title: Sample 9_Macrophages exposed to VE-UHMWPE particles

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped by alignment to human genome (hg19) using TopHat and Bowtie, normalized using the Trimmed Mean of M values (TMM) process, and then annotated using Cufflinks and Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html). Low calculated fragments per kilobase of transcript per million mapped reads (FPKM) were removed
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Mononuclear cells (PMCs) were separated from the blood samples by density gradient centrifugation (Ficoll-Paque™ PLUS: GE Healthcare, Waukesha, WI, USA) and cultured in RPMI-1640 supplemented with 10% heat-inactivated fetal calf serum (FCS), 25 mg/l penicillin/streptomycin and incubated in a humidified atmosphere containing 5% CO2 for 3 hr. Adherent cells were washed twice with ice-cold phosphate-buffered saline buffer (PBS) and cultured in medium supplemented with 50 ng/ml human recombinant macrophage colony-stimulating factor for 7 days. Cultures were regularly replenished with fresh medium every 3 days. Differentiated macrophages were detached on day 7 of culture by treatment with 1% trypsin-EDTA solution for 5 min, washed with ice-cold PBS, counted, and then seeded onto 48-well culture plates at 2 × 105 cells/well.

extract_protocol:
Differentiated macrophages cultured with or without UHMWPE and  VE-UHMWPE particles were lysed with TRIzol Reagent and harvested for RNA purification. RNA was purified using RNeasy Mini kit columns according to the manufacturer’s instructions, and integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer.
High-quality DNA-free RNA with integrity score > 9.0 was further used for RNA-seq. Each library was generated from 0.5-1 μg pooled RNA of 3 donors (equal quantity) using the TruSeq® Stranded mRNA Sample Preparation Kit. Quality of libraries was examined by Bioanalyzer High sensitivity DNA kit, and then paired-end reads (101 bp) were obtained by Illumina HiSeq 2500, with an average of 69 million reads per sample. Reads were mapped by alignment to human genome (hg19) using TopHat and Bowtie, normalized using the Trimmed Mean of M values (TMM) process, and then annotated using Cufflinks and Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html).

treatment_protocol: Macrophages were co-cultured with free-endotoxin UHMWPE or VE-UHMWPE particles at ratio of 1:4000 µm3 for 24 h using inverted cell culture technique that allows particles to directly interact with macrophages. Control macrophages were cultured alone. Ratio of particles to cells was initially optimized to get high biological response of macrophages. Suspended particles in RPMI-1640 supplemented with 10% FCS and 25 mg/l penicillin/streptomycin were added to macrophages culture to completely fill the wells, and a round-shape 12-mm-coverslips were gently placed onto each well without forming bubbles. Plates were then covered by two breathable sealing membranes, inverted and incubated in a humidified atmosphere containing 5% CO2 for 24 h.

tag: subject status

value: Healthy Asian donor

value: 30-40 years old

value: Blood

tag: cell type

value: Primary macrophage

tag: cultured with

value: VE-UHMWPE particles


title: Sample 8_Macrophages exposed to VE-UHMWPE particles

status: Public on May 06 2019

type: SRA

country: Japan

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: age

tag: tissue


title: Sample 7_Macrophages exposed to VE-UHMWPE particles


title: D39_C14

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

country: USA

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2
Gene expression estimates obtained using RSEM v 1.2.1, with Bowtie 0.12.8 for alignment.
Genome_build: Genome Reference: hg19
Supplementary_files_format_and_content: 2d.tpm.csv (comma-delimited RSEM-generated gene expression estimates in Transcripts per Million)

extract_protocol:
Qiagen Rneasy 96 kit with RLT lysis buffer
Refer to document ‘TruSeq RNA Sample Preparation v2 Guide 15026495F’ from the Illumina site, (URL: https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqrna/truseq-rna-sample-prep-v2-guide-15026495-f.pdf)

tag: compound

value: Ficoll 400

tag: classification

value: non-toxic

tag: concentration

tag: time

value: 39 days exposure

tag: cell line


title: FL lymph node biopsy, untreated, 1022

type: RNA

city: Stanford

first: Aaron

middle: M

last: Newman

state: California

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

institute: Stanford University

hyb_protocol: cRNA was hybridized to HGU133 Plus 2.0 microarrays (Affymetrix) according to the manufacture's protocol.

scan_protocol: standard Affymetrix protocol

data_processing: MAS5 normalized using the affy package in R/Bioconductor.

label: biotin

source_name: FL lymph node biopsy, untreated, 1022

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA and genomic DNA were prepared and stored using TRIzol and RNeasy Midi Kits (Qiagen, Valencia, CA). Total cellular RNA (at least 300 ng) was assessed for yield (NanoDrop 2000, Thermo Scientific) and quality (2100 Bioanalyzer, Agilent).

value: lymph node


title: FL lymph node biopsy, untreated, 1005

source_name: FL lymph node biopsy, untreated, 1005


title: D39_C15

value: Naproxen sodium


title: D39_C16

value: DMSO


title: FL lymph node biopsy, untreated, 1010

source_name: FL lymph node biopsy, untreated, 1010


title: D39_C11

value: Glycerol


title: FL lymph node biopsy, untreated, 1009

source_name: FL lymph node biopsy, untreated, 1009


title: FL lymph node biopsy, untreated, 1006

source_name: FL lymph node biopsy, untreated, 1006


title: FL lymph node biopsy, untreated, 1008

source_name: FL lymph node biopsy, untreated, 1008


title: DOHH-2_control

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ

hyb_protocol: Samples were prepared for and measured on Affymetrix HG-U133-plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the scanner GCS3000 and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction, quantile normalisation of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

source_name: lymphoma cell line

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using Trizol reagent.

