title: Mouse Lung, KO, Dose 120, 26wk, biological replicate 1

description:
SIRC_120_26w_611_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_611_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_A04.CEL

value: Whole Lung


title: C3H, Liver, 21 days HFD, rep3 reanalysis

status: Public on Mar 08 2018

type: RNA

city: Munich

first: Barbara

last: Fridrich

address: Ingolstädter Landstraße 1

country: Germany

institute: Hemholtz Center Munich

description: Gene expression data from liver of radnom fed C3H mice, 21 days HFD

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.1) including median polish and Sketch-Quantile normalisation

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: C3H, Liver, 21 days HFD

label_protocol: GeneChip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix)

growth_protocol: Single housed animals

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: As described in the paper. Briefly, mice were fed with a HFD (7, 14 or 21 days) or LFD (≤ 21 days) and gene transcription analyses in liver was performed.

tag: strain

tag: age

value: 17 weeks

tag: gender

value: male

tag: genotype

value: WT

tag: treatment

value: high fat diet

tag: time


title: C3H, Liver, 21 days HFD, rep6 reanalysis

scan_protocol: According to the Affymetrix expression protocol


title: Mouse Lung, KO, Dose 120, 26wk, biological replicate 3

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

country: USA

institute: Scitovation, LLC.

description:
SIRC_120_26w_614_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_614_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C05.CEL

hyb_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit, page40-42 and GeneTitan® Instrument User Guide for Expression Array Plates.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6.

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 120ppm, 26w

label_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit.

growth_protocol: Adult male C57Bl/6 WT, KO and TG and CD-1 mice were acquired from Taconic (Germantown, NY). Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room. The room was maintained on a 12-hr light-dark cycle (7 AM-7 PM) at approximately 20-25°C with a relative humidity of approximately 35-65%. All animals were allowed access to Certified LabDiet 5002 diet and reverse osmosis water ad libitum.

extract_protocol: Trizol® (ThermalFisher) organic extraction with Phase Lock Gel™ -Heavy- tubes (5Prime). Aqueous phase placed in RB (QiaCube sample) tubes and loaded into QiaCube, the RNeasy Mini Protocol used.

treatment_protocol: During exposure periods, animals were placed individually in stainless-steel wire-mesh cages and exposed to styrene or air 5 days per week for 6 hours per day for either 1 or 4 weeks. On the morning following the last inhalation exposure, mice were euthanized by sodium pentobarbital and exsanguination. Doses were 0 ppm (air only), and 120 ppm styrene.

tag: strain/background

tag: genotype/variation

value: adult

tag: tissue

value: styrene inhalation

tag: dose (ppm)

tag: time of exposure


title: C3H, Liver, 21 days HFD, rep5 reanalysis


title: C3H, Liver, 14 days HFD, rep4

description: Gene expression data from liver of radnom fed C3H mice, 14 days HFD

source_name: C3H, Liver, 14 days HFD

value: 16 weeks


title: Mouse Lung, KO, Dose 120, 26wk, biological replicate 2

description:
SIRC_120_26w_612_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_612_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C04.CEL


title: C3H, Liver, 14 days HFD, rep1


title: C3H, Liver, 14 days HFD, rep2


title: C3H, Liver, 7 days HFD, rep8

description: Gene expression data from liver of radnom fed C3H mice, 7 days HFD

source_name: C3H, Liver, 7 days HFD

value: 15 weeks

value: 7 d


title: Mouse Lung, KO, Dose 0, 26wk, biological replicate 2

description:
SIRC_0_26w_512_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_512_ACO3_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_B12.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 0ppm, 26w


title: Mouse Lung, KO, Dose 0, 26wk, biological replicate 5

description:
SIRC_0_26w_515_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_515_ACO3_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C03.CEL


title: Mouse Lung, KO, Dose 0, 26wk, biological replicate 4

description:
SIRC_0_26w_514_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_514_ACO3_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C02.CEL


title: Mouse Lung, KO, Dose 0, 26wk, biological replicate 1

description:
SIRC_0_26w_511_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_511_ACO3_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_A03.CEL


title: Mouse Lung, KO, Dose 0, 26wk, biological replicate 3

description:
SIRC_0_26w_513_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_513_ACO3_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C01.CEL


title: C3H, Liver, 7 days HFD, rep7


title: C3H, Liver, 7 days HFD, rep6


title: C3H, Liver, 7 days HFD, rep1


title: Mouse Lung, TG, Dose 120, 104wk, biological replicate 5

description:
SIRC_120_104w_856_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_856_Tu_TG_DEDSTY141-1_(HT_MG-430_PM)_H07.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 120ppm, 104w

value: CYP2F2(-/-) + 2F1,SA13,2B6-transgenic (TG)


title: Mouse Lung, TG, Dose 120, 104wk, biological replicate 2

description:
SIRC_120_104w_828_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_828_TG_DEDSTY141-1_(HT_MG-430_PM)_G07.CEL


title: C3H, Liver, 7 days HFD, rep3


title: C3H, Liver, 7 days HFD, rep2


title: Mouse Lung, TG, Dose 120, 104wk, biological replicate 4

description:
SIRC_120_104w_842_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_842_TG_DEDSTY141-1_(HT_MG-430_PM)_H05.CEL


title: Mouse Lung, KO, Dose 120, 52wk, biological replicate 1

description:
SIRC_120_52w_616_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_616_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_F06.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 120ppm, 52w


title: Mouse Lung, TG, Dose 120, 104wk, biological replicate 1

description:
SIRC_120_104w_826_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_826_TG_DEDSTY141-1_(HT_MG-430_PM)_G05.CEL


title: Mouse Lung, TG, Dose 0, 104wk, biological replicate 2

description:
SIRC_0_104w_735_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_735_TG_DEDSTY141-1_(HT_MG-430_PM)_H05.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 0ppm, 104w


title: Mouse Lung, TG, Dose 120, 104wk, biological replicate 6

description:
SIRC_120_104w_860_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_860_TG_DEDSTY141-1_(HT_MG-430_PM)_H09.CEL


title: C3H, Liver, 7 days HFD, rep5


title: C3H, Liver, control, rep17 reanalysis

description: Gene expression data from liver of random fed C3H mice, control

source_name: C3H, Liver, control

value: 15-17 weeks

value: control


title: C3H, Liver, control, rep16 reanalysis


title: C3H, Liver, control, rep18 reanalysis


title: Mouse Lung, TG, Dose 0, 104wk, biological replicate 5

description:
SIRC_0_104w_759_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_759_TG_DEDSTY141-1_(HT_MG-430_PM)_A05.CEL


title: C3H, Liver, control, rep15 reanalysis


title: C3H, Liver, 7 days HFD, rep4


title: Mouse Lung, TG, Dose 120, 104wk, biological replicate 3

description:
SIRC_120_104w_832_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_832_TG_DEDSTY141-1_(HT_MG-430_PM)_G09.CEL


title: Mouse Lung, TG, Dose 0, 104wk, biological replicate 3

description:
SIRC_0_104w_737_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_737_TG_DEDSTY141-1_(HT_MG-430_PM)_H07.CEL


title: Mouse Lung, TG, Dose 0, 104wk, biological replicate 1

description:
SIRC_0_104w_733_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_733_TG_DEDSTY141-1_(HT_MG-430_PM)_G09.CEL


title: C3H, Liver, control, rep13 reanalysis


title: Mouse Lung, TG, Dose 0, 104wk, biological replicate 4

description:
SIRC_0_104w_739_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_739_TG_DEDSTY141-1_(HT_MG-430_PM)_H09.CEL


title: Mouse Lung, TG, Dose 120, 78wk, biological replicate 3

description:
SIRC_120_78w_823_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_823_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_F07.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 120ppm, 78w


title: Mouse Lung, TG, Dose 120, 78wk, biological replicate 2

description:
SIRC_120_78w_822_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_822_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_F05.CEL


title: C3H, Liver, control, rep14 reanalysis


title: C3H, Liver, control, rep12 reanalysis


title: Mouse Lung, TG, Dose 0, 78wk, biological replicate 5

description:
SIRC_0_78w_725_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_725_ACO12_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_H07.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 0ppm, 78w


title: C3H, Liver, control, rep10 reanalysis


title: C3H, Liver, control, rep11 reanalysis


title: C3H, Liver, control, rep8 reanalysis


title: Mouse Lung, TG, Dose 0, 78wk, biological replicate 2

description:
SIRC_0_78w_722_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_722_ACO12_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_H04.CEL


