illumina) or the ChAMP package in R 3.4.3.
In processing with GenomeStudio, normalization was performed using negative control probes to generate average β values of early or advanced stage degeneration group. And then, the methylation data were filtered for probes with a detection P > 0.01 or sex chromosomes.
In processing with the ChAMP package,  Raw methylation data were imported with the minfi method, and normalized with the SWAN method. By default setting, raw data were filtered for probes with a detection P > 0.01, non-CpG site, SNP-related probe list(PMID: 27924034), the multi-hit probe list(PMID: 24063430) or sex chromosomes.

label: Cy5 and Cy3

source_name: Advanced stage degeneration 8

extract_protocol: Frozen NP tissue samples (200-250 mg wet weight) were pulverized in the presence of liquid nitrogen using a cryopress (Microtech Nichion, Chiba, Japan). DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega, City, WI, USA) according to the manufacturer's instruction.

value: Female

tag: age

tag: grades of degeneration

value: Pfirrmann grades IV

tag: disease

value: Lumbar degenerative spondylolisthesis

value: intervertebral disc (IVD)


title: N_089

city: Shanghai

institute: Fudan University

tag: disease state


title: P143


title: P144


title: CML361

first: Junling

last: Pang

address: No.12 Zhongguancun South St.,Haidian District

data_processing:
Sequenced reads were cleaned after removing low quality sequences and adapter. Then cleaned reads were mapped to maize B73 AGPv3 reference genome using tophat2 software with the following key parameters: “-i 5 -I 60000 --library-type fr-unstranded -r 250 --mate-std-dev 60 --no-novel-juncs --microexon-search”. The insertion size (-r) and standard deviation (--mate-std-dev) of paired reads were estimated using “CollectInsertSizeMetrics.jar” plugin in picard tools (http://picard.sourceforge.net). Only reads that are uniquely mapped to the genome were retained for further analysis
Reads count of annotated genes (AGPv3.27) were calculated using R packages “GenomicFeatures” and “GenomicAlignments”. DESeq2 package were used to normalize the reads count among samples and to calculate the FPKM value of genes.
Genome_build: maize B73 (AGPv3 )
Supplementary_files_format_and_content: tab-delimited text files include reads counts or FPKM values for each Sample


title: GEMS49


title: SAMPLE 14: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_6

source_name: Advanced stage degeneration 6

label_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip array. The primer hybridized to the DNA was extended and labeled using labeled nucleotides.


title: N_087


title: CML338


title: P145


title: CML411


title: SAMPLE 15: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_7

source_name: Advanced stage degeneration 7


title: SAMPLE 13: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_5

source_name: Advanced stage degeneration 5

value: Lumbar degenerative scoliosis


title: SAMPLE 12: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_4

source_name: Advanced stage degeneration 4

value: Male


title: CML32


title: CML325


title: SAMPLE 10: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_2

source_name: Advanced stage degeneration 2

value: Lumbar spinal stenosis


title: P139


title: N_083

source_name: Blood extracellular vesicle

value: plasma


title: N_086


title: N_085


title: P141

value: Borderline


title: N_084


title: CML327


title: SAMPLE 11: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_3

source_name: Advanced stage degeneration 3


title: P140


title: N_082


title: SAMPLE 8: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_8

source_name: Early stage degeneration 8

value: Pfirrmann grades II

value: Spinal trauma


title: CML323

value: kernel

value: 5 day after pollination


title: SAMPLE 9: Human_IVD tissues_Advanced stage degeneration (Pfirrmann grades IV–V)_1

source_name: Advanced stage degeneration 1


title: P137


title: N_081

value: healthy


title: CML31


title: SAMPLE 7: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_7

source_name: Early stage degeneration 7

value: Pfirrmann grades III


title: CML304


title: P138

value: ACR


title: P142