tag: genotype

value: DLBCL cells

tag: infection

value: control


title: D39_C10

value: Ibuprofen


title: FL lymph node biopsy, untreated, 1012

source_name: FL lymph node biopsy, untreated, 1012


title: D39_C9


title: D39_C8

value: PVP


title: D39_C3

value: Glyphosate


title: D39_C6

value: Sucrose


title: D39_C5

value: Sorbitol


title: D39_C4

value: Saccharin


title: D39_C2

value: Amoxicillin


title: FL lymph node biopsy, untreated, 1016

source_name: FL lymph node biopsy, untreated, 1016


title: D27_C16

value: 27 days exposure


title: D27_C10


title: D27_C9


title: D27_C14

value: Ficoll 400


title: D27_C8

value: non-toxic


title: D27_C6


title: D27_C5


title: D27_C7

value: Fructose


title: FL lymph node biopsy, untreated, 1004

source_name: FL lymph node biopsy, untreated, 1004

value: lymph node


title: D27_C2


title: D27Hi_29

value: Dexamethasone

value: toxic


title: D27Hi_26


title: D27_C3


title: D27Hi_28


title: D27Hi_24


title: D27Hi_23

value: Bis-I


title: D27Hi_21

value: Accutane or Isotretinoin


title: D27Hi_22

value: Lead acetate


title: D39_C7

value: 39 days exposure


title: D27Hi_20

value: Carbamazepine


title: D27Hi_18

value: Thalidomide


title: D27Hi_19

value: Amiodarone


title: D39_C1

value: Acetaminophen


title: D27Hi_17

value: (trans) Retinoic acid


title: D27_C15

value: Naproxen sodium


title: D27Hi_15

value: 27 days exposure


title: D27Hi_10


title: D27Hi_12

value: Dioxin


title: D27Hi_8

value: L-phenylalanine


title: D27_C1

value: non-toxic


title: D27Hi_9

value: Propylthiouracil


title: D27Hi_7

value: Permethrin


title: D27Hi_6

value: Monosodium glutamate

value: toxic


title: D27Hi_3

value: Diazinon


title: D21_C16

value: DMSO

value: 21 day exposure


title: D27Hi_4

value: Hydroxyurea


title: D27Hi_1

value: Benzene


title: D21_C10

value: Ibuprofen


title: D21_C8

value: PVP


title: D27Hi_2

value: Bioallethrin


title: D21_C14

value: Ficoll 400


title: D21_C2

value: Amoxicillin


title: D21_C9


title: D21_C3

value: Glyphosate


title: D21_C7

value: Fructose


title: D15_C15

value: Naproxen sodium

value: non-toxic

value: 15 days exposure


title: D15_C16


title: D21_C1

value: Acetaminophen


title: D39Hi_29

value: Dexamethasone

value: toxic

value: 39 days exposure


title: D15_C14


title: D39Hi_28


title: D39Hi_26


title: D21_C15

value: 21 day exposure


title: D39Hi_23

value: Bis-I


title: D39Hi_21

value: Accutane or Isotretinoin


title: D39Hi_22

value: Lead acetate


title: D15_C2


title: D15_C6

value: Sucrose


title: D39Hi_20

value: Carbamazepine


title: D21_C6


title: D39Hi_18

value: Thalidomide


title: D39Hi_19

value: Amiodarone


title: D39Hi_15


title: D39Hi_12

value: Dioxin


title: D39Hi_10


title: DOHH-2_EBV

value: DLBCL cells

value: EBV


title: D39Hi_7

value: Permethrin


title: D39Hi_9

value: Propylthiouracil


title: D39Hi_6

value: Monosodium glutamate


title: D39Hi_8

value: L-phenylalanine


title: D39Hi_4

value: Hydroxyurea

value: toxic


title: D39Hi_2

value: Bioallethrin

value: 39 days exposure


title: D39Hi_3

value: Diazinon


title: D21Hi_29

value: Dexamethasone

value: 21 day exposure


title: D21Hi_24


title: D15_C8

value: PVP

value: non-toxic

value: 15 days exposure


title: FL lymph node biopsy, untreated, 1080

source_name: FL lymph node biopsy, untreated, 1080

value: lymph node


title: D39Hi_1

value: Benzene


title: D21Hi_23

value: Bis-I


title: D15_C7

value: Fructose


title: D21Hi_22

value: Lead acetate


title: D21Hi_21

value: Accutane or Isotretinoin


title: D21Hi_20

value: Carbamazepine


title: D21Hi_19

value: Amiodarone


title: D21Hi_17

value: (trans) Retinoic acid

value: toxic


title: D21Hi_8

value: L-phenylalanine


title: D21Hi_12

value: Dioxin


title: D21Hi_9

value: Propylthiouracil


title: D21Hi_10

value: 21 day exposure


title: D21Hi_18

value: Thalidomide


title: D21Hi_1


title: D21Hi_2

value: Bioallethrin


title: D21Hi_3

value: Diazinon


title: D21Hi_6

value: Monosodium glutamate


title: D15Hi_26

value: 15 days exposure


title: D21Hi_7

value: Permethrin


title: D15Hi_29

value: Dexamethasone


title: D15Hi_28


title: D21Hi_4

value: Hydroxyurea


title: D15Hi_24


title: D15Hi_23

value: Bis-I


title: D15Hi_22

value: Lead acetate


title: D15Hi_18


title: D15Hi_19

value: Amiodarone


title: D15Hi_21

value: Accutane or Isotretinoin


title: D15Hi_20

value: Carbamazepine

value: toxic


title: D15Hi_12

value: Dioxin


title: D15Hi_17

value: (trans) Retinoic acid


title: D15Hi_10


title: D15Hi_8

value: L-phenylalanine


title: D15Hi_9

value: Propylthiouracil


title: D15Hi_6


title: D15Hi_4


title: D15Hi_3


title: D15Hi_1

value: Benzene


title: D10Hi_29

value: 10 days exposure


title: D39Hi_24

value: 39 days exposure


title: D10Hi_26


title: D10Hi_21


title: D10Hi_24


title: D10Hi_10


title: D10Hi_19


title: D10Hi_20


title: D10Hi_22


title: D10Hi_17


title: D10Hi_7


title: D10Hi_23


title: D10Hi_8


title: D10Hi_4


title: D10Hi_9


title: D10Hi_6

value: Monosodium glutamate


title: D10Hi_2

value: Bioallethrin


title: D10Hi_3

value: Diazinon


title: D10Hi_1


title: D8Hi_29

value: Dexamethasone

value: 8 days exposure


title: D8Hi_28


title: D10Hi_28


title: D15Hi_2

value: 15 days exposure


title: D8Hi_23

value: Bis-I


title: D8Hi_24


title: D10Hi_12


title: D8Hi_22

value: Lead acetate


title: D10Hi_18

value: Thalidomide


title: D8Hi_21

value: Accutane or Isotretinoin

value: toxic


title: D8Hi_20

value: Carbamazepine


title: D8Hi_19

value: Amiodarone


title: D8Hi_17

value: (trans) Retinoic acid


title: D8Hi_12

value: Dioxin


title: D8Hi_9

value: Propylthiouracil


title: D8Hi_4

value: Hydroxyurea


title: D8Hi_6

value: Monosodium glutamate


title: D8Hi_7

value: Permethrin


title: D8Hi_3

value: Diazinon


title: D8Hi_2

value: Bioallethrin


title: D8Hi_26

value: 8 days exposure


title: D10_C14

value: Ficoll 400

value: non-toxic

value: 10 days exposure


title: D10_C12

value: Glucosamine


title: D10_C15

value: Naproxen sodium


title: D10_C16

value: DMSO


title: D8Hi_1

value: Benzene

value: toxic


title: D10_C10

value: Ibuprofen


title: D10_C11

value: Glycerol


title: D10_C8

value: PVP


title: D10_C6

value: Sucrose


title: D10_C7

value: Fructose


title: D10_C9


title: D10_C3

value: Glyphosate


title: D10_C4

value: Saccharin


title: D10_C5

value: Sorbitol


title: D8Hi_18

value: Thalidomide

value: 8 days exposure


title: D10_C2

value: Amoxicillin

value: non-toxic


title: D8Hi_8

value: L-phenylalanine


title: D10_C1

value: Acetaminophen

value: 10 days exposure


title: D8_C15

value: Naproxen sodium


title: D8_C14

value: Ficoll 400


title: D8_C10

value: Ibuprofen


title: D6Hi_9

value: Propylthiouracil

value: toxic

value: 6 days exposure


title: D6Hi_10


title: D8_C12

value: Glucosamine


title: D8_C9


title: D8_C8

value: PVP


title: D8_C6

value: Sucrose


title: D6Hi_8


title: D6Hi_7

value: Permethrin


title: D39Hi_17

value: (trans) Retinoic acid

value: 39 days exposure


title: D6Hi_4

value: Hydroxyurea


title: D8_C2

value: Amoxicillin

value: non-toxic

value: 8 days exposure


title: D8_C7

value: Fructose


title: D6Hi_6

value: Monosodium glutamate


title: D4Hi_21

value: Accutane or Isotretinoin

value: 4 days exposure


title: D4Hi_19

value: Amiodarone


title: D4Hi_18

value: Thalidomide

value: toxic


title: D4Hi_17


title: D4Hi_15


title: D8_C16

value: DMSO


title: D4Hi_13

value: Arsenic


title: D4Hi_14

value: Cadmium


title: D4Hi_12

value: Dioxin


title: D4Hi_11

value: Cytosine Beta-D-arabinofuranoside


title: D4Hi_10


title: D4Hi_8

value: L-phenylalanine


title: D4Hi_7

value: Permethrin


title: D4Hi_6


title: D4Hi_4

value: Hydroxyurea


title: D4Hi_3

value: Diazinon


title: D4Hi_2

value: Bioallethrin


title: D4Hi_1

value: Benzene


title: D4Hi_22

value: Lead acetate


title: D6Hi_29

value: Dexamethasone

value: 6 days exposure


title: D6Hi_27

value: Vincristine


title: D6Hi_28


title: D6Hi_25

value: Okadaic acid


title: D4Hi_20

value: Carbamazepine

value: toxic

value: 4 days exposure


title: D6Hi_23

value: Bis-I


title: D6Hi_26


title: D4Hi_16

value: Busulfan


title: D6Hi_21

value: Accutane or Isotretinoin


title: D6Hi_24


title: D6Hi_20


title: D6Hi_22


title: D6Hi_19

value: Amiodarone


title: D6Hi_16


title: D4Hi_9

value: Propylthiouracil


title: D6Hi_18

value: Thalidomide


title: D6Hi_14

value: Cadmium


title: D6Hi_15


title: D6Hi_17

value: (trans) Retinoic acid


title: D6Hi_12

value: Dioxin


title: D4Hi_29


title: D4Hi_28


title: D6Hi_11

value: Cytosine Beta-D-arabinofuranoside


title: D4Hi_25


title: D4Hi_26


title: D6Hi_3

value: Diazinon


title: D6Hi_2

value: Bioallethrin

value: 6 days exposure


title: D6Hi_1

value: Benzene


title: D4Hi_27

value: Vincristine


title: D6_C14

value: Ficoll 400

value: non-toxic


title: D6_C13

value: Aspirin


title: D6_C11

value: Glycerol


title: D6_C12

value: Glucosamine


title: D4Hi_23

value: Bis-I

value: toxic

value: 4 days exposure


title: D6_C10

value: Ibuprofen


title: D6_C9


title: D6_C7

value: Fructose


title: D6_C8

value: PVP


title: D6_C6

value: Sucrose


title: D6Hi_13

value: Arsenic


title: D6_C5

value: Sorbitol


title: D6_C4

value: Saccharin

value: 6 days exposure


title: D6_C3

value: Glyphosate


title: D6_C2

value: Amoxicillin


title: ßTC3_PB31-ALK7sh1/2_dox + 24hrs activin B #2

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.4.2, trimming for TrueSeq and polyA sequences. Reads were aligned to mouse genome build mm10 using HISAT2 aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR TMM method.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID

molecule: polyA RNA

organism: Mus musculus

source_name: ßTC3 cells

growth_protocol: Cells were plated in 6-well plates in triplicate.

extract_protocol:
Cells were isolated and RNA was harvested using Trizol reagent. TruSeq stranded mRNA kit (Illumina) was used to prepare sequencing libraries, starting from 500ng total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in media containing DOX (1µg/ml) for 24 hours. When indicated they were treated with Activin B (50ng/ml) for 24hrs.

tag: plasmid

tag: group

value: ALK7 knock-down

tag: treatment 1

value: 24hrs DOX

tag: treatment 2

value: 24hrs Activin B

tag: replicate

tag: batch


title: ßTC3_PB31-ALK7sh1/2_dox + 24hrs activin B #3


title: D6_C1

value: Acetaminophen

value: non-toxic


title: ßTC3_PB31-ALK7sh1/2_dox + 24hrs activin B #1


title: ßTC3_PB31-ALK7sh1/2_dox alone #3

value: NO


title: D4Hi_24

value: toxic

value: 4 days exposure


title: D6_C16

value: DMSO


title: D4_C15

value: Naproxen sodium


title: ßTC3_PB31-ALK7sh1/2_dox alone #2


title: D4_C14

value: Ficoll 400


title: ßTC3_PB31-ALK7sh2_dox + 24hrs activin B #3

value: PB-31 ALK7-sh2


title: ßTC3_PB31-ALK7sh2_dox + 24hrs activin B #2


title: D4_C12

value: Glucosamine


title: ßTC3_PB31-ALK7sh2_dox alone #3


title: D4_C11

value: Glycerol


title: D4_C9


title: D4_C10

value: Ibuprofen


title: ßTC3_PB31-ALK7sh2_dox alone #1


title: ßTC3_PB31-ALK7sh2_dox alone #2


title: D4_C7

value: Fructose


title: ßTC3_PB33-ALK7-DN_dox + 24hrs activin B #3

value: PB-33 ALK7-DN

value: ALK7-DN expression


title: D4_C8

value: PVP


title: ßTC3_PB33-ALK7-DN_dox + 24hrs activin B #1

value: 24hrs DOX

value: 24hrs Activin B


title: ßTC3_PB33-ALK7-DN_dox + 24hrs activin B #2


title: D4_C5

value: Sorbitol

value: non-toxic


title: D4_C6

value: Sucrose


title: D4_C16

value: 4 days exposure


title: D4_C4

value: Saccharin


title: ßTC3_PB31-ALK7sh1/2_dox alone #1

value: ALK7 knock-down

value: NO


title: ßTC3_PB33-ALK7-DN_dox alone #2


title: ßTC3_PB33-ALK7-DN_dox alone #1


title: D4_C2

value: Amoxicillin


title: ßTC3_PB33-ALK7_dox + 24hrs activin B #3

value: PB-33 ALK7

value: ALK7 expression


title: D4_C13

value: Aspirin


title: D4_C1

value: Acetaminophen


title: D3_C15

value: Naproxen sodium

value: 3 days exposure


title: D3_C14

value: Ficoll 400


title: ßTC3_PB33-ALK7_dox alone #2

value: 24hrs DOX


title: ßTC3_PB33-ALK7_dox + 24hrs activin B #1

value: 24hrs Activin B


title: ßTC3_PB33-ALK7_dox alone #3


title: ßTC3_PB33-ALK7-DN_dox alone #3

value: PB-33 ALK7-DN

value: ALK7-DN expression


title: ßTC3_PB33_dox + 24hrs activin B #3

value: Control cells


title: ßTC3_PB33_dox + 24hrs activin B #2


title: ßTC3_PB33_dox alone #3


title: ßTC3_PB33_dox + 24hrs activin B #1


title: D4_C3

value: Glyphosate

value: non-toxic

value: 4 days exposure


title: D3_C11

value: Glycerol


title: D3_C9


title: D3_C8

value: PVP


title: ßTC3_PB33-ALK7_dox + 24hrs activin B #2

value: PB-33 ALK7


title: D3_C6

value: Sucrose


title: D3_C7

value: Fructose


title: D3_C5

value: Sorbitol


title: AJ_PB33 ALK7+AcB dox 24hrs 2 [1263]

source_name: AJ5257-1 cells

treatment_protocol: Cells were cultured in media containing DOX (2µg/ml) for 0, 2 and 24 hours. When indicated they were treated with Activin B (50ng/ml) for 24hrs.