title: C3H, Liver, control, rep9 reanalysis


title: Mouse Lung, TG, Dose 0, 78wk, biological replicate 3

description:
SIRC_0_78w_723_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_723_ACO12_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_H05.CEL


title: C3H, Liver, control, rep7 reanalysis


title: Mouse Lung, TG, Dose 0, 78wk, biological replicate 1

description:
SIRC_0_78w_721_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_721_ACO12_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_H03.CEL


title: C3H, Liver, control, rep5 reanalysis


title: C3H, Liver, control, rep2 reanalysis


title: C3H, Liver, control, rep1 reanalysis


title: C3H, Liver, control, rep4 reanalysis


title: Mouse Lung, TG, Dose 0, 78wk, biological replicate 4

description:
SIRC_0_78w_724_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_724_ACO12_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_H06.CEL


title: C3H, Liver, control, rep6 reanalysis


title: Mouse Lung, TG, Dose 120, 78wk, biological replicate 1

description:
SIRC_120_78w_821_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_821_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_E07.CEL


title: C3H, Liver, control, rep3 reanalysis


title: Mouse Lung, TG, Dose 120, 52wk, biological replicate 3

description:
SIRC_120_52w_818_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_818_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_G01.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 120ppm, 52w


title: Mouse Lung, TG, Dose 0, 52wk, biological replicate 5

description:
SIRC_0_52w_720_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_720_ACO8_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_E09.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 0ppm, 52w


title: Mouse Lung, TG, Dose 120, 52wk, biological replicate 5

description:
SIRC_120_52w_857_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_857_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_G03.CEL


title: Mouse Lung, TG, Dose 120, 52wk, biological replicate 4

description:
SIRC_120_52w_819_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_819_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_G02.CEL


title: Mouse Lung, TG, Dose 120, 52wk, biological replicate 1

description:
SIRC_120_52w_816_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_816_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_F11.CEL


title: T_HC_C3 [Human LncRNA Array v3.0]

city: Hefei

first: Lian-Ju

last: Li

state: Anhui

address: 81 Meishan Road

department: Department of Epidemiology and Biostatistics, School of Public Health

country: China

institute: Anhui Medical University

description: lncRNA expression in T cells from healthy volunteer C3

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: The Agilent Scanner G2505B was used to scan the slides

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering.

organism: Homo sapiens

source_name: T cell, HC

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from T cells by using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacture’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: CD3+ T cell was positively labeled with anti-human CD3 magnetic Particles-DM (BD IMag™, San Jose, USA) and selected by IMag magnetic cell separation system (BD IMagnet™, San Jose, USA).

value: Peripheral Blood Mononuclear Cells

value: female


title: Mouse Lung, TG, Dose 120, 52wk, biological replicate 2

description:
SIRC_120_52w_817_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_817_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_F12.CEL


title: T_HC_C2 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from healthy volunteer C2


title: Mouse Lung, TG, Dose 0, 52wk, biological replicate 3

description:
SIRC_0_52w_718_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_718_ACO8_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_E07.CEL


title: T_HC_C1 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from healthy volunteer C1


title: Mouse Lung, TG, Dose 0, 52wk, biological replicate 4

description:
SIRC_0_52w_719_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_719_ACO8_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_E08.CEL


title: T_SLE_S25 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from patient S25

source_name: T cell, SLE


title: Mouse Lung, TG, Dose 0, 52wk, biological replicate 1

description:
SIRC_0_52w_716_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_716_ACO8_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_E05.CEL


title: T_SLE_S15 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from patient S15


title: T_SLE_S5 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from patient S5


title: T_SLE_S18 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from patient S18


title: Mouse Lung, TG, Dose 120, 26wk, biological replicate 4

description:
SIRC_120_26w_814_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_814_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_C12.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 120ppm, 26w


title: T_SLE_S11 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from patient S11


title: Mouse Lung, TG, Dose 120, 26wk, biological replicate 3

description:
SIRC_120_26w_813_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_813_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_C11.CEL


title: Mouse Lung, TG, Dose 0, 26wk, biological replicate 4

description:
SIRC_0_26w_715_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_715_ACO4_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_C09.CEL

source_name: Whole lung, C57Bl/6, TG, styrene inhalation, 0ppm, 26w


title: T_SLE_S9 [Human LncRNA Array v3.0]

description: lncRNA expression in T cells from patient S9


title: Mouse Lung, TG, Dose 120, 26wk, biological replicate 5

description:
SIRC_120_26w_815_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_815_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_D01.CEL


title: Mouse Lung, WT, Dose 120, 104wk, biological replicate 4

description:
SIRC_120_104w_438_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_438_WT_DEDSTY141-1_(HT_MG-430_PM)_E07.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 120ppm, 104w

value: Wild Type (WT)


title: Mouse Lung, TG, Dose 0, 26wk, biological replicate 3

description:
SIRC_0_26w_714_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_714_ACO4_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_C08.CEL


title: dSur -/-, elavGal4/RNAi104241, biological replicate 3 Day-RNAi-C)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: Gene expression profiling of dSur -/- flies (Day-RNAi-C).

hyb_protocol: 1.65 μg of labeled cRNA were used in each reaction and the hybridization was carried out at 65°C for 17 hours in an hybridization oven rotator (Agilent Technologies, Palo Alto, CA). The arrays were washed by Agilent Gene expression washing buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with quantile to correct possible experimental distortions. Normalization function was applied to expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provides spot quality measures in order to evaluate the quality and the reliability of the hybridization. In particular, flag glsFound (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as null. So, in order to make more robust and unbiased statistical analyses, probes with a high proportion of null values were removed from the dataset. About forty percent (38%) of null was used as threshold in the filtering process, and a total of 22,523 available Drosophila transcripts were obtained.

organism: Drosophila melanogaster

source_name: Heads of 30 dSur-/- flies sampled at the time point Day (pooled samples every three hours over a 24h period).

label_protocol: 800 ng of total RNA were labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labeled with Cy3-dCTP. Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE).

extract_protocol: Total RNA was extracted from 30 heads (males) larvae for each genotype using Trizol (Life Technologies) according to the manufacter's instructions and further purified with LiCl 8M. All RNA samples were checked for quality by capillary electrophoresis (RNA 6000 Nano LabChip, Agilent Bioanalyzer 2100, Agilent Technologies).

value: heads

value: dSur-/-

tag: time point

value: day

tag: Sex


title: wt, RNAi104241, biological replicate 4 (Day-wt-D)

description: Gene expression profiling of parental control flies (Day-wt-D).

source_name: Heads of 30 parental control flies (wt) sampled at the time point Day (pooled samples every three hours over a 24h period).

value: parental control (wt)

value: male


title: wt, RNAi104241, biological replicate 3 (Day-wt-C)

description: Gene expression profiling of parental control flies (Day-wt-C).


title: wt, RNAi104241, biological replicate 4 (Night-wt-D)

description: Gene expression profiling of parental control flies (Night-wt-D).

source_name: Heads of 30 parental control flies (wt) sampled at the time point Night ( ZT15, three hours in the dark phase)

value: night


title: Mouse Lung, WT, Dose 120, 52wk, biological replicate 5

description:
SIRC_120_52w_419_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_419_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_F04.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 120ppm, 52w

value: adult

value: Whole Lung


title: Mouse Lung, TG, Dose 120, 26wk, biological replicate 2

description:
SIRC_120_26w_812_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_812_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_C10.CEL

value: styrene inhalation


title: Mouse Lung, TG, Dose 120, 26wk, biological replicate 1

description:
SIRC_120_26w_811_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_811_STY_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_A06.CEL


title: dSur -/-, elavGal4/RNAi104241, biological replicate 2 Day-RNAi-B)

description: Gene expression profiling of dSur -/- flies (Day-RNAi-B).


title: Mouse Lung, TG, Dose 0, 26wk, biological replicate 1

description:
SIRC_0_26w_711_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_711_ACO4_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_A05.CEL


title: dSur -/-, elavGal4/RNAi104241, biological replicate 1 (Day-RNAi-A)

description: Gene expression profiling of dSur -/- flies (Day-RNAi-A).


title: dSur -/-, elavGal4/RNAi104241, biological replicate 4 Day-RNAi-D)

description: Gene expression profiling of dSur -/- flies (Day-RNAi-D).