value: AJ5257-1 cells

tag: genotype/variation

value: ALK7  + Activin B


title: AJ_PB33 ALK7+AcB dox 24hrs 3 [1264]


title: ßTC3_PB31-ALK7sh2_dox + 24hrs activin B #1

value: PB-31 ALK7-sh2

value: ALK7 knock-down


title: D3_C16

value: DMSO

value: 3 days exposure


title: D3_C4

value: Saccharin


title: D15Hi_7

value: Permethrin

value: toxic

value: 15 days exposure


title: D3_C10

value: Ibuprofen

value: non-toxic


title: D2_C16

value: 2 days exposure


title: D3_C2

value: Amoxicillin


title: AJ_PB33 ALK7 dox 24hrs 3 [1240]

value: PB-33 ALK7

value: 24hrs DOX

value: NO


title: D2_C15

value: Naproxen sodium


title: ßTC3_PB33_dox alone #2

value: Control cells


title: AJ_PB33 AcB  dox 0hrs 3 [1258]

value: AJ5257-1 cells

value: Activin B

value: 0hrs DOX

value: 24hrs Activin B


title: AJ_PB33 ALK7+AcB dox 24hrs 1 [1262]

value: ALK7  + Activin B


title: AJ_PB33 AcB  dox 0hrs 2 [1257]


title: AJ_PB33 AcB  dox 0hrs 1 [1256]


title: ßTC3_PB33_dox alone #1


title: D2_C14

value: Ficoll 400


title: AJ_PB33 dox 0hrs 3 [1234]


title: D2_C12

value: Glucosamine


title: AJ_PB33 dox 0hrs 2 [1233]


title: D3_C3

value: Glyphosate

value: 3 days exposure


title: AJ_PB33 dox 0hrs 1 [1232]


title: AJ_PB33 dox 0hrs 3 [1015]


title: AJ_PB33 dox 0hrs 2 [1014]


title: D2_C9

value: non-toxic


title: D2_C10

value: Ibuprofen

value: 2 days exposure


title: AJ_PB33 dox 0hrs 1 [1013]


title: D2_C5

value: Sorbitol


title: D2_C3


title: ßTC3_PB33 dox 0hrs 2 [1293]


title: D2_C1

value: Acetaminophen


title: ßTC3_PB33 AcB  dox 0hrs 3 [1306]


title: ßTC3_PB33 AcB  dox 0hrs 2 [1305]


title: D3_C13

value: Aspirin


title: ßTC3_PB33 AcB  dox 0hrs 1 [1304]


title: D2_C4

value: Saccharin


title: ßTC3_PB33 dox 0hrs 3 [1294]

value: Control cells

value: NO


title: ßTC3_PB33 dox 0hrs 3 [1006]


title: D1_C15

value: Naproxen sodium

value: 1 day exposure


title: D2_C2

value: Amoxicillin


title: AJ_PB33 ALK7-CA dox 24hrs Rep2 [1038]

value: AJ5257-1 cells

value: PB-33 ALK7-CA

value: ALK7-CA expression

value: 24hrs DOX


title: D1_C16

value: DMSO


title: AJ_PB33 ALK7-CA dox 24hrs Rep3 [1039]


title: AJ_PB33 ALK7-CA dox 24hrs Rep1 [1037]


title: AJ_PB33 ALK7-CA dox 2hrs Rep3 [1036]

value: 2hrs DOX


title: D1_C10

value: Ibuprofen

value: non-toxic


title: AJ_PB33 ALK7-CA dox 2hrs Rep2 [1035]


title: D2_C7

value: Fructose

value: 2 days exposure


title: D1_C14

value: Ficoll 400


title: ßTC3_PB33 dox 0hrs 2 [1005]

value: 0hrs DOX


title: D1_C9


title: ßTC3_PB33 dox 0hrs 1 [1292]

value: Control cells


title: D1_C12

value: Glucosamine


title: D1_C11

value: Glycerol


title: ßTC3_PB33 dox 0hrs 1 [1004]

value: NO


title: AJ_PB33 dox 24hrs Rep3 [1030]


title: D1_C7

value: 1 day exposure


title: AJ_PB33 ALK7-CA dox 2hrs Rep1 [1034]

value: AJ5257-1 cells


title: D3_C12

value: 3 days exposure


title: D1_C2

value: Amoxicillin


title: D1_C6

value: Sucrose


title: D1_C5

value: Sorbitol


title: AJ_PB33 dox 24hrs Rep1 [1028]

value: 24hrs DOX


title: ßTC3_PB33 ALK7-CA dox 24hrs Rep2 [1020]

value: PB-33 ALK7-CA

value: ALK7-CA expression


title: AJ_PB33 dox 2hrs Rep1 [1016]

value: 2hrs DOX


title: ßTC3_PB33 ALK7-CA dox 24hrs Rep1 [1019]


title: D1_C4

value: Saccharin

value: non-toxic


title: D1_C1

value: Acetaminophen


title: ßTC3_PB33 ALK7-CA dox 24hrs Rep3 [1021]


title: AJ_PB33 ALK7 dox 24hrs 2 [1239]

value: PB-33 ALK7


title: D3Hi_28

value: toxic


title: D3Hi_29

value: Dexamethasone


title: AJ_PB33 dox 2hrs Rep2 [1017]

value: NO

value: Control cells


title: D1_C3

value: Glyphosate

value: 1 day exposure


title: D3Hi_26

value: 3 days exposure


title: D2_C8

value: PVP

value: 2 days exposure


title: ßTC3_PB33 ALK7-CA dox 2hrs Rep2 [1026]


title: D2_C11

value: Glycerol


title: ßTC3_PB33 ALK7-CA dox 2hrs Rep1 [1025]

value: PB-33 ALK7-CA


title: D2_C6

value: Sucrose


title: D3Hi_27

value: Vincristine


title: AJ_PB33 ALK7 dox 24hrs 1 [1238]

value: AJ5257-1 cells

value: 24hrs DOX


title: ßTC3_PB33 ALK7-CA dox 2hrs Rep3 [1027]

value: ALK7-CA expression

value: 2hrs DOX


title: D3Hi_25

value: Okadaic acid

value: toxic


title: ßTC3_PB33 dox 24hrs Rep3 [1012]

value: NO


title: D3Hi_23

value: Bis-I


title: D3Hi_22

value: Lead acetate


title: D3Hi_24


title: D3Hi_21

value: Accutane or Isotretinoin


title: ßTC3_PB33 dox 24hrs Rep2 [1011]

value: Control cells


title: ßTC3_PB33 dox 2hrs Rep3 [1009]


title: ßTC3_PB33 dox 24hrs Rep1 [1010]


title: D3Hi_20

value: Carbamazepine

value: 3 days exposure


title: ßTC3_PB33 dox 2hrs Rep2 [1008]


title: ßTC3_PB33 dox 2hrs Rep1 [1007]


title: ßTC3_PB33-ALK7_dox alone #1

value: PB-33 ALK7

value: ALK7 expression


title: D3Hi_19

value: Amiodarone


title: D3Hi_18

value: Thalidomide


title: D3Hi_16

value: Busulfan


title: D3Hi_13

value: Arsenic


title: D3Hi_11

value: Cytosine Beta-D-arabinofuranoside


title: D3Hi_12

value: Dioxin


title: D2_C13

value: Aspirin

value: non-toxic

value: 2 days exposure


title: D3Hi_8

value: L-phenylalanine

value: toxic


title: D3Hi_17

value: (trans) Retinoic acid


title: D3Hi_10


title: D1_C13

value: 1 day exposure


title: D3Hi_15


title: D1_C8

value: PVP


title: D3Hi_7

value: Permethrin

value: 3 days exposure


title: D3Hi_4

value: Hydroxyurea


title: D3Hi_3

value: Diazinon


title: D2Hi_28


title: D3Hi_2

value: Bioallethrin


title: D3Hi_1

value: Benzene


title: D2Hi_27

value: Vincristine


title: D2Hi_26


title: AJ_PB33 dox 24hrs Rep2 [1029]

value: NO

value: AJ5257-1 cells

value: Control cells

value: 24hrs DOX


title: D2Hi_23

value: Bis-I

value: 2 days exposure


title: D2Hi_24

value: toxic


title: D3_C1

value: Acetaminophen

value: non-toxic


title: AJ_PB33 dox 2hrs Rep3 [1018]

value: 2hrs DOX


title: D3Hi_9

value: Propylthiouracil


title: D2Hi_22

value: Lead acetate


title: D3Hi_14

value: Cadmium

value: 3 days exposure


title: D2Hi_21

value: Accutane or Isotretinoin


title: D2Hi_17

value: (trans) Retinoic acid


title: D2Hi_20

value: Carbamazepine


title: D2Hi_16

value: Busulfan


title: D2Hi_18

value: Thalidomide


title: D3Hi_6

value: Monosodium glutamate


title: D2Hi_12

value: Dioxin


title: D2Hi_14


title: D2Hi_15


title: D2Hi_19

value: Amiodarone


title: D2Hi_29

value: Dexamethasone

value: 2 days exposure


title: D2Hi_13

value: Arsenic

value: toxic


title: D2Hi_10


title: D2Hi_11

value: Cytosine Beta-D-arabinofuranoside


title: D2Hi_9

value: Propylthiouracil


title: D2Hi_6


title: D2Hi_7

value: Permethrin


title: D2Hi_25

value: Okadaic acid


title: D2Hi_8

value: L-phenylalanine


title: D2Hi_4

value: Hydroxyurea


title: shFTO Mel624 rep2 IP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: Melanoma cells

data_processing:
Library strategy: m6A-seq
The adapters were removed by using cutadapt
for m6A-seq, reads were aligned to the reference genome using Tophat v2.0.14 with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene had multiple isoforms. Aligned reads were extended to 150 bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from introns in peak calling. The peak calling method was modified from published work (Dominissini et al., 2012). To call m6A peaks, the longest isoform of each gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with read counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. A Fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the FDR < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP samples in the current peak/window (a), median read counts of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c), and median read counts of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c).
Genome_build: hg38
Supplementary_files_format_and_content: Excel, m6A peaks

source_name: Skin

growth_protocol: 10% FBS DMEM

extract_protocol:
RNA extraction with trizol and mRNA purification with Dynabeads mRNA Purification Kit. m6A IP with standard protocol
RNA libraries were prepared for sequencing Illumina stranded mRNA library preparetion kit

treatment_protocol: No treatment

value: Melanoma

value: FTO knockdown


title: shFTO Mel624 rep2 Input

description: Melanoma cells


title: D2Hi_1

value: Benzene


title: shFTO Mel624 rep1 Input

description: Melanoma cells


title: scRNA-Seq PBMCs from a patient with non-small cell lung cancer (NSCLC)

data_processing: Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 1.2 (10x Genomics).

source_name: NSCLC PBMCs

extract_protocol: Single cell libraries were prepared from cryopreserved NSCLC PBMC single cell suspensions using Chromium with v2 chemistry (10x Genomics), and were sequenced on a NextSeq 500 (Illumina).

tag: cell type

value: peripheral blood mononuclear cells

tag: disease state

value: non-small cell lung cancer


title: D2Hi_2

value: Bioallethrin


title: shNC Mel624 rep2 IP

description: Melanoma cells

tag: tissue

value: Control


title: D2Hi_3

tag: compound

value: Diazinon


title: shFTO Mel624 rep1 IP

description: Melanoma cells


title: D1Hi_29

value: Dexamethasone

tag: classification

value: 1 day exposure


title: shNC Mel624 rep1 IP

description: Melanoma cells


title: D1Hi_27

value: Vincristine

value: toxic

tag: concentration


title: D1Hi_26

tag: time


title: D1Hi_24

tag: cell line


title: D1Hi_28


title: D1Hi_25


title: D1Hi_23

value: Bis-I


title: shNC Mel624 rep2 Input

description: Melanoma cells


title: D1Hi_22

value: Lead acetate


title: D1Hi_21

value: Accutane or Isotretinoin


title: D1Hi_19

value: Amiodarone


title: D1Hi_18

value: Thalidomide


title: D1Hi_17

value: (trans) Retinoic acid


title: D1Hi_16

value: Busulfan


title: shNC Mel624 rep1 Input

description: Melanoma cells

value: Melanoma


title: D1Hi_14

value: Cadmium


title: D1Hi_12

value: Dioxin


title: D1Hi_13

value: Arsenic


title: D1Hi_10


title: D1Hi_9

value: Propylthiouracil


title: D1Hi_11

value: Cytosine Beta-D-arabinofuranoside


title: eWAT94_NO NR

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description:
94_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturer's procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 8*60K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequentially following Agilent's recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed and were used for normalization. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: eWAT

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, split in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent linear amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). The two dietary groups are part of a larger animal study, but we focus here only on NO-NR and Ctrl-NR. All Cy3-labeled samples were used for the reference pool. This reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

extract_protocol: Total RNA was isolated from epididymal white adipose tissue using Trizol isolation combined with RNeasy Mini kit (Qiagen), quantified using Nanodrop (IsoGen Life Science) and qualified using TapeStation (Agilent).

treatment_protocol: The C57BL/6JRcc male mice (8 or 9 weeks old) were individually housed (12h light–dark cycle, 23±1°C, 55±15% humidity), with ad libitum access to feed and water. A semi-synthetic diet (40% energy from fat, 19% energy from protein, 41% energy from carbohydrates) was designed to contain a low, but sufficient amount of tryptophan (calculated 0.115% L-tryptophan) and either 0 or 30 mg nicotinamide riboside (NR) per kg diet as vitamin B3 (referred to as No NR and Ctrl NR, respectively). Mice were accustomed to this diet (Ctrl NR) for two weeks. Subsequently, mice were stratified into 2 experimental groups on mean body weight (n=12/group) and received the Ctrl NR or No NR diet for 18 weeks. Mice were provided with a limited amount of diet (with 0.8 gram of fresh experimental diet) at start of dark phase to have them fasted at end of dark phase; they were subsequently refed at start of light phase with 1.8 gram of diet for four hours and then sacrificed by decapitation. Tissues were immediately isolated, frozen in liquid nitrogen and stored at -80C until analysis.

tag: strain/background

tag: gender

value: Male

tag: age

value: 28 or 29 weeks

value: epididymal white adipose tissue

tag: diet

value: No NR

source_name: eWAT reference pool

value: Pooled male and female

value: mix

tag: sample type

value: Reference pool


title: eWAT74_NO NR

description:
74_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT90_NO NR

description:
90_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT98_NO NR

description:
98_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: D1Hi_8

value: L-phenylalanine

value: toxic

value: 1 day exposure


title: eWAT61_NO NR

description:
61_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: D1Hi_15


title: D1Hi_20

value: Carbamazepine


title: eWAT110_NO NR

description:
110_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT101_NO NR

description:
101_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT70_NO NR

description:
70_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: D1Hi_7

value: Permethrin


title: eWAT78_NO NR

description:
78_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT114_NO NR

description:
114_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT81_NO NR

description:
81_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT77_Ctrl NR

description:
77_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

value: Ctrl NR


title: D1Hi_6

value: Monosodium glutamate


title: eWAT95_Ctrl NR

description:
95_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT118_NO NR

description:
118_NO NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT97_Ctrl NR

description:
97_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT68_Ctrl NR

description:
68_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: D1Hi_5

value: Maneb


title: eWAT75_Ctrl NR

description:
75_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: eWAT88_Ctrl NR

description:
88_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.


title: D1Hi_4

value: Hydroxyurea


title: D1Hi_2

value: Bioallethrin


title: D1Hi_3

value: Diazinon


title: eWAT64_Ctrl NR

description:
64_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

value: Male

value: 28 or 29 weeks


title: amiR519_lettuce

city: Nanjing

last: Zhang

state: Jiangsu

address: 163 Xianlin Road

department: Life of Science

country: China

institute: Nanjing University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean reads are obtained after that raw reads were removed the adaptor sequence, evaluated sequence quality and filtered out contaminated sequences
Genome_build: Legassy_V2
txt files are generated for clean reads.
Supplementary_files_format_and_content: sequences and their abundance measurements

organism: Lactuca sativa

source_name: Leaves

growth_protocol: Lettuce was grown in a growth room at 25℃ under long-day conditions (16 h light/8 h dark).

extract_protocol:
Total RNA from fresh lettuce leaves was extracted using TRIzol Reagent (Invitrogen, USA)
Small RNA molecules (18-30 bp) were excised from total RNA after a denaturing polyacrylamide gel used for sequencing analysis using an Illumina Genome Analyzer (Illumina, San Diego, CA, USA).

tag: strain

value: Dasusheng

value: leaves

value: 40 days after seeding planted into soil

tag: genotype

value: amiR519 transgenic


title: D1Hi_1

value: Benzene


title: eWAT104_Ctrl NR

description:
104_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

value: epididymal white adipose tissue

value: Pooled male and female

value: mix

value: Reference pool


title: amiR471_lettuce

value: amiR471 transgenic


title: Sample 2_Macrophages exposed to UHMWPE particles

data_processing:
llumina HiSeq 2500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped by alignment to human genome (hg19) using TopHat and Bowtie, normalized using the Trimmed Mean of M values (TMM) process, and then annotated using Cufflinks and Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html). Low calculated fragments per kilobase of transcript per million mapped reads (FPKM) were removed
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Macrophages exposed to UHMWPE particles

extract_protocol:
Differentiated macrophages cultured with or without UHMWPE particles were lysed with TRIzol Reagent and harvested for RNA purification. RNA was purified using RNeasy Mini kit columns according to the manufacturer’s instructions, and integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer.
High-quality DNA-free RNA with integrity score > 9.0 was further used for RNA-seq. Each library was generated from 0.5-1 μg pooled RNA of 3 donors (equal quantity) using the TruSeq® Stranded mRNA Sample Preparation Kit. Quality of libraries was examined by Bioanalyzer High sensitivity DNA kit, and then paired-end reads (101 bp) were obtained by Illumina HiSeq 2500, with an average of 69 million reads per sample. Reads were mapped by alignment to human genome (hg19) using TopHat and Bowtie, normalized using the Trimmed Mean of M values (TMM) process, and then annotated using Cufflinks and Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html).

treatment_protocol: Macrophages were co-cultured with free-endotoxin UHMWPE particles at ratio of 1:4000 µm3 for 24 h using inverted cell culture technique that allows particles to directly interact with macrophages. Control macrophages were cultured alone. Ratio of particles to cells was initially optimized to get high biological response of macrophages. Suspended particles in RPMI-1640 supplemented with 10% FCS and 25 mg/l penicillin/streptomycin were added to macrophages culture to completely fill the wells, and a round-shape 12-mm-coverslips were gently placed onto each well without forming bubbles. Plates were then covered by two breathable sealing membranes, inverted and incubated in a humidified atmosphere containing 5% CO2 for 24 h.

tag: subject

value: Healthy Asian donors

value: 30-40 years old

value: Blood

value: Primary macrophage

tag: cultured with

value: free-endotoxin UHMWPE particles


title: Sample 2_Control macrophages

source_name: Control macrophages

tag: cell type

value: none (control)


title: Sample 1_Macrophages exposed to UHMWPE particles


title: Sample 3_Macrophages exposed to UHMWPE particles


title: C2G3R8

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description: Genotype_3_Treatment_2_Cond_6_Repl_8_ID_245

data_processing:
reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013)
the reads per position were determined using HTSeq (Anders et al. 2015)
statistics were performed using the DeSeq2 R package (Love et al. 2014)
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Gene wise read countings in tabular separated plain text format

source_name: Tph2 -/-_maternal separation_amygdala

extract_protocol:
brains were extracted, snapfrozen in isopentane, subsequently the amygdala was dissected, amygdalae of both hemispheres were poderised at - 80 ͦC, blended and split in two equal portions. RNA was extracted from one portion, using a combination of the classical phenol-chloroform (QIAZOL) method and the column-based protocol of the commercial miRNeasy Mini kit (Qiagen, Hilden, Germany) for fatty tissue.
library preparation was performed by IGA Technologies (Undine, Italy) using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, US)
RNA seq 125 bp, paired-end; 60 million reads/sample

treatment_protocol: pups were separated from their respective dams for 3h per day from postnatal day 2 until postnatal day 15, adult males were investigated

tag: Sex

value: male

value: 4 months

tag: condition

value: maternal separation

value: amygdala


title: Sample 3_Control macrophages

tag: tissue


title: C2G3R6

description: Genotype_3_Treatment_2_Cond_6_Repl_6_ID_197


title: WT_lettuce

value: Dasusheng

value: leaves

value: 40 days after seeding planted into soil

value: wide type


title: eWAT117_Ctrl NR

description:
117_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

value: Male

value: 28 or 29 weeks

value: epididymal white adipose tissue

value: Ctrl NR

value: Pooled male and female

value: mix


title: C2G3R5

description: Genotype_3_Treatment_2_Cond_6_Repl_5_ID_188


title: C2G3R3

description: Genotype_3_Treatment_2_Cond_6_Repl_3_ID_133


title: C2G3R4

description: Genotype_3_Treatment_2_Cond_6_Repl_4_ID_151


title: Sample 1_Control macrophages

value: Healthy Asian donors

value: 30-40 years old

value: Blood

value: Primary macrophage


title: GSCs-U87MG vehicle hypoxia rep1 (condition C)

city: Valdivia

first: Carlos

last: Spichiger

state: Región de los Rios

address: Instituto de Bioquímica y Microbiología, campus Isla Teja, UACh

department: Instituto de Bioquímica y Microbiología

country: Chile

institute: Universidad Austral de Chile

description:
Cell line derived from: brain, male.
Processed data file: RESULTS.c_d.total.txt

data_processing:
The bcl files were obtained directly from BaseCaller Illumina software, which were used to generate fastq files with CASAVA (v 1.8.2).
Trimmomatic v. 0.36 was used to remove low quality reads, using default settings for paired-end reads.
The fastQC software (version 0.10.0, Babraham Bioinformatics) was used to check reads quality.
The sequences were mapped to HS_GRCh38 human genome (ensembl.org) using TopHat2.
Test for differential expression based on raw counts were performed using DESeq2 R library.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.single_*, counts.pair_*: Excel files include raw counts.
Supplementary_files_format_and_content: RESULTS.c_d.total.txt: Tab-delimited text file includes differential expression.

source_name: U87MG human glioblastoma cell line

growth_protocol: Neurobasal medium (cat. 21103049; GibcoTM) was supplemented with EGF (20ng/mL; PeproTech ©), bFGF (20ng/mL; PeproTech ©), 1x B27 (w/o vitamin A; Gibco®), 100 units/mL of penicillin/streptomycin, and 2 mM L-glutamine.

extract_protocol:
Total RNA was isolated using a commercial kit, Nucleospin RNA ii mn (Macherey-Nagel) following
Library preparation for RNA-seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. RS-122-2102) using at least 0.5 ug of total RNA and following the manufacturer’s instructions. Library quantitation was performed by qPCR using the Library Quant Kit Illumina GA (KAPA, Cat KK4824). The size range of the libraries was determined using the High Sensitivity NGS Kit on the Fragment Analyzer (Advanced Analytical Technologies, Cat DNF-474).