title: Mouse Lung, WT, Dose 120, 104wk, biological replicate 2

description:
SIRC_120_104w_433_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_433_WT_DEDSTY141-1_(HT_MG-430_PM)_D09.CEL


title: wt, RNAi104241, biological replicate 1 (Day-wt-A)

description: Gene expression profiling of parental control flies (Day-wt-A).


title: Mouse Lung, TG, Dose 0, 26wk, biological replicate 2

description:
SIRC_0_26w_713_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_713_ACO4_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_C07.CEL


title: Mouse Lung, WT, Dose 120, 104wk, biological replicate 5

description:
SIRC_120_104w_467_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_467_WT_DEDSTY141-1_(HT_MG-430_PM)_E09.CEL


title: wt, RNAi104241, biological replicate 2 (Day-wt-B)

description: Gene expression profiling of parental control flies (Day-wt-B).


title: Mouse Lung, WT, Dose 120, 104wk, biological replicate 3

description:
SIRC_120_104w_434_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_434_WT_DEDSTY141-1_(HT_MG-430_PM)_E05.CEL


title: Mouse Lung, TG, Dose 0, 52wk, biological replicate 2

description:
SIRC_0_52w_717_TG
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_717_ACO8_TG_DEDSTY141-1_2016_(HT_MG-430_PM)_E06.CEL


title: wt, RNAi104241, biological replicate 1 (Night-wt-A)

description: Gene expression profiling of parental control flies (Night-wt-A).


title: Bacillus amyloliquefaciens; B425_T5A

type: SRA

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description:
B425_T5A
Processed_data_rpkm.txt

library_source: transcriptomic

data_processing:
mapping of reads was done using: bowtie2  -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Bacillus subtilis subsp. subtilis str. 168 chromosome, complete genome NC_000964.3
Genome_build: Bacillus amyloliquefaciens sB4140 sGCF_001587325.1sLQYO00000000sPRJNA270600
Genome_build: Bacillus subtilissB4146 sGCF_000830645.1sJXHR00000000s
Genome_build: Bacillus amyloliquefaciens sB425 sGCF_001587435.1sLQYP00000000sPRJNA270600
Genome_build: Bacillus subtilis HR3sB4417sGCF_001619535.1sASM161953v1s
Genome_build: Bacillus subtilissB4067 sGCF_000828495.1sJSXS00000000s
Genome_build: Bacillus subtilissB4072 sGCF_000830595.1sJXHO00000000s
Genome_build: Bacillus subtilissB4143 sGCF_000832195.1 sJXLQ00000000s
Supplementary_files_format_and_content: Tab delimited text file

organism: Bacillus amyloliquefaciens

source_name: Cell culture

growth_protocol: Bacterial cells were grown in M17 broth (containing 0,5% (w/v) glucose ) at 30°C

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton

treatment_protocol: Samples were followed in time during the sporulation process

value: Wild type

tag: growth stage


title: Bacillus amyloliquefaciens; B425_T8A

description:
B425_T8A
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 0, 104wk, biological replicate 2

description:
SIRC_0_104w_335_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_335_WT_DEDSTY141-1_(HT_MG-430_PM)_D05.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 0ppm, 104w


title: Bacillus amyloliquefaciens; B425_T4B

description:
B425_T4B
Processed_data_rpkm.txt


title: wt, RNAi104241, biological replicate 2 (Night-wt-B)

description: Gene expression profiling of parental control flies (Night-wt-B).


title: Bacillus amyloliquefaciens; B425_T6B

description:
B425_T6B
Processed_data_rpkm.txt


title: dSur -/-, elavGal4/RNAi104241, biological replicate 4 (Night-RNAi-D)

description: Gene expression profiling of dSur -/- flies (Night-RNAi-D).

source_name: Heads of 30 dSur-/- flies sampled at the time point Night ( ZT15, three hours in the dark phase)


title: Bacillus amyloliquefaciens; B425_T5B

description:
B425_T5B
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 0, 104wk, biological replicate 3

description:
SIRC_0_104w_345_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_345_WT_DEDSTY141-1_(HT_MG-430_PM)_D07.CEL


title: dSur -/-, elavGal4/RNAi104241, biological replicate 3 (Night-RNAi-C)

description: Gene expression profiling of dSur -/- flies (Night-RNAi-C).


title: Bacillus amyloliquefaciens; B425_T4A

description:
B425_T4A
Processed_data_rpkm.txt


title: dSur -/-, elavGal4/RNAi104241, biological replicate 2 (Night-RNAi-B)

description: Gene expression profiling of dSur -/- flies (Night-RNAi-B).


title: Mouse Lung, WT, Dose 0, 104wk, biological replicate 4

description:
SIRC_0_104w_373_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_373_WT_DEDSTY141-1_(HT_MG-430_PM)_D09.CEL


title: Mouse Lung, WT, Dose 120, 78wk, biological replicate 1

description:
SIRC_120_78w_421_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_421_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_H11.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 120ppm, 78w


title: dSur -/-, elavGal4/RNAi104241, biological replicate 1 (Night-RNAi-A)

description: Gene expression profiling of dSur -/- flies (Night-RNAi-A).


title: wt, RNAi104241, biological replicate 3 (Night-wt-C)

description: Gene expression profiling of parental control flies (Night-wt-C).


title: Mouse Lung, WT, Dose 120, 104wk, biological replicate 1

description:
SIRC_120_104w_429_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_429_WT_DEDSTY141-1_(HT_MG-430_PM)_D07.CEL


title: Mouse Lung, WT, Dose 120, 78wk, biological replicate 5

description:
SIRC_120_78w_425_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_425_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B07.CEL


title: Bacillus amyloliquefaciens; B425_T6A

description:
B425_T6A
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B425_T8B

description:
B425_T8B
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 120, 78wk, biological replicate 2

description:
SIRC_120_78w_422_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_422_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_A05.CEL


title: Mouse Lung, WT, Dose 0, 104wk, biological replicate 1

description:
SIRC_0_104w_326_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_326_Tu_WT_DEDSTY141-1_(HT_MG-430_PM)_C09.CEL


title: Mouse Lung, WT, Dose 120, 78wk, biological replicate 4

description:
SIRC_120_78w_424_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_424_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B05.CEL


title: Mouse Lung, WT, Dose 0, 78wk, biological replicate 2

description:
SIRC_0_78w_324_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_324_ACO10_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_G10.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 0ppm, 78w


title: Mouse Lung, WT, Dose 120, 78wk, biological replicate 3

description:
SIRC_120_78w_423_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_423_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_A07.CEL


title: Mouse Lung, WT, Dose 120, 52wk, biological replicate 4

description:
SIRC_120_52w_450_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_450_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_F02.CEL


title: Mouse Lung, WT, Dose 0, 78wk, biological replicate 1

description:
SIRC_0_78w_323_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_323_ACO10_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_G09.CEL


title: Mouse Lung, WT, Dose 120, 52wk, biological replicate 3

description:
SIRC_120_52w_439_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_439_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_F01.CEL


title: Bacillus amyloliquefaciens; B425_T2A

description:
B425_T2A
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B425_T3B

description:
B425_T3B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B425_T0A

description:
B425_T0A
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B425_T3A

description:
B425_T3A
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B425_T0B

description:
B425_T0B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B425_T2B

description:
B425_T2B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T8B

description:
B4140_T8B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T6B

description:
B4140_T6B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T6A

description:
B4140_T6A
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T5B

description:
B4140_T5B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T4B

description:
B4140_T4B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T3B

description:
B4140_T3B
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 0, 52wk, biological replicate 5

description:
SIRC_0_52w_320_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_320_ACO6_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_D10.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 0ppm, 52w


title: Mouse Lung, WT, Dose 120, 52wk, biological replicate 1

description:
SIRC_120_52w_418_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_418_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_F03.CEL


title: Mouse Lung, WT, Dose 0, 52wk, biological replicate 3

description:
SIRC_0_52w_318_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_318_ACO6_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_D08.CEL


title: Mouse Lung, WT, Dose 120, 26wk, biological replicate 1

description:
SIRC_120_26w_411_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_411_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_A02.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 120ppm, 26w


title: Mouse Lung, WT, Dose 0, 26wk, biological replicate 4

description:
SIRC_0_26w_315_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_315_ACO2_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B07.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 0ppm, 26w


title: Mouse Lung, WT, Dose 120, 26wk, biological replicate 5

description:
SIRC_120_26w_415_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_415_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B11.CEL


title: Bacillus amyloliquefaciens; B4140_T5A

description:
B4140_T5A
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 120, 26wk, biological replicate 2