treatment_protocol: Vehicle (0.001% DMSO) and MRS1220 (10 µM) for 24 hrs under hypoxia.

tag: originating cell line

value: U-87 MG (ATCC HTB-14)

value: Glioblastoma stem-like cells (GSCs)

tag: treatment

value: vehicle

value: hypoxia


title: GSCs-U87MG MRS1220 hypoxia rep1 (condition D)


title: GSCs-U87MG MRS1220 hypoxia rep2 (condition D)


title: eWAT108_Ctrl NR

description:
108_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

value: Reference pool


title: C2G3R2

description: Genotype_3_Treatment_2_Cond_6_Repl_2_ID_106

value: male

value: 4 months

value: maternal separation

value: amygdala


title: GSCs-U87MG vehicle hypoxia rep2 (condition C)


title: C2G3R1

description: Genotype_3_Treatment_2_Cond_6_Repl_1_ID_103


title: BWTG3 TNF 2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm10 version of the reference genome using a reference structural annotation as a guide with tophat2 -i 50 -I 500000 -p 4 --b2-sensitive -G Ensembl71.gtf
Counts were obtained with the subread package (featurecounts) and only uniquely mapping reads were retained. Differentially expressed genes were detected with DESeq2 starting from raw counts.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count files containing two columns: Gene_id count_value

source_name: BWTG3 cell line

growth_protocol: cells were maintained and grown in Dulbecco’s modified Eagles medium (DMEM; house-made) containing 10% fetal calf serum (FCS), 1mM sodium pyruvate, 0.1mM non-essential amino acids and 2mM L-glutamine. Before performing experiments, cells were starved for 24h in optimem medium (Gibco, Invitrogen)

extract_protocol:
total RNA extraction was performed with TRIzol and the chloroform-isopropanol separation method followed by a DNAse treatment accoring to the manufacturers instructions (Thermo Scientific). Final purification was done using the InviTrap ® Spin Universal RNA Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols (truseq)

treatment_protocol: Cells were then exposed to 1µM Dex (Sigma, D-2915) and/or 1000U/ml recombinant TNF (produced in E. coli and purified in our department) in optimem given 1h before Dex stimulation. Cells were stimulated for three hours in total

value: mouse hepatoma derived cells

value: TNF


title: RAW264.7 cells_vehicle_repeat1

city: Chongqing

first: Yawei

last: Wang

address: 30 gaotanyan center street

institute: Third Millitary Medical University

description: Gene expression after 24h in vehicle-treated RAW264.7 cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner ( Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.0.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: RAW264.7 cells, vehicle, repeat1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RAW264.7 cells were treated with vehicle control or IR-61 for 24 h and then RNA was extracted, reverse transcription and analyzed.

treatment_protocol: RAW264.7 cells was treated with vehicle control or IR-61 for 24h in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: Abelson murine leukemia virus-induced tumor; ascites

tag: agent

value: BALB/c

value: adult


title: C1G3R8

description: Genotype_3_Treatment_1_Cond_5_Repl_8_ID_274

source_name: Tph2 -/-_no stress_amygdala

value: no stress


title: RAW264.7 cells_IR-61_repeat1

description: Gene expression after 24h in IR-61-treated RAW264.7 cells

source_name: RAW264.7 cells, IR-61, repeat1

tag: cell line


title: C1G3R7

description: Genotype_3_Treatment_1_Cond_5_Repl_7_ID_273


title: BWTG3 TNFDEX 2

value: TNFDEX


title: BWTG3 TNFDEX 3


title: BWTG3 TNF 1


title: C1G3R5

description: Genotype_3_Treatment_1_Cond_5_Repl_5_ID_49


title: BWTG3 TNFDEX 1


title: BWTG3 DEX 3

value: DEX


title: BWTG3 DEX 1


title: C1G3R2

description: Genotype_3_Treatment_1_Cond_5_Repl_2_ID_19


title: C1G3R3

description: Genotype_3_Treatment_1_Cond_5_Repl_3_ID_39


title: C1G3R4

description: Genotype_3_Treatment_1_Cond_5_Repl_4_ID_43


title: BWTG3 DEX 2


title: eWAT115_Ctrl NR

description:
115_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

tag: strain/background

value: Male

value: 28 or 29 weeks

value: epididymal white adipose tissue

value: Ctrl NR

value: Pooled male and female

value: mix


title: BWTG3 NI 3

value: Control


title: BWTG3 TNF 3


title: C2G2R8

description: Genotype_2_Treatment_2_Cond_4_Repl_8_ID_239

source_name: Tph2 +/-_maternal separation_amygdala

value: male

value: 4 months

value: maternal separation


title: BWTG3 NI 2

value: mouse hepatoma derived cells


title: C2G2R6

description: Genotype_2_Treatment_2_Cond_4_Repl_6_ID_192

value: amygdala


title: BWTG3 NI 1


title: C2G2R7

description: Genotype_2_Treatment_2_Cond_4_Repl_7_ID_219


title: C2G2R5

description: Genotype_2_Treatment_2_Cond_4_Repl_5_ID_182


title: C2G2R4

description: Genotype_2_Treatment_2_Cond_4_Repl_4_ID_167


title: Input_synblast_250 (rRNA-depleted)

city: Cambridge

first: Jamie

last: Kwasnieski

state: Massachusetts

address: 455 Main Street

department: Biology

institute: Whitehead Institute/MIT

data_processing:
Illumina 1.5 base calls
Recover spike-in reads from HEK293 RNA: Align to Human genome with STAR, keep unmapped reads
Align reads to dm6 with STAR
Use HT-seq count to tally reads overlapping exons
Calculate RPKM values and normalize to HEK read number
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each normalized sample

organism: Drosophila melanogaster

source_name: Oregon R embryo

growth_protocol: Embryos were injected with 5-ethynyl uridine, allowed to develop, then morphologically staged. Total RNA was isolated, RNA containing the labeled nucleoside was biotinylated and pulled on with streptavidin beads. Eluate, flow-through and input samples were sequenced.

extract_protocol:
After injection with 5-ethynyl uridine, halocarbon oil was drained from embryos, embryos were liberated from glue tape with heptane, homogenized in Trizol and frozen at -80C. RNA was extracted with Trizol followed by an additional extraction with acid phenol and chloroform rinse.
RNA libraries were prepared for sequencing using the SMARTer Stranded RNA-Seq kit

tag: developmental stage

value: Syncytial blastoderm

tag: pull-down sample

value: Input

tag: concentration of injected 5-eu


title: C2G2R3

description: Genotype_2_Treatment_2_Cond_4_Repl_3_ID_156

tag: age


title: C2G2R1

description: Genotype_2_Treatment_2_Cond_4_Repl_1_ID_125

tag: strain


title: Input_nc7-9_250 (rRNA-depleted)


title: C1G3R1

description: Genotype_3_Treatment_1_Cond_5_Repl_1_ID_16

tag: genotype

value: no stress


title: Ft_synblast_250 (rRNA-depleted)

value: Flow-through


title: Ft_nc9-10_250 (rRNA-depleted)


title: Ft_nc7-9_250 (rRNA-depleted)


title: Eluate_cellblast_250 (rRNA-depleted)

value: Cellular blastoderm

value: Eluate


title: C1G2R6

description: Genotype_2_Treatment_1_Cond_3_Repl_6_ID_76

source_name: Tph2 +/-_no stress_amygdala


title: Eluate_nc9-10_250 (rRNA-depleted)


title: Eluate_synblast_250 (rRNA-depleted)


title: C1G2R5

description: Genotype_2_Treatment_1_Cond_3_Repl_5_ID_61


title: C1G2R7

description: Genotype_2_Treatment_1_Cond_3_Repl_7_ID_287


title: C1G2R4

description: Genotype_2_Treatment_1_Cond_3_Repl_4_ID_40


title: Input_cellblast_250 (rRNA-depleted)


title: C1G2R3

description: Genotype_2_Treatment_1_Cond_3_Repl_3_ID_37


title: Input_nc9-10_250 (rRNA-depleted)


title: C1G2R2

description: Genotype_2_Treatment_1_Cond_3_Repl_2_ID_29


title: Eluate_nc7-9_250 (rRNA-depleted)


title: Input_cellblast_50 (polyA)

value: 50 mM 5-EU


title: C1G2R1

description: Genotype_2_Treatment_1_Cond_3_Repl_1_ID_18


title: C1G3R6

description: Genotype_3_Treatment_1_Cond_5_Repl_6_ID_272


title: Input_synblast_50 (polyA)


title: C2G1R8

description: Genotype_1_Treatment_2_Cond_2_Repl_8_ID_263

source_name: Tph2 +/+_maternal separation_amygdala


title: C1G2R8

description: Genotype_2_Treatment_1_Cond_3_Repl_8_ID_294


title: Ft_cellblast_250 (rRNA-depleted)


title: Input_cellblast_250 (polyA)


title: eWAT84_Ctrl NR

description:
84_Ctrl NR
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool. The reference pool also included additional Cy-3 labelled samples from other dietary groups including 4 female samples to enlarge total Cy3-labelled pool of transcripts.

tag: gender

value: Male

value: 28 or 29 weeks

value: epididymal white adipose tissue

tag: diet

tag: sample type

value: Reference pool


title: Input_synblast_250 (polyA)


title: C2G1R6

description: Genotype_1_Treatment_2_Cond_2_Repl_6_ID_181

tag: Sex


title: C2G2R2

description: Genotype_2_Treatment_2_Cond_4_Repl_2_ID_148

tag: condition


title: C2G1R5

description: Genotype_1_Treatment_2_Cond_2_Repl_5_ID_172

tag: tissue


title: Input_nc9-10_250_rep2 (polyA)


title: C2G1R4

description: Genotype_1_Treatment_2_Cond_2_Repl_4_ID_158


title: Input_nc9-10_250 (polyA)


title: Input_nc7-9_250 (polyA)


title: Ft_cellblast_250 (polyA)


title: Ft_cellblast_50 (polyA)


title: C2G1R3

description: Genotype_1_Treatment_2_Cond_2_Repl_3_ID_153


title: C2G1R1

description: Genotype_1_Treatment_2_Cond_2_Repl_1_ID_107


title: C2G1R2

description: Genotype_1_Treatment_2_Cond_2_Repl_2_ID_129


title: C1G1R8

description: Genotype_1_Treatment_1_Cond_1_Repl_8_ID_295

source_name: Tph2 +/+_no stress_amygdala


title: Ft_synblast_250 (polyA)


title: C1G1R7

description: Genotype_1_Treatment_1_Cond_1_Repl_7_ID_290


title: Ft_nc9-10_250_rep2 (polyA)


title: C1G1R6

description: Genotype_1_Treatment_1_Cond_1_Repl_6_ID_74


title: Ft_nc9-10_250 (polyA)


title: C1G1R5

description: Genotype_1_Treatment_1_Cond_1_Repl_5_ID_70


title: Ft_nc7-9_250 (polyA)


title: Breast cancer cell line, cSrcKO, 9327 KO input DNA

city: Montreal

first: Harvey

middle: Wilmore

last: Smith

state: Quebec

address: Life Sciences Complex, Room 602, 1160 Pine Avenue West

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Data was assayed for quality through the use of FASTQC and processed using trimmomatic
D. melanogaster and mouse sequences were aligned to the BDGP6 and mm10 reference genomes, respectively, through the use of BWA
D. melanogaster sequence data were used to normalize mouse sequence data to remove background noise from random reads as previously described (PMID: 27875550, Egan et al.).
PCR bias and other artifacts were removed through the use of SAMtools and PICARDtools using default parameters
Broad peaks were called through the use of MACS2 and HOMER with default parameters
Genome_build: Mus musculus: mm10, D. melanogaster: BDGP6
Supplementary_files_format_and_content: bedgraph files were generated using MACS2 with default parameters

molecule: genomic DNA

source_name: Breast cancer cell line

growth_protocol: Breast cancer cell lines were established from the MMTV-NIC (ErbB2-IRES-Cre) model (PMID: 18273058, Ursini-Siegel et al.) and routinely cultured in DMEM supplemented with 5% FBS, EGF (5 ng/ml), Hydrocortisone (1 μg/ml), Insulin (5 μg/ml) and Bovine Pituitary Extract (BPE) (35μg/ml)). Cells were grown in a humidified, 5% CO2, 37°C incubator.

extract_protocol:
NIC cells in 15 cm plates were fixed with a 1% final concentration of formaldehyde for 5 min at room temperature and then lysed and sonicated. Three plates of cells were pooled for each sample (approximately 3x107 cells). Equal amounts of chromatin from 2 individual cell lines of each genotype were diluted in 2.5X ChIP dilution buffer (EDTA 2 mM, NaCl 100 mM, Tris 20 mM, Triton 0.5%) + 100 μL of PBS+0.5% BSA and 750 ng of D. melanogaster chromatin and 0.4 µg of a D. melanogaster H2Av-specific antibody (Active Motif) were added to each sample. 5 μg of anti-H3K27me3 antibody immobilized overnight at 4ºC on 20 μl of Magna ChIP Protein A+G magnetic beads (Millipore) were added to each sample and immunoprecipitation was performed overnight at 4ºC. Beads were washed 3 times for 3 min at 4ºC with 1 mL LiCl buffer (Tris 100mM, LiCl 500 mM, Na-deoxycholate 1%) then once with 1 mL TE buffer. DNA was eluted with 150 μL of elution buffer (0.1M NaHCO3, 0.1% SDS) overnight at 65ºC. Chromatin immunoprecipitated DNA was purified using a QIAquick PCR purification kit (Qiagen) and eluted in 35 μL of elution buffer.
Libraries were constructed with the Illumina TruSeq ChIP Library Preparation Kit using Illumina's standard protocols.

value: FVB/N

value: Breast cancer cell line

value: MMTV-NIC/c-Src LoxP/LoxP

tag: passages

value: mammary gland

tag: chip antibody


title: Breast cancer cell line, cSrcKO, 4447 KO input DNA


title: Eluate_cellblast_50 (polyA)


title: Breast cancer cell line, cSrcKO, 9327 KO H3K27me3 ChIP-Seq

value: Anti-H3K27me3 (C36B11), Cell Signaling, Cat. #9733 + Anti-Drosophila H2Av, Active Motif, Cat. #39715


title: Eluate_cellblast_250 (polyA)


title: Breast cancer cell line, WT, 9822 WT input DNA

value: MMTV-NIC/c-Src WT/WT


title: Breast cancer cell line, cSrcKO, 4447 KO H3K27me3 ChIP-Seq


title: C2G1R7

description: Genotype_1_Treatment_2_Cond_2_Repl_7_ID_241

value: male

value: 4 months

value: maternal separation

value: amygdala


title: Breast cancer cell line, WT, 8905 WT input DNA


title: Ft_synblast_50 (polyA)

value: Syncytial blastoderm

value: Flow-through


title: C1G1R3

description: Genotype_1_Treatment_1_Cond_1_Repl_3_ID_35

value: no stress


title: C1G1R2

description: Genotype_1_Treatment_1_Cond_1_Repl_2_ID_28


title: Breast cancer cell line, WT, 9822 WT H3K27me3 ChIP-Seq


title: BMP4+Pyr 16mM_6 Days

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing: Data was normalized by quantile normalization (computed using www.arrayanalysis.org)

source_name: H1_BMP4+Pyr 16mM_6 Days

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change. Cell culture of <70% confluence is designated as low density, and >90% confluence as high density.

extract_protocol: Toatal RNA was isolated by RNAiso Plus.

treatment_protocol: E8_2 Days: normal E8 medium. Pyr 16mM_2 Days: E8 medium supplemented with 16 mM pyruvate for 2 days.  BMP4_2 Days: E8 medium supplemented with BMP4 for 2 days. BMP4+Pyr 16mM_2 Days: E8 medium supplemented with BMP4 and 16mM pyruvate for 2 days. BMP4+Pyr 16mM_6 Days: E8 medium supplemented with BMP4 and 16mM pyruvate for 6 days.

tag: cell type

value: Human embryonic stem cell line

tag: treatment

value: BMP4+Pyr 16mM_6 Days


title: BMP4+Pyr 16mM_2 Days

source_name: H1_BMP4+Pyr 16mM_2 Days

tag: cell line

value: BMP4+Pyr 16mM_2 Days


title: YYHe-A-1 (shNC Mel624 rep1)

first: Yu-Ying

last: He

address: 5841 S Maryland Ave, AMB N011

department: Medicine

description: Negative control

data_processing: Performed by the Functional Genomics core facility at the University of Chicago according to manufacturer's instructions. Data were quantile normalized.

source_name: Melanoma

growth_protocol: 10% FBS in DMEM medium.

extract_protocol: RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed.

treatment_protocol: Mel624 cells were infected with lentiviral vector expressing negative control shRNA (shNC) or shRNA targeting FTO (shFTO) for FTO knockdown.

value: Melanoma cell line

tag: shRNA

value: shNC


title: C1G1R1

description: Genotype_1_Treatment_1_Cond_1_Repl_1_ID_17


title: BMP4_2 Days

source_name: H1_BMP4_2 Days

value: BMP4_2 Days


title: YYHe-B-1 (shFTO Mel624 rep1)

description: FTO knockdown

hyb_protocol: Performed by the Functional Genomics core facility at the University of Chicago according to manufacturer's instructions.

value: shFTO


title: YYHe-A-2 (shNC Mel624 rep2)

description: Negative control

scan_protocol: Performed by the Functional Genomics core facility at the University of Chicago according to manufacturer's instructions.


title: E8_2 Days

source_name: H1_E8_2 Days

value: E8_2 Days


title: Eluate_synblast_50 (polyA)

tag: developmental stage

tag: pull-down sample

value: Eluate

value: 50 mM 5-EU


title: YYHe-B-2 (shFTO Mel624 rep2)

description: FTO knockdown

label_protocol: Performed by the Functional Genomics core facility at the University of Chicago according to manufacturer's instructions.


title: C1G1R4

description: Genotype_1_Treatment_1_Cond_1_Repl_4_ID_52

value: male

tag: age


title: Eluate_synblast_250 (polyA)

tag: concentration of injected 5-eu


title: mock inoculated plant mock-2

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

data_processing:
fastqc was used to assess quality
Trimmomatic and sortmeRNA was used to remove low quality and ribosome matching reads respectively
The Tuxado protocol (bowtie, cufflinks, cummRbund) was used for alignment, and statistical evaluation.
Genome_build: SL2.5
Supplementary_files_format_and_content: data matrix
Supplementary_files_format_and_content: gene_exp.diff: text (gene level compression of samples + basic statistics)
Supplementary_files_format_and_content: genes.fpkm_rep.txt: text (fpkm values of all gene in all samples)

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Plants were grown in soil under 16 h light /8 h dark regime at 21°C .

extract_protocol:
The total RNA from control leaves and virus infected, systemically symptomatic leaves was extracted with phenol-chloroform methods (White and Kaper 1989)
Strand specific, polyA fractionated, Illumina RNA-Seq library preparation protocol

treatment_protocol: S. lycopersicum was infected with potato virus x (PVX) and tobacco mosaic virus (TMV) U1 strain. Host plants were used for infections using a sap inoculation with in vitro transcripts of the viruses (PVX and TMVU1).

tag: infection

value: mock


title: mock inoculated plant mock-1


title: Eluate_nc9-10_250_rep2 (polyA)


title: Eluate_nc9-10_250 (polyA)


title: Eluate_nc7-9_250 (polyA)


title: mock inoculated plant mock-0


title: Pyr 16mM_2 Days

source_name: H1_Pyr 16mM_2 Days

value: Pyr 16mM_2 Days


title: TNF 1

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v1.0.0 with parameters -q -p 12 -n 0 -m 1 --best --strata
peak calling was performed using HOMER v4.6 using the 'factor' preset and with a minimum 4 fould enrichment over local background and input control
Genome_build: mm10
Supplementary_files_format_and_content: Peak files and bedgraph files were generated with the HOMER software. Bedgraph values were normalized to 1e7 tags

source_name: BWTG3 cell line

extract_protocol:
Immunoprecipitation (IP) was performed on 100μl lysates diluted 1:3 in incubation buffer.Immunoprecipitated material was collected the next day by centrifugation and washed once each with WBI, WBII, LiCl buffer, and twice with EDTA/HEPES buffer (0.5M EDTA and 1M HEPES) using spin columns with 0.35μM pore size filters (MoBiTec).The recovered DNA was purified by the PCR purification kit (Qiagen) according to the manufacturer’s protocol, eluting in 50μl of Qiagen Elution buffer
RNA libraries were prepared for sequencing using standard Illumina protocols (truseq)

value: mouse hepatoma derived cells

value: rabbit anti-GR antibody; Santa Cruz Biotechnolgoy, sc-8992


title: TNF 2


title: Input

value: none:input DNA


title: Tobacco mosaic virus infected plant TMV-3

value: Tobacco mosaic virus


title: Tobacco mosaic virus infected plant TMV-2


title: mock inoculated plant mock-3


title: TNFDEX 2


title: leaf_CymRSV inoculated_rep2

hyb_protocol: One-Color Microarray-Based Gene Expression AnalysisLow Input Quick Amp Labeling

scan_protocol: Agilent scanner, FE SW 9.5 Extended Dynamic Range (with laser intensity at 100% and 10%; with 5 micron resolutino)

data_processing: Feature Extraction Software 10.01., default one color, high density, protocol (GE1-v5_95_Feb07)

organism: Nicotiana benthamiana

label_protocol: Low Input QuickAmp 6.5

growth_protocol: Plants were grown in soil under 16 h light /8 h dark regime at 21°C.

extract_protocol: The total RNA from control leaves and virus infected, systemically symptomatic leaves was extracted with phenol-chloroform methods (White and Kaper 1989)

treatment_protocol: N. benthamiana was infected with Cymbidium ring spot virus (CymRSV), turnip crinkle virus (TCV), crucifer infecting tobacco mosaic virus (crTMV). Host plants were used for infections using a sap inoculation with in vitro transcripts of the viruses  (crTMV) or with purified virions (CymRSV, TCV).

value: CymRSV


title: leaf_CymRSV inoculated_rep3


title: DEX 3


title: TNFDEX 1


title: leaf_crTMV inoculated_rep1

value: crTMV


title: leaf_CymRSV inoculated_rep1


title: Tobacco mosaic virus infected plant TMV-1


title: Sfwc-1(∆lov) 15 min light treatment (A15)

city: Taipei

first: Kulsumpun

last: krobanan

address: No.1, Sec. 4, Roosevelt Rd., Zhongzheng Dist.