description:
SIRC_120_26w_412_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_412_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B08.CEL


title: Bacillus amyloliquefaciens; B4140_T4A

description:
B4140_T4A
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 0, 26wk, biological replicate 3

description:
SIRC_0_26w_313_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_313_ACO2_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B06.CEL


title: Mouse Lung, WT, Dose 0, 52wk, biological replicate 4

description:
SIRC_0_52w_319_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_319_ACO6_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_D09.CEL


title: Mouse Lung, WT, Dose 0, 26wk, biological replicate 2

description:
SIRC_0_26w_312_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_312_ACO2_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B05.CEL


title: Bacillus amyloliquefaciens; B4140_T0B

description:
B4140_T0B
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T0A

description:
B4140_T0A
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 120, 26wk, biological replicate 4

description:
SIRC_120_26w_414_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_414_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B10.CEL


title: Mouse Lung, WT, Dose 0, 26wk, biological replicate 1

description:
SIRC_0_26w_311_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_311_ACO2_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_A01.CEL


title: Bacillus amyloliquefaciens; B4140_T8A

description:
B4140_T8A
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 120, 26wk, biological replicate 3

description:
SIRC_120_26w_413_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_413_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_B09.CEL


title: Bacillus amyloliquefaciens; B4140_T2A

description:
B4140_T2A
Processed_data_rpkm.txt


title: Bacillus amyloliquefaciens; B4140_T2B

description:
B4140_T2B
Processed_data_rpkm.txt


title: Mouse Lung, WT, Dose 0, 52wk, biological replicate 1

description:
SIRC_0_52w_316_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_316_ACO6_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_D06.CEL


title: Mouse Lung, WT, Dose 0, 52wk, biological replicate 2

description:
SIRC_0_52w_317_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_317_ACO6_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_D07.CEL


title: Minus_Si roots biological rep1, technical rep2

city: Seeland / OT Gatersleben

first: Martin

last: Becker

state: Lower Saxony

department: Plant Reproductive Biology

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

hyb_protocol: 10 μg of fragmented aRNA was added to a 300 μl hybridization cocktail also containing hybridization controls. 200 μl of the mixture was hybridized on GeneChips for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit; Affymetrix, Santa Clara, CA, USA) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Intensity values were summarized using Robust Multiarray Averaging (RMA) method. Normalization was performed by Quantile normalization approach. Statistics were done by applying unpaired T-Test. Multiplicity adjustment was conducted with Benjamini-Hochberg algorithm giving rise to corrected p-values.

organism: Oryza sativa Japonica Group

source_name: Rice adventitious roots segment between 2-6cm behind the root tip 28d in nutrient solution with 3mgL-1 SiOH4

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Rice US Gene 1.0 ST Array, Product Code 901992, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA with by a RIN number (Agilent 2100 Bioanalyzer, Agilent, Böblingen, Germany) of at least 9.5 containing spiked-in poly-A+ RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After secondstrand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix).

growth_protocol: Oryza sativa ssp. Japonica cv. Selenio seeds were surface-sterilized, germinated for 7d and transferred into nutrient solution. Plants were grown in the climate chamber (humidity: 70%; photosynthetic photon flux: 220 µmol m-2 s-1) at a 16 h light (25°C) and 8 h dark (20°C) regime. Nutrient solution was refreshed twice a week with a pH of 6. The pH was adjusted daily.

extract_protocol: Root section 2-6 cm from the root tip were taken from frozen stocks and ground using a swing mil prior to RNA extractions. Total RNA isolation and DNase I on-column digestion was performed via RNA Plant extraction kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. RNA preparations were quality-checked both via spectrophotometry (NanoDrop ND-1000, Peqlab, Erlangen, Germany) and via capillary electrophoresis in RNA Nano chips (Agilent 2100 Bioanalyzer, Agilent, Böblingen, Germany), as recommended by the manufacturers.

value: Root without root tip

tag: cultivar

value: Selenio

value: 28 days


title: Minus_Si roots biological rep4, technical rep2


title: Plus_Si roots biological rep4, technical rep2

source_name: Rice adventitious roots segment between 2-6cm behind the root tip 28d in nutrient solution with 30mgL-1 SiOH4


title: Minus_Si roots biological rep3, technical rep2


title: Bacillus amyloliquefaciens; B4140_T3A

description:
B4140_T3A
Processed_data_rpkm.txt


title: Minus_Si roots biological rep4, technical rep1


title: Minus_Si roots biological rep3, technical rep1


title: Plus_Si roots biological rep1, technical rep2


title: Minus_Si roots biological rep2, technical rep2


title: MFS_54T

type: genomic

city: Tokyo

first: Koichi

last: Ogura

address: 5-1-1 Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center

description: SAMPLE 39

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System

data_processing: The data were analyzed using GenomeStudio Methylation Module Softwarev.1.9.0

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Tumor tissue 54

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from fresh-frozen tissues tissues using the standard phenol-chloroform methodDNA was extracted from fresh-frozen tissues or FFPE tissues using the standard phenol-chloroform genomic DNA was extracted from fresh-frozen tissues or FFPE tissues using the standard phenol-chloroform method.

value: Female

value: Myxofibrosarcoma


title: Minus_Si roots biological rep2, technical rep1


title: Plus_Si roots biological rep3, technical rep2


title: Plus_Si roots biological rep2, technical rep2


title: MFS_55T

description: SAMPLE 40

source_name: Tumor tissue 55


title: MFS_56T

description: SAMPLE 41

source_name: Tumor tissue 56


title: K9

city: Boston

first: Robert

last: Husson

state: MA

address: 300 Longwood Ave.

department: Division of Infectious Diseases

institute: Boston Children's Hospital

data_processing:
Basecalls using Illumina bcl2fastq v2.15
Fastq files aligned to mycobaterium_tuberculosis h37_rv2 using STAR v2.3.1z4.  Index built using genomeSAindexNbases=4
Reads quantified to genes using subRead FeatureCounts v1.4.4.  Reads counted at exon level (-t exon arg) and reported gene name
Genes added to genome build: socA (we annotated as Rv000X1), socB (we annotated as Rv000X2) and mymT
Genome_build: M_tuberculosis h37_rv2
Supplementary_files_format_and_content: Sample-specific quantification files concatenated into raw count matrix using custom script.  Saved in tab-delimited (tsv) format

organism: Mycobacterium tuberculosis H37Rv

source_name: bacterial culture

extract_protocol:
total RNAs extracted using the Direct-zol  RNA MiniPrep kit (Zymo Research #R2052) according to the manufacturer's instructions.
2 µg of total RNAs were subjected to rRNA  depletion using the Ribo-Zero rRNA Removal kit (Illumina #MRZB12424). The reaction clean-up was performed using the RNeasy Mini kit (Qiagen #74104). The cDNA library was prepared using the NEBNext^® Ultra™ Directional RNA Library Prep kit for Illumina^® (New England Biolabs #E7420S), NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (New England Biolabs #E7335S)*, *NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 2) (New England Biolabs #E7500S) according to the manufacturer’s instructions.

tag: bacterial lysate

value: ΔpknD, T10 20 µM, TP 48h

tag: replicate # in experiment #

value: replicate #3 / experiment #K


title: MFS_50T

description: SAMPLE 35

source_name: Tumor tissue 50


title: MFS_53T

description: SAMPLE 38

source_name: Tumor tissue 53


title: MFS_51T

description: SAMPLE 36

source_name: Tumor tissue 51


title: Plus_Si roots biological rep3, technical rep1


title: MFS_49T

description: SAMPLE 34

source_name: Tumor tissue 49


title: Plus_Si roots biological rep2, technical rep1


title: Plus_Si roots biological rep1, technical rep1


title: K8

value: replicate #2 / experiment #K


title: Plus_Si roots biological rep4, technical rep1


title: Minus_Si roots biological rep1, technical rep1


title: MFS_48T

description: SAMPLE 33

source_name: Tumor tissue 48


title: K7

value: replicate #1 / experiment #K


title: K5

value: WT, T4 20 µM, TP 48h


title: MFS_46T

description: SAMPLE 31

source_name: Tumor tissue 46


title: MFS_47T

description: SAMPLE 32

source_name: Tumor tissue 47


title: K6


title: K3

value: WT, T10 20 µM, TP 48h


title: K4


title: K2


title: Mouse Lung, WT, Dose 120, 52wk, biological replicate 2

description:
SIRC_120_52w_420_WT
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_420_STY_WT_DEDSTY141-1_2016_(HT_MG-430_PM)_F05.CEL