country: Taiwan

institute: National Taiwan University

data_processing:
De novo assembly by using trinity
Map reads to assembled sequence by bowtie
Estimate abundance with RSEM
Normalize RSEM-estimated abundances weighted by Trimmed Mean of M values (TMM) method
Identify differentially expressed gene with edgeR
Please note that  feature Ids like “TR4637|c0_g1” (in the processed data files) are generated in this study (de novo transciptome assembly: SF_denovo_trinity.fasta) and the corresponding public gene Id was included in the last column (https://www.ncbi.nlm.nih.gov/bioproject/13841). However, as the species Sordaria fimicola and the reference Neurospora crassa OR74A genome (used for annotation) are closely related but different species, there are 26 out of 53,338 transcripts which do not  match to the reference genome.
Genome_build: De novo assembly
Supplementary_files_format_and_content: tab-delimited text files include raw eastimated abundance and RPKM values for each sample

organism: Sordaria fimicola

source_name: Mycelium

growth_protocol: The S. fimiocla wild type and Sfwc-1(∆lov) mutant were grown on malt extract agar I in constant dark for 2 days.

extract_protocol:
RNA extraction of frozen mycelium was carried out using Trizol reagent according to manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The dark grown mycellium were exposed to blue light for 15 and 45 min and immediately dipped in liquid nitrogen

tag: strain

value: dark grown for  2 days

tag: genotype/variation

value: Sfwc-1(deltalov) mutant

value: vegetative mycelium


title: DEX 2


title: DEX 1


title: Sfwc-1(∆lov) constant dark  (ADD)


title: WT 45 min light treatment (WT45)

value: Wild Type


title: NI 3


title: Sfwc-1(∆lov) 45 min light treatment (A45)


title: leaf_mock inoculated_rep2

value: uninfected


title: Potato virus x infected plant PVX-2

value: Potato virus x


title: NI 2


title: leaf_TCV inoculated_rep3

value: TCV


title: leaf_TCV inoculated_rep1


title: leaf_mock inoculated_rep3


title: Tobacco mosaic virus infected plant TMV-0


title: Potato virus x infected plant PVX-1


title: WT constant dark  (WTDD)


title: NI 1


title: leaf_mock inoculated_rep1


title: Potato virus x infected plant PVX-0


title: RNAseq_NCAPH2_Rep4

status: Public on May 05 2019

first: Nezar

last: Abdennur

state: MA

address: 77 Massachusetts Ave

institute: MIT

description:
rRNA-depleted RNA
NCAPH2_all_star_genome_minusAll.bw
NCAPH2_all_star_genome_minusUniq.bw
NCAPH2_all_star_genome_plusAll.bw
NCAPH2_all_star_genome_plusUniq.bw
TAMVsNCaph2.genes_de.xlsx

data_processing:
Hi-C: Hi-C datasets were processed using a portable pipeline called distiller, available at https://github.com/mirnylab/distiller-nf. Briefly, Hi-C sequencing reads were mapped to the mouse reference assembly mm9 using bwa mem (Li 2013) with flags -SP. Alignments were parsed, filtered for duplicates and pairs were classified using the pairtools package (https://github.com/mirnylab/pairtools). Hi-C pairs were aggregated into contact matrices in the cooler format using the cooler package (https://github.com/mirnylab/cooler) at multiple resolutions. fter binning, low-coverage bins were removed using a maximum allowed median absolute deviation (MAD) filter on log genomic coverage, set to five MADs. All contact matrices were normalized using the iterative correction procedure (Imakaev et al., 2012) such that the genome-wide sum of contact probability for each row/column equals 1.0.
RNA-seq: We mapped the RNA-seq data to mm9 reference mouse genome assembly and GENCODE vM1 transcriptome using STAR v.2.5.0a and adapted scripts from the ENCODE RNA-Seq pipeline [https://www.encodeproject.org/pipelines/ENCPL002LSE/]. To obtain the tracks of local transcription, we aggregated the uniquely mapped reads into RPKM-normalized bigWig files using the built-in STAR functionality. To find differentially expressed genes, we aggregated the read counts at the gene level using HTSeq  with the “union” option and called DE genes with DESeq2. Alignment with STAR v2.5.0.a was done using parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1. Signal tracks were generated using STAR with parameters: --runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded  --outWigReferencesPrefix chr.
Genome_build: mm9
Supplementary_files_format_and_content: Cooler files (extension .cool for single-resolution, .mcool for multi-resolution) contain contact matrices and were generated using the cooler Python package; RNA-seq bigWig files were generated using STAR in units of RPM; The xlsx file contains estimated transcript abundances and differential expression statistics between TAM control and the Ncaph2 mutant. The TAM control Samples are in Series GSE93431 listed as GSM2453295, GSM2453296, GSM2453297, and GSM2453298.

source_name: Liver

extract_protocol:
Liver was dissected and the left lateral lobe was prepped for a two-step perfusion adapted from (Li et al 2010 & Goncalves et al 2007): First, the liver was perfused with an EDTA-containing buffer to remove Ca2+ from the tissue in order to weaken the integrity of the desmosomes, which were subsequently digested using a Ca2+ rich buffer containing collagenase. The freed hepatocytes were rinsed through a cell strainer and washed four times with ice-cold Ca2+ rich buffer without collagenase. For each wash, the cells were spun at low centrifugal force (60g for 1min) to enrich intact hepatocytes and reduce non-mesenchymal debris. Part of each sample was fixed with 1% PFA for 10 minutes at room temperature. Fixed and unfixed hepatocytes were aliquoted and frozen in liN2 for later use.
Hi-C: Roughly 100 million fixed hepatocytes per sample were processed according to (Kalhor et al, 2012) using HindIII. TCC libraries were PCR-amplified (12 cycles) and size selected. Equimolar pools of libraries were sequenced; RNA-seq: RNA integrity was tested with Bioanalyzer (Agilent RNA Nano Kit) and ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Illumina) prior to library preparation.  Strand-specific libraries were prepared with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. After amplification and size selection with Agencourt AMPure XP beads (Beckmann Coulter) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end).
Tethered Chromosome Capture (TCC) variant of Hi-C; RNA-seq

treatment_protocol: Treated 12 week old mice were injected with 1mg Tamoxifen (100μl of 10mg/ml Tamoxifen in corn oil) on 5 consecutive days. After keeping these mice for another 5 days without injection, they were sacrificed and the hepatocytes were harvested.

tag: genotype

value: tamoxifen

value: 12 weeks

value: liver


title: Tumor_angiosarcoma-like

type: genomic

city: Saarbrucken

first: Sonja

last: Kessler

address: Campus C2 3

institute: Saarland University

hyb_protocol: The samples were hybridized on an 8x15k CGH Array under the conditions of the Agilent protocol (Version 7.2).

scan_protocol: The arrays were analyzed with an Agilent DNA Microarray Scanner G2505C.

data_processing: For analysis extraction software Agilent Feature Extraction 11.0.1.1 was used.

organism: Sus scrofa

source_name: liver tumor tissue

label_protocol: Labeling was performed according to the BioPrime aCGH Genomic Labeling Module protocol (Invitrogen).

growth_protocol: Pigs Sus scrofa were kept in boxes of two to four animals and fed twice a day with G-22 food for fattening (Gsellmann, Austria).

extract_protocol: Paraffin-embedded liver tumors were micro-dissected and gDNA was isolated using the QiaAmp DNA Mini Kit

treatment_protocol: Diethynitrosamine (DENA) was applied was injected 200 mg DENA by a single i.p. shot.

tag: disease state

value: Tumor angiosarcoma-like

tag: gender

value: female

source_name: reference liver tissue


title: Potato virus x infected plant PVX-3


title: C2G3R7

description: Genotype_3_Treatment_2_Cond_6_Repl_7_ID_218

source_name: Tph2 -/-_maternal separation_amygdala

tag: Sex

value: male

value: 4 months

tag: condition

value: maternal separation

tag: tissue

value: amygdala


title: RNAseq_NCAPH2_Rep3


title: Fertile sib (of am1-489), maize anthers 1.25 mm, rep 3

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
All reads from small RNA, PARE or RNA-seq libraries were trimmed to remove adapter sequences using a Perl script.
Genome_build: None
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts

organism: Zea mays

source_name: maize anthers

extract_protocol:
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described. All libraries were sequenced on an Illumina Hi-Seq 2000 instrument

value: maize anthers 125 mm

value: Fertile sib


title: leaf_crTMV inoculated_rep2

value: crTMV


title: RNAseq_NCAPH2_Rep1


title: Fertile sib (of am1-489), maize anthers 1.25 mm, rep 2


title: Non-tumor control tissue

source_name: liver tissue

value: control


title: Fertile sib (of am1-praI), maize anthers 1.25 mm, rep 3


title: Fertile sib (of am1-489), maize anthers 1.25 mm, rep 1


title: am1-489 maize anthers 1.25 mm, rep 1


title: WT 15 min light treatment (WT15)

value: dark grown for  2 days

value: Wild Type

value: vegetative mycelium


title: Fertile sib (of am1-praI), maize anthers 1.25 mm, rep 2


title: RNAseq_NCAPH2_Rep2


title: ameiotic1 (praI) maize anthers 1.25 mm, rep 2

value: ameiotic1 (praI)


title: Fertile sib (of am1-praI), maize anthers 1.25 mm, rep 1


title: ameiotic1 (praI) maize anthers 1.25 mm, rep 3


title: am1-489 maize anthers 1.25 mm, rep 2


title: ameiotic1 (praI) maize anthers 1.25 mm, rep 1


title: Fertile sib (of am1-489), maize anthers, 1.5 mm rep 2.

value: maize anthers 15 mm


title: Fertile sib (of am1-489), maize anthers, 1.5 mm rep 3.


title: leaf_crTMV inoculated_rep3


title: Fertile sib (of am1-489), maize anthers, 1.5 mm rep 1.


title: leaf_TCV inoculated_rep2

value: TCV


title: ameiotic1 (praI) maize anthers, male sterile, 1.5 mm rep 1

value: male sterile 15 mm


title: ameiotic1 (praI) maize anthers, male sterile, 1.0 mm rep 3.

value: male sterile 10 mm


title: ameiotic1 (praI) maize anthers, male sterile, 1.5 mm rep 2.


title: ameiotic1 (praI) maize anthers, male sterile, 1.0 mm rep 1.


title: ameiotic1 (praI) maize anthers, male sterile, 1.0 mm rep 2.


title: ameiotic1 (489) maize anthers, male sterile, 1.5 mm rep 2

value: ameiotic1 (489)


title: ameiotic1 (489) maize anthers, male sterile, 1.5 mm rep 1


title: DMS-MaPseq on denatured E. coli total RNA (Replicate #1)