source_name: Whole lung, C57Bl/6, WT, styrene inhalation, 120ppm, 52w

value: Wild Type (WT)

value: male


title: MFS_44T

description: SAMPLE 30

source_name: Tumor tissue 44


title: K18

value: ΔpknL, T4 20 µM, TP 48h


title: MFS_41T

description: SAMPLE 28

source_name: Tumor tissue 41


title: MFS_33T

description: SAMPLE 22

source_name: Tumor tissue 33


title: K17


title: K16


title: MFS_39T

description: SAMPLE 26

source_name: Tumor tissue 39


title: MFS_43T

description: SAMPLE 29

source_name: Tumor tissue 43


title: K15

value: ΔpknL, T10 20 µM, TP 48h


title: K14


title: MFS_30T

description: SAMPLE 19

source_name: Tumor tissue 30


title: MFS_40T

description: SAMPLE 27

source_name: Tumor tissue 40


title: MFS_36T

description: SAMPLE 24

source_name: Tumor tissue 36


title: MFS_32T

description: SAMPLE 21

source_name: Tumor tissue 32


title: MFS_29T

description: SAMPLE 18

source_name: Tumor tissue 29


title: Adipocyte yes OVCAR5 3

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

description:
Subcutaneous, primary
Adipo_Yes_3

data_processing:
NextSeq read sequences were cleaned using Trimmomatic version 0.32 with the paramaters “2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17” to remove adapter sequences and perform quality trimming.
Custom perl scripts along with FASTX-Toolkit version 0.0.13.2 with the following parameters, “-l 17 -v -M 1 -i “ was also used to look for partial adapters within the read.
FASTX-Toolkit was then used to reverse complement the reads.
The resulting reads were mapped against GRCh38.p5 using TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100”. Tophat uses Bowtie, which is based on the Burrows-Wheeler transform algorithm, for sequence alignment and allows for mapping across exon junctions
Read counts for each gene were created using custom perl scripts and Gencode v24 as the annotation
Custom perl scripts were used for estimation of transcript abundances based on RPKM.
Initial differential expression analysis was carried out using the DESeq2 package (version 1.12.4) in R/Bioconductor (R version 3.3.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include counts and RPKM values for each sample

source_name: SGBS adipocytes

growth_protocol: Simpson-Golabi-Behman syndrome (SGBS) human adipocyte cells were (provided by Dr. Martin Wabitsch) differentiated as described in Wabitsch M, Brenner R, Melzner I, Braun M, Möller P, Heinze E, et al. Characterization of a human preadipocyte cell strain with high capacity for adipose differentiation. International Journal of Obesity 2001;25:8. OVCAR5 (high-grade serous ovarian) cancer cells were maintained in media supplemented with 10% fetal bovine serum (FBS), antibiotic-antimycotic, 25mM HEPES, MEM vitamins, and MEM nonessential amino acids.

extract_protocol:
On day 4, RNA was harvested from the adipocytes using the RNAEasy kit (Qiagen)
RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina #RS-122-2101) according to manufacter's protocol.
Poly-A tail mRNA library

treatment_protocol: In triplicate, we indirectly cocultured OVCAR5-RFP cells using a 0.45 micron Boyden chamber with or without adipocytes seeded in the bottom chamber for 4 days.

tag: cell type

value: SGBS adipocytes

tag: agent


title: MFS_37T

description: SAMPLE 25

source_name: Tumor tissue 37

tag: gender


title: Adipocyte no OVCAR5 3

description:
Subcutaneous, primary
Adipo_No_3


title: K13

source_name: bacterial culture


title: K12

value: ΔpknD, T4 20 µM, TP 48h


title: Adipocyte yes OVCAR5 1

description:
Subcutaneous, primary
Adipo_Yes_1


title: Adipocyte no OVCAR5 2

description:
Subcutaneous, primary
Adipo_No_2


title: Adipocyte yes OVCAR5 2

description:
Subcutaneous, primary
Adipo_Yes_2


title: Adipocyte no OVCAR5 1

description:
Subcutaneous, primary
Adipo_No_1


title: MFS_52T

description: SAMPLE 37

source_name: Tumor tissue 52


title: MFS_34T

description: SAMPLE 23

source_name: Tumor tissue 34


title: K11


title: K1


title: K10


title: I87

value: T4 20 µM, TP 48h

value: replicate #3 / experiment #I


title: Bacillus subtilis; T53

description:
T53
Processed_data_rpkm.txt

organism: Bacillus subtilis

source_name: Cell culture

tag: strain

tag: genotype

value: Wild type


title: MFS_27T

description: SAMPLE 16

source_name: Tumor tissue 27


title: Bacillus subtilis; T54

description:
T54
Processed_data_rpkm.txt


title: Bacillus subtilis; T56

description:
T56
Processed_data_rpkm.txt


title: MFS_25T

description: SAMPLE 14

source_name: Tumor tissue 25

value: Female


title: I85

tag: treatment

value: replicate #1 / experiment #I


title: Bacillus subtilis; T51

description:
T51
Processed_data_rpkm.txt


title: MFS_13T

description: SAMPLE 9

source_name: Tumor tissue 13

value: Myxofibrosarcoma


title: MFS_19T

description: SAMPLE 11

source_name: Tumor tissue 19


title: MFS_21T

description: SAMPLE 12

source_name: Tumor tissue 21


title: MFS_18T

description: SAMPLE 10

source_name: Tumor tissue 18


title: MFS_26T

description: SAMPLE 15

source_name: Tumor tissue 26


title: MFS_22T

description: SAMPLE 13

source_name: Tumor tissue 22


title: MFS_11T

description: SAMPLE 8

source_name: Tumor tissue 11


title: Bacillus subtilis; T55

description:
T55
Processed_data_rpkm.txt


title: I86

value: replicate #2 / experiment #I


title: I75


title: Bacillus subtilis; T52

description:
T52
Processed_data_rpkm.txt


title: I73


title: Bacillus subtilis; T50

description:
T50
Processed_data_rpkm.txt


title: Bacillus subtilis; T49

description:
T49
Processed_data_rpkm.txt


title: Bacillus subtilis; T48

description:
T48
Processed_data_rpkm.txt


title: MFS_07T

description: SAMPLE 6

source_name: Tumor tissue 07


title: MFS_31T

description: SAMPLE 20

source_name: Tumor tissue 31


title: Bacillus subtilis; T46

description:
T46
Processed_data_rpkm.txt


title: MFS_28T

description: SAMPLE 17

source_name: Tumor tissue 28


title: MFS_05T

description: SAMPLE 4

source_name: Tumor tissue 05


title: I74

source_name: bacterial culture


title: Bacillus subtilis; T47

description:
T47
Processed_data_rpkm.txt


title: MFS_01T

description: SAMPLE 1

source_name: Tumor tissue 01


title: I62

value: T4 20 µM, TP 24h


title: I51


title: Bacillus subtilis; T43

description:
T43
Processed_data_rpkm.txt


title: I63


title: I61


title: Bacillus subtilis; T45

description:
T45
Processed_data_rpkm.txt


title: MFS_06T

description: SAMPLE 5

source_name: Tumor tissue 06


title: I50


title: Bacillus subtilis; T41

description:
T41
Processed_data_rpkm.txt

source_name: Cell culture


title: Bacillus subtilis; T40

description:
T40
Processed_data_rpkm.txt


title: I61_failed

description: Sample failed in sequencing, was rerun


title: Bacillus subtilis; T38

description:
T38
Processed_data_rpkm.txt


title: I49


title: Bacillus subtilis; T39

description:
T39
Processed_data_rpkm.txt


title: Bacillus subtilis; T42

description:
T42
Processed_data_rpkm.txt


title: I37

value: T4 20 µM, TP 12h


title: I39


title: MFS_04T

description: SAMPLE 3

source_name: Tumor tissue 04


title: I38


title: MFS_03T

description: SAMPLE 2

source_name: Tumor tissue 03


title: Bacillus subtilis; T44

description:
T44
Processed_data_rpkm.txt


title: I26


title: Bacillus subtilis; T36

description:
T36
Processed_data_rpkm.txt


title: I27


title: MFS_08T

description: SAMPLE 7

source_name: Tumor tissue 08


title: I25


title: Bacillus subtilis; T34

description:
T34
Processed_data_rpkm.txt


title: I13

value: DMSO 0.4%, TP 0h

value: replicate #4 / experiment #I


title: I14

value: replicate #5 / experiment #I


title: Bacillus subtilis; T35

description:
T35
Processed_data_rpkm.txt


title: I15

value: replicate #6 / experiment #I


title: Bacillus subtilis; T33

description:
T33
Processed_data_rpkm.txt


title: I12


title: I11


title: Bacillus subtilis; T30

description:
T30
Processed_data_rpkm.txt


title: Bacillus subtilis; T32

description:
T32
Processed_data_rpkm.txt


title: Bacillus subtilis; T31

description:
T31
Processed_data_rpkm.txt


title: Bacillus subtilis; T37

description:
T37
Processed_data_rpkm.txt


title: H87

value: replicate #3 / experiment #H


title: I10


title: Bacillus subtilis; T29

description:
T29
Processed_data_rpkm.txt


title: Bacillus subtilis; T28

description:
T28
Processed_data_rpkm.txt


title: H86

value: replicate #2 / experiment #H


title: Bacillus subtilis; T27

description:
T27
Processed_data_rpkm.txt


title: H85

value: replicate #1 / experiment #H


title: H75


title: Bacillus subtilis; T26

description:
T26
Processed_data_rpkm.txt


title: H74


title: Bacillus subtilis; T25

description:
T25
Processed_data_rpkm.txt


title: H73


title: Jurkat at sim ug, rep6

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

hyb_protocol: DNA targets were hybridized for 17h at 45°C on GeneChip Human Transcriptome Arrays 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol (Affymetrix GeneChip Wash, Stain and Scan Kit, 900720).

scan_protocol: Subsequently, the GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: For microarray data analysis, the Affymetrix Expression Console and Transcriptome Analysis Console was used. The robust multi-array (RMA) averaging method was applied for background correction, quantile normalization, and probe summarization.

source_name: Jurkat cells (ATCC Clone E6-1, TIB152™)

label_protocol: The fragmented and biotinylated DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol (Affymetrix GeneChip® WT PLUS Reagent Kit, 902280) from 100 ng total RNA starting material and 5.5 µg cDNA intermediate product.

growth_protocol: Jurkat T cells were cultivated in RPMI 1640 medium, supplemented with 10% fetal bovine serum, 2 mM glutamine and 100 U/ml penicillin as well as 100 µg/ml streptomycin. Cells were cultured with a density of 0.2x106 cells/ml and medium exchange was performed every 48 hours.

extract_protocol: Jurkat cells were lysed with Trizol LS and total RNA was extracted following the Rneasy Midi Kit protocol (Qiagen).

treatment_protocol: Human Jurkat T cells were exposed for 5 min to simulated microgravity and hypergravity (9g)  during ground based facility experiments.

tag: cell line

value: Jurkat T cells


title: Jurkat at 9g, rep1


title: Bacillus subtilis; T23

description:
T23
Processed_data_rpkm.txt


title: Jurkat at 9g, rep4


title: Jurkat at 1g  ground control  rep5


title: Jurkat at 1g  ground control  rep4


title: H63


title: Jurkat at 1g  ground control  rep6


title: Jurkat at sim ug, rep7


title: Jurkat at sim ug, rep5


title: H62


title: Jurkat at sim ug, rep2


title: Jurkat at 1g ground control rep1


title: Bacillus subtilis; T22

description:
T22
Processed_data_rpkm.txt


title: Jurkat at sim ug, rep4


title: Jurkat at 1g  ground control  rep3


title: Jurkat at 1g  ground control  rep2


title: Jurkat at sim ug, rep3


title: Bacillus subtilis; T24

description:
T24
Processed_data_rpkm.txt


title: Jurkat at 9g, rep2


title: Jurkat at 9g, rep5


title: Jurkat at 9g,  rep3


title: Jurkat at 1g baseline, rep6


title: Jurkat at 1g baseline, rep5


title: Bacillus subtilis; T21

description:
T21
Processed_data_rpkm.txt


title: H61


title: Bacillus subtilis; T20

description:
T20
Processed_data_rpkm.txt


title: Bacillus subtilis; T19

description:
T19
Processed_data_rpkm.txt


title: Bacillus subtilis; T18

description:
T18
Processed_data_rpkm.txt


title: Bacillus subtilis; T17

description:
T17
Processed_data_rpkm.txt


title: H49


title: H50


title: H39


title: H38


title: Bacillus subtilis; T16

description:
T16
Processed_data_rpkm.txt


title: H37


title: Bacillus subtilis; T14

description:
T14
Processed_data_rpkm.txt


title: H27


title: AT2_H3K4me3

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

library_source: genomic

data_processing:
Illumina v1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using gSNAP -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap
Mapped reads then were assessed for peaks relative to the input controls using Macs2 (version 2.1.0.20150420) call peak function.
Peakfold enrichment was calculated using Macs2, using a sliding window across the genome and assessing read counts relative to expected background.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files

source_name: AT2 cells

extract_protocol:
AT2 cells (2 × 107) were isolated from 10- to 12-wk-old C57BL/6 mice. Active Motif Epigenetic Services performed ChIP assays. Cells fixed with 1% formaldehyde for 11 min were quenched with 0.25 M glycine and then were swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300–500 bp. Input and immunoprecipitated DNAs were treated with RNase, proteinase K, and heat for de-crosslinking, followed by ethanol precipi- tation.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: age

value: 10-12 weeks

value: Alveolar type II (AT2) cells

tag: chip antibody

value: anti-H3K4me3 (Abcam, ab8580)


title: AT2_ETV5

value: ETV5 (Proteintech, 13011-1-AP)


title: AT2_Input

value: none (Input)


title: Jurkat at 1g baseline, rep4


title: Bacillus subtilis; T15

description:
T15
Processed_data_rpkm.txt

value: Wild type


title: H26


title: Bacillus subtilis; T12

description:
T12
Processed_data_rpkm.txt


title: Jurkat at 1g baseline rep7


title: Jurkat at 1g baseline, rep3


title: Jurkat at 1g baseline,rep2


title: Jurkat at 1g baseline, rep1


title: H25


title: Bacillus subtilis; T11

description:
T11
Processed_data_rpkm.txt


title: H14

value: replicate #5 / experiment #H


title: H13

value: replicate #4 / experiment #H


title: Bacillus subtilis; T09

description:
T09
Processed_data_rpkm.txt


title: H12


title: Bacillus subtilis; T08

description:
T08
Processed_data_rpkm.txt


title: Bacillus subtilis; T07

description:
T07
Processed_data_rpkm.txt


title: Bacillus subtilis; T13

description:
T13
Processed_data_rpkm.txt


title: F9

value: replicate #3 / experiment #F


title: H11

value: DMSO 0.4%, TP 0h


title: H51


title: Bacillus subtilis; T06

description:
T06
Processed_data_rpkm.txt


title: H10


title: Bacillus subtilis; T05

description:
T05
Processed_data_rpkm.txt


title: F7

value: replicate #1 / experiment #F


title: F8

value: replicate #2 / experiment #F


title: Bacillus subtilis; T02

description:
T02
Processed_data_rpkm.txt


title: F63

value: T4 20 µM, TP 48h


title: H15

value: replicate #6 / experiment #H


title: Bacillus subtilis; T04

description:
T04
Processed_data_rpkm.txt


title: Bacillus subtilis; T01

description:
T01
Processed_data_rpkm.txt


title: Bacillus subtilis; T03

description:
T03
Processed_data_rpkm.txt


title: Bacillus subtilis; T10

description:
T10
Processed_data_rpkm.txt


title: F62


title: Bacillus subtilis; HR3_T9B

description:
HR3_T9B
Processed_data_rpkm.txt


title: Bacillus subtilis; HR3_T9A

description:
HR3_T9A
Processed_data_rpkm.txt


title: F54


title: Bacillus subtilis; HR3_T7B

description:
HR3_T7B
Processed_data_rpkm.txt


title: F52


title: F53


title: Bacillus subtilis; HR3_T6B

description:
HR3_T6B
Processed_data_rpkm.txt


title: Bacillus subtilis; HR3_T7A

description:
HR3_T7A
Processed_data_rpkm.txt


title: F45

value: T4 20 µM, TP 24h


title: F44


title: control siRNA(cy3) vs siADSL(cy5) biological replicate 2 dyeswap

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: control siRNA(cy3) vs siADSL(cy5) biological eplicate 2 dyeswap

hyb_protocol: After washing in GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2505C.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: HEC1B cells transfected with siADSL

label_protocol: Differentially labeled 825 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4 × 44KWhole Human Genome Oligo Microarray ver. 2 (G4845A) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.