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

description: E. coli denatured (Replicate #1)

data_processing:
Library strategy: DMS-MaPseq
All the relevant analysis steps, from reads alignment to data normalization and structure modeling, were performed using the RNA Framework (Incarnato et al., 2018). Briefly, sequencing reads were clipped from adapter sequences and terminal positions with Phred qualities <20 were trimmed. Alignment was performed using the rf-map tool and the Bowtie v2 algorithm (Langmead et al., 2012), with soft-clipping enabled (parameters: -b2 -cp -b5 5 -mp "--very-sensitive-local"). Before proceeding to DMS-MaPseq data analysis, sequencing of an untreated IAV sample was performed in order to annotate eventual mutations with respect to the reference strain. Positions with mutations exceeding a frequency of 50% were annotated. All the subsequent analysis steps were then performed using this updated reference. Per-base mutation count and coverage were calculated using the rf-count tool (parameters: -nm -r -m -mq 0 -na -md 3 -ni). A ratiometric score was then calculated as ri = (mi / Ci) where ri, mi, and Ci are respectively the raw reactivity, the mutation count and the coverage at position i. Reactivity normalization was performed as a 2-step process. First, each sample was normalized by 90% Winsorizing, in order to smooth the contribution of both over and under-reactive residues, using the rf-norm tool (parameters: -sm 4 -nm 2 -rb AC). Briefly, each reactivity value above the 95th percentile was set to the 95th percentile and each reactivity value below the 5th percentile was set to the 5th percentile, then the reactivity at each position of the transcript was divided by the value of the 95th percentile. Reactivity data from targeted DMS-MaPseq analysis of probe pairing regions was independently Winsorized and then used to replace original RAPiD-MaPseq data. Second, both the in vitro and the in vivo datasets were normalized to the respective denatured controls as Ri = min(Si/Di,1) where Ri, Si, and Di are respectively the normalized reactivity, the sample reactivity (either in vivo or in vitro), and the denatured control reactivity at position i. This normalization yielded reactivity values comprised between 0 (low single-strandedness probability) and 1 (high single-strandedness probability). Given the high correlation of all the datasets, biological replicates were combined using the rf-combine utility following normalization. Combined datasets were then used for all downstream analyses.
Genome_build: A/Puerto Rico/8/1934(H1N1) from NC_002016 to NC_002023
Supplementary_files_format_and_content: For each DMS-MaPseq sample (but the untreated controls) a Wiggle track file is provided, reporting the mutation frequency of A/C residues for each Influenza A vmRNA. For the untreated controls, a multi-Fasta file is provided with the sequence of Influenza A vmRNAs, annotated with the detected SNVs. Additional processed files are available at: http://www.incarnatolab.com/datasets/IAV_Simon_2019.php

organism: Escherichia coli

growth_protocol: LB medium, 37°C, 300 RPM

extract_protocol:
Cell pellets from exponential phase E. coli were resuspended in 1 ml of Resuspension Buffer [15 mM Tris-HCl pH 8.0; 450 mM Sucrose; 8 mM EDTA], and 18,500 U of Ready-Lyse Lysozyme (Epicentre, #R1810M) were added. After incubation at 22 °C for 5 min and on ice for 10 min, protoplasts were collected by centrifugation at 5000 x g (4 °C) for 5 min. Pellets were resuspended in 120 µl Protoplast Lysis Buffer [50 mM HEPES pH 8.0; 200 mM NaCl; 5 mM MgCl2; 1.5% SDS]. Samples were incubated for 5 min at 22 °C and for 5 min on ice, followed by addition of 30µl SDS precipitation buffer (50mM HEPES pH8, 1M KOAc, 5mM MgCl2). The precipitate was removed by centrifugation at 17000g (4 °C) for 5min and the supernatant was the extracted with TRIzol reagent, as per manufacturer instructions.
RNA was fragmented in 64 mM Tris-HCl pH 8.3, 96 mM KCl, 3.9 mM MgCl2 for 8 min at 94 °C and subsequently purified on RNA Clean & Concentrator-5 columns. Reverse transcription (RT) was performed using the TGIRT-III enzyme (InGex, #TGIRT50) as described previously (Zubradt et al., 2016). Briefly, to the 5 µl of fragmented RNA, 1 µl 10 mM dNTPs and 0.5 µl 10 µM random hexamers were added, and the mixture was heated to 70 °C for 5 min and immediately placed on ice for 1 min. 2 µl of 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], DTT to 5 mM, 10 U SUPERase In RNase Inhibitor, and 100 U TGIRT-III were added. Reverse transcription was then allowed to proceed at 25 °C for 5 min, followed by 1.5 h at 57 °C. To remove TGIRT-III from the RNA-DNA duplex, 1 µl of proteinase K was added to a final concentration of 0.1 µg/µl and the reaction incubated at 37 °C for 15 min., 1 µl of a 1:2 dilution of protease inhibitor cocktail (Sigma Aldrich, #P8340) was then added to inhibit proteinase K activity. The reaction volume was then adjusted to 25 µl by adding 3 µl of 5X RT Buffer and 10 µl water. Libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, #15025063), starting from second strand synthesis.

treatment_protocol: RNA was heated to 95 °C for 1 min in a total volume of 90 µl with 55 mM HEPES pH 7.9, 4.4 mM EDTA, 55% formamide. 10 µl of 0.5 M DMS in ethanol were then added to obtain a probing concentration of 50 mM. Probing was allowed to proceed at 95 °C for 1 min. Reactions were quenched by adding 200 µl RNA Binding Buffer (from RNA Clean & Concentrator-5 columns) supplemented with DTT to a final concentration of 750 mM. Samples were then purified on RNA Clean & Concentrator-5 columns.


title: DMS-MaPseq on ex vivo native deproteinized E. coli total RNA (Replicate #1)

description: E. coli ex vivo (Replicate #1)

extract_protocol:
Cell pellets from exponential phase E. coli were resuspended in 1 ml of Resuspension Buffer [15 mM Tris-HCl pH 8.0; 450 mM Sucrose; 8 mM EDTA], and 18,500 U of Ready-Lyse Lysozyme (Epicentre, #R1810M) were added. After incubation at 22 °C for 5 min and on ice for 10 min, protoplasts were collected by centrifugation at 5000 x g (4 °C) for 5 min. Pellets were resuspended in 120 µl Protoplast Lysis Buffer [50 mM HEPES pH 8.0; 200 mM NaCl; 5 mM MgCl2; 1.5% SDS]. Samples were incubated for 5 min at 22 °C and for 5 min on ice, followed by addition of 30µl SDS precipitation buffer (50mM HEPES pH8, 1M KOAc, 5mM MgCl2). The precipitate was removed by centrifugation at 17000g (4 °C) for 5min and the supernatant was subjected to gel filtration on ProbeQuant G-50 Micro Columns (GE Healthcare, #28-9034-08) pre-equilibrated 3 times with RNA folding buffer (RFB) [50 mM HEPES pH 8.0; 200 mM KOAc; 5 mM MgCl2]. The eluate was then extracted 2 times with phenol:chloroform:isoamyl alcohol (25:24:1, pre-equilibrated 3 times with RFB), and once with chloroform. 20 U of SUPERase In RNase Inhibitor (ThermoFisher Scientific, #AM2696) were added.
RNA was fragmented in 64 mM Tris-HCl pH 8.3, 96 mM KCl, 3.9 mM MgCl2 for 8 min at 94 °C and subsequently purified on RNA Clean & Concentrator-5 columns. Reverse transcription (RT) was performed using the TGIRT-III enzyme (InGex, #TGIRT50) as described previously (Zubradt et al., 2016). Briefly, to the 5 µl of fragmented RNA, 1 µl 10 mM dNTPs and 0.5 µl 10 µM random hexamers were added, and the mixture was heated to 70 °C for 5 min and immediately placed on ice for 1 min. 2 µl of 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], DTT to 5 mM, 10 U SUPERase In RNase Inhibitor, and 100 U TGIRT-III were added. Reverse transcription was then allowed to proceed at 25 °C for 5 min, followed by 1.5 h at 57 °C. To remove TGIRT-III from the RNA-DNA duplex, 1 µl of proteinase K was added to a final concentration of 0.1 µg/µl and the reaction incubated at 37 °C for 15 min., 1 µl of a 1:2 dilution of protease inhibitor cocktail (Sigma Aldrich, #P8340) was then added to inhibit proteinase K activity. The reaction volume was then adjusted to 25 µl by adding 3 µl of 5X RT Buffer and 10 µl water. Libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, #15025063), starting from second strand synthesis.

treatment_protocol: RNA was equilibrated at 37 °C for 20 min prior to probing with 200 mM DMS for 3 min at 30 °C with moderate shaking. The probing reactions were then quenched by DTT addition to a final concentration of 0.7M and RNA extracted with TRIzol.


title: DMS-MaPseq on untreated in vitro-transcribed Influenza A vmRNA

description: Influenza untreated in vitro

organism: Influenza A virus

source_name: A/Puerto Rico/8/1934(H1N1)

extract_protocol:
A T7 promoter was introduced 5’ to each segment via PCR using pDZ-PB2, PB1, PA, HA, NP, NA, M1/2, NS1/NEP plasmids as a template. Segments were then in vitro transcribed using T7-FlashScribe kit (CellScript, #C-ASF3507). Transcription products were verified by capillary electrophoresis on a Fragment Analyzer (Advanced Analytical). For in vitro refolding, segments were pooled equimolarly and 240 ng of the pool were used per replicate.
RNA was fragmented in 64 mM Tris-HCl pH 8.3, 96 mM KCl, 3.9 mM MgCl2 for 8 min at 94 °C and subsequently purified on RNA Clean & Concentrator-5 columns. Reverse transcription (RT) was performed using the TGIRT-III enzyme (InGex, #TGIRT50) as described previously (Zubradt et al., 2016). Briefly, to the 5 µl of fragmented RNA, 1 µl 10 mM dNTPs and 0.5 µl 10 µM random hexamers were added, and the mixture was heated to 70 °C for 5 min and immediately placed on ice for 1 min. 2 µl of 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], DTT to 5 mM, 10 U SUPERase In RNase Inhibitor, and 100 U TGIRT-III were added. Reverse transcription was then allowed to proceed at 25 °C for 5 min, followed by 1.5 h at 57 °C. To remove TGIRT-III from the RNA-DNA duplex, 1 µl of proteinase K was added to a final concentration of 0.1 µg/µl and the reaction incubated at 37 °C for 15 min., 1 µl of a 1:2 dilution of protease inhibitor cocktail (Sigma Aldrich, #P8340) was then added to inhibit proteinase K activity. The reaction volume was then adjusted to 25 µl by adding 3 µl of 5X RT Buffer and 10 µl water. Libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, #15025063), starting from second strand synthesis.

value: A/Puerto Rico/8/1934(H1N1)


title: LLC cells wild type - replica 2

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

data_processing:
Sequenced reads were trimmed for adaptor sequence
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR software to generate read alignments.
The annotation file Mus_musculus.GRCm38.84.gtf was obtained from the ftp.Ensembl.org server
Following transcript assembly, gene level counts were obtained using HTSeq
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample.

source_name: Wild type Lewis lung carcinoma cells

growth_protocol: LLC cells were inoculated subcutaneously into the back of syngeneic C57BL/6 mice. Tumors were collected after 5 days for further analysis.

extract_protocol:
Tumor tissue was lysed in TRIzol reagent (Life Technologies, Carlsbad, CA, US). Total RNA was extracted with the RNAeasy micro kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols

tag: cells

value: Lewis lung carcinoma cells

value: wild type

tag: tumor stage

value: 5 days following graft subcutaneously


title: ameiotic1 (489) maize anthers, male sterile, 0.4 mm rep 1.

value: male sterile 04 mm


title: ameiotic1 (489) maize anthers, male sterile, 0.7 mm rep 1

value: male sterile 07 mm