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

treatment_protocol: HEC1B cells seeded at 20% confluence were transfected with ADSL-targeting siRNA or non-targeting control siRNA (Thermo Fisher Scientific) using Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific) at a final concentration of 50 nM.

source_name: HEC1B cells transfected with control siRNA

value: ASS1 wild-type


title: Bacillus subtilis; HR3_T5B

description:
HR3_T5B
Processed_data_rpkm.txt


title: control siRNA(cy3) vs siADSL(cy5) biological replicate 1 dyeswap


title: F36


title: F43


title: Bacillus subtilis; HR3_T5A

description:
HR3_T5A
Processed_data_rpkm.txt


title: F35


title: Bacillus subtilis; HR3_T4B

description:
HR3_T4B
Processed_data_rpkm.txt


title: F34


title: F61


title: Bacillus subtilis; HR3_T4A

description:
HR3_T4A
Processed_data_rpkm.txt


title: F27

value: T4 20 µM, TP 12h


title: Bacillus subtilis; HR3_T6A

description:
HR3_T6A
Processed_data_rpkm.txt


title: Bacillus subtilis; HR3_T2A

description:
HR3_T2A
Processed_data_rpkm.txt


title: F26


title: F25


title: F18


title: Bacillus subtilis; B4146_T7B

description:
B4146_T7B
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T7A

description:
B4146_T7A
Processed_data_rpkm.txt


title: F16


title: D6-C1-8h

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description: DC cell culture in different time point

hyb_protocol: Hybridization was carried  out in a water bath at 42°C for 18 to 24 hours and  the arrays were then washed

scan_protocol: scanned on a GenePix  scanner Pro 4.0 (Axon, Sunnyvale, CA) with a variable  photomultiplier tube to obtain optimized signal intensities  with minimum (<1% spots) intensity saturation.

data_processing: The raw data set was filtered according to a standard  procedure to exclude spots below a minimum intensity  that arbitrarily was set to an intensity parameter of 200 for both channels

label_protocol: Total RNA (3 μg) from the  DCs was amplified into anti-sense RNA (aRNA). While  total RNA from PBMCs pooled from the 6 normal  donors was extracted and amplified into aRNA to serve  as the reference. Pooled reference and test aRNA were  isolated and amplified using identical conditions and the  same amplification/hybridization procedures to avoid  possible interexperimental biases. Both reference and  test aRNA were directly labeled using ULS aRNA Fluorescent  Labeling kit (Kreatech, Amsterdam, Netherlands)  with Cy3 for reference and Cy5 for test samples.

growth_protocol: The elutriated monocytes from each donor were suspended  at 6.7 × 10^6/mL with RPMI 1640 (Invitrogen,  Carlsbad, CA) supplemented with 10% fetal calf serum  (FSC) (Invitrogen), 2 mM L-glutamine (Invitrogen), 1%  nonessential amino acids (Invitrogen), 1% pyruvate  (Invitrogen), 100 units/mL penicillin/streptomycin (Invitrogen),  and 50 μM 2-mercaptoethanol (Sigma, St  Louis, MO). A total of 10 mL of monocyte suspension  was cultured in T25 culture flasks (Nalge Nunc International,  Rochester, NY) overnight in a humidified incubator  with 5% CO2 at 37°C. On Day 1, 2000 IU/mL  human IL-4 (R&D Systems) and 2000 IU/mL GM-CSF  (R&D Systems) were added to the culture. On Day 3,  an additional 2000 IU/mL IL-4 and GM-CSF were  added.

extract_protocol: Total RNA was extracted from the DCs using Trizol  (Invitrogen, Carlsbad, CA). RNA integrity was assessed  using an Agilent 2100 Bioanalyzer (Agilent Technologies,  Waldbronn, Germany).

treatment_protocol: To induce DC maturation, on day 4, 100 ng/mL  LPS (Sigma) and 1000 IU/mL IFN-g (R&D Systems)  were added. The DCs were harvested at 0, 4, 8 and 24  hours (h) after the addition of LPS and IFN-g. To  remove the adherent DCs, 2 mM EDTA-PBS was added  to each flask on ice. The harvested cells were pelleted,  washed twice with HBSS, and resuspended in RPMI  1640. The total number of cells harvested and their viability  was measured microscopically after adding Trypan  Blue.

value: immature DCs (iDCs)

value: cultured with LPS and IFN-g

tag: time

source_name: PBMC

tag: reference

value: PBMCs pooled from the 6 normal donors


title: Bacillus subtilis; B4146_T5B

description:
B4146_T5B
Processed_data_rpkm.txt


title: D6-C1-0h

description: DC cell culture in different time point

value: control


title: Bacillus subtilis; HR3_T2B

description:
HR3_T2B
Processed_data_rpkm.txt


title: D6-C1-24h

description: DC cell culture in different time point


title: D6-C1-4h

description: DC cell culture in different time point


title: Bacillus subtilis; HR3_T0B

description:
HR3_T0B
Processed_data_rpkm.txt


title: D4-C1-24h

description: DC cell culture in different time point


title: D5-C1-0h

description: DC cell culture in different time point


title: D5-C1-24h

description: DC cell culture in different time point


title: siADSL(cy3) vs control siRNA(cy5) biological replicate 1


title: D5-C1-4h

description: DC cell culture in different time point


title: D5-C1-8h

description: DC cell culture in different time point


title: Bacillus subtilis; HR3_T0A

description:
HR3_T0A
Processed_data_rpkm.txt


title: D4-C1-4h

description: DC cell culture in different time point


title: D4-C1-8h

description: DC cell culture in different time point


title: D4-C1-0h

description: DC cell culture in different time point


title: Bacillus subtilis; B4146_T5A

description:
B4146_T5A
Processed_data_rpkm.txt


title: siADSL(cy3) vs control siRNA(cy5) biological replicate 2


title: Bacillus subtilis; B4146_T4B

description:
B4146_T4B
Processed_data_rpkm.txt


title: F17


title: D3-C1-24h

description: DC cell culture in different time point


title: D3-C1-8h

description: DC cell culture in different time point


title: Bacillus subtilis; B4146_T4A

description:
B4146_T4A
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T3B

description:
B4146_T3B
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T2B

description:
B4146_T2B
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T3A

description:
B4146_T3A
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T2A

description:
B4146_T2A
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T0B

description:
B4146_T0B
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T1A

description:
B4146_T1A
Processed_data_rpkm.txt


title: Bacillus subtilis; B4146_T1B

description:
B4146_T1B
Processed_data_rpkm.txt


title: Macrophages

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Macrophages

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Following cells were deferentiated to macrophages and oligodendrocytes, mRNA was isolated and gene expressions were tested.

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: No stimulation was added.

tag: cell

value: Macrophages


title: Bacillus subtilis; B4146_T0A

description:
B4146_T0A
Processed_data_rpkm.txt

value: Wild type

tag: growth stage


title: Oligodendrocytes

source_name: Oligodendrocytes

value: Oligodendrocytes


title: D1-C1-24h

description: DC cell culture in different time point


title: D2-C1-0h

description: DC cell culture in different time point


title: D3-C1-4h

description: DC cell culture in different time point


title: MeDIP_seq_WIS_female_3

status: Public on Mar 07 2018

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: mapped reads (RN6) were binned across 150bp windows.

data_processing:
Reads mapped to RN6 rat genome build in the cloud using TMAP software
Data binned into 150bp windows across the genome
data normalised by read count
antibody enriched datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: Rn6

organism: Rattus norvegicus

source_name: Wistar Rat liver

extract_protocol:
Sheared gDNA was enriched using antibodies of choice. prior to enrichment through magnetic IgG beads . Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 18 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

tag: tissue

value: liver

value: female

value: Wistar

tag: antibody

value: Anti 5mc - Eurogentec BI-MECY-0100


title: D2-C1-8h

description: DC cell culture in different time point


title: hMeDIP_seq_WIS_female_5

value: Anti 5-hmC - Active Motif (cat# 39769)


title: hMeDIP_seq_WIS_female_2


title: Input_seq_WIS_female_2

value: None (input)


title: Input_seq_WIS_female_1


title: hMeDIP_seq_WIS_female_4


title: MeDIP_seq_WIS_female_1


title: hMeDIP_seq_WIS_female_1


title: MeDIP_seq_WIS_female_5


title: MeDIP_seq_WIS_female_4


title: D2-C1-4h

description: DC cell culture in different time point


title: D3-C1-0h

description: DC cell culture in different time point


title: D1-C1-4h

description: DC cell culture in different time point


title: D2-C1-24h

description: DC cell culture in different time point


title: hMeDIP_seq_WIS_male_3

value: male


title: hMeDIP_seq_WIS_male_4


title: hMeDIP_seq_WIS_male_2


title: hMeDIP_seq_WIS_male_1


title: D1-C1-8h

description: DC cell culture in different time point


title: MeDIP_seq_WIS_female_2


title: hMeDIP_seq_WIS_female_3


title: MeDIP_seq_WIS_male_5


title: MeDIP_seq_WIS_male_4


title: hMeDIP_seq_WIS_male_5


title: MeDIP_seq_WIS_male_3


title: MeDIP_seq_WIS_male_2


title: MeDIP_seq_WIS_male_1


title: Input_seq_WIS_male_1


title: hMeDIP_seq_SD_female_3

source_name: Sprague Dawley Rat liver

value: Sprague Dawley


title: hMeDIP_seq_SD_female_5


title: hMeDIP_seq_SD_female_4


title: hMeDIP_seq_SD_female_2


title: MeDIP_seq_SD_female_5


title: MeDIP_seq_SD_female_3


title: hMeDIP_seq_SD_female_1


title: MeDIP_seq_SD_female_4


title: MeDIP_seq_SD_female_1


title: Input_seq_SD_female_2


title: Input_seq_SD_female_1


title: hMeDIP_seq_SD_male_2


title: hMeDIP_seq_SD_male_5


title: hMeDIP_seq_SD_male_1


title: hMeDIP_seq_SD_male_4


title: MeDIP_seq_SD_male_3


title: MeDIP_seq_SD_male_1


title: MeDIP_seq_SD_male_2


title: Input_seq_WIS_male_2


title: Input_seq_SD_male_1


title: MeDIP_seq_SD_female_2


title: hMeDIP_seq_SD_male_3


title: D1-C1-0h

description: DC cell culture in different time point


title: MeDIP_seq_SD_male_4


title: MeDIP_seq_SD_male_5


title: HUVEC 2

city: Harbin

first: SIMING

last: YU

address: No.194 XueFu Road

institute: Department of Pharmacology,Harbin Medical University,

description: The cell lines were purchased from the American Type Culture Collection

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

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

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: Human Umbilical Vein Endothelial Cells

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: The cells weremaintained in RPMI-1640 Medium (SH30027.01, Hyclone, Utah, USA), supplemented with 10% fetal bovine serum (FBS) and 1% Antibiotic-Antimycotic solution (Beyotime, China)

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: The cells were starved overnight, then we added the PEP06 and glucose for 24 h.

value: HUVEC

tag: disease state

value: normal cells


title: HUVEC 4


title: HUVEC 3

value: treated with PEP06


title: HUVEC 1


title: Input_seq_SD_male_2


title: SW620+1-2

source_name: colorectal cells

value: colorectal tumor cells


title: SW620C1-2


title: SW620C1-1


title: HCT116+2


title: HCT116C1


title: ESC_NKO_3

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

data_processing:
Standard Illumina Sequencing Pipeline
Reads were trimmed using trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the Illumina adapter sequence.
Reads were mapped to the mouse genome assembly using TopHat guided by the gene models from Ensembl.
BAM files were imported to Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Read counts per transcript were calculated using the RNA-Seq quantitation pipeline using non-directional counts. Raw read counts per transcript were calculated using the RNA-seq quantitation pipeline on the Ensembl v70 gene set using non-directional counts.
Differential analysis of gene expression was performed using the default settings in DESeq2 (Love et al., 2014) without independent filtering of the results. Differentially expressed genes were called at padj < 0.05 and log2 fold change above 1.5 or below −1.5.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Matrix of normalised expression values by sample/gene

source_name: embryonic stem cells

growth_protocol: E14Tg2a (129P2/OlaHsd) and RCNβH-B(t) (E14Tg2a-derived Nanog–/–, passages 20-30) ESCs were cultured on gelatin-coated surfaces in standard ESC media (DMEM supplemented with 15% FBS, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol, 0.1mM non-essential amino acids, 2mM glutamax and 1000 U/ml LIF), and 25µg/ml hygromycin was added during RCNβH-B(t) ESC expansion to select for Nanog–/– cells. Embryo-derived 129S2 (Brons et al. 2007) EpiSC were cultured on fibronectin (10µg/ml) in N2B27 media supplemented with 20ng/ml Activin A and 12ng/ml bFGF.

extract_protocol:
Total RNA was purified using an RNeasy kit (Qiagen). Indexed mRNA-Seq libraries were constructed from 500ng total  RNA using the TruSeq RNA Library Prep Kit v2 (Illumina).
Library fragment size and concentration was determined using an Agilent Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina HiSeq as 50bp or 100bp single-end libraries at the Babraham Institute Sequencing Facility.

tag: cell type

value: embryonic stem cells

value: NANOG knockout


title: ESC_NKO_2


title: ESC_NKO_1


title: EpiSC_4

source_name: epiblast-derived stem cells

value: epiblast-derived stem cells


title: EpiSC_3


title: HCT116C2

value: control


title: SW620+1-1


title: HCT116+1


title: EpiSC_1


title: EpiSC_2


title: ESC_WT_2

value: wild type


title: ESC_WT_1


title: t_HFD_wt_2

city: Cologne

first: thomas

last: wunderlich

state: NRW

address: Gleueler Str. 50

institute: MPI for Metabolism Research

description: Gene expression data from colitis-associated colon tumour from 17 weeks old IL-6RaFl/ctrl mouse

hyb_protocol: RNA was processed to be hybridized to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) according to the manufacture`s instruction.

scan_protocol: scanning was performed on a Gene Chip scanner 3000 7G affimetrix

data_processing: Affymetrix Powertools and the robust multiarray average method were used for background correction, quantile normalization and summerization of the raw intensity values. R software (version 2.13.1) along with the Bioconducter software package were used for robust multiarray average method, statistical analysis (Student`s t-test), calculation of the change in intensity and illustration. Genes were considered significantly deregulated when they had difference in expresion with a P value of <0.025. Genes with a fold change of <1.5 were removed from the data.

source_name: Tumour from control, biological rep 2

label_protocol: Biotin labeled cDNA was synthezied with a Gene Chip whole Transcript Sense Target Labeling Assay according to the manufacture s guidelines (affimetrix)

growth_protocol: Mice were housed in groups of three to five in single ventilated cages at 22-24 °C

extract_protocol: RNA was isolated with an Rneasy Kit from Qiagen according to the manufacture`s instruction.

treatment_protocol: Mice were fed a high fat diet from weaning on. 8 weeks old animals were i.p. injected with 10 mg/kg body weight azoxymethane. 4 days later animals were exposed to 1,5% dextrane sodium sulfate (MW=36000-50000) in the drinking water for 5 days and then provided with normal drinking water until the end of the experiment with 17 weeks of age.

tag: background strain

value: colitis-associated colon tumor

value: 17 weeks old


title: CD4T_Ezh2 [RNA-seq]

city: New York

first: Marc-Werner

last: Dobenecker

state: New York

address: 1230 York Ave, Box 301

institute: The Rockefeller University

description: mRNA-seq

data_processing:
Illumina Hiseq 2000
Illumina bcl2fastq
Bowtie v 0.12.7
Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq samples were quantified via cuffdiff
Supplementary_files_format_and_content: ChIP-seq samples were binned in 25 bp bins via igvtools count, coverage in regions +/- 3kb of  transcriptional start site was calculated, normalized via quantile normalization

source_name: naïve CD4+ T cell

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Goldberg et al., 2010; Lee et al., 2006). Briefly, 1x107 cells were cross-linked with 0.5% formaldehyde at room temperature for 10 min. Chromatin was sonicated to 300-500 bp in RIPA buffer with 0.3 M NaCl. 5-10 ug antibodies were pre-incubated with Dynabead Protein A/G (Invitrogen) for at least 8 hrs before incubating with sonicated chromatin overnight. After overnight incubation, beads were washed in modified RIPA wash buffer (100 mM LiCl) and 1x in TE. After overnight cross-link reversal at 65°C, RNase digestion and Proteinase K digestion, ChIP DNA and input DNA were purified using the Quiaquick PCR purification kit. For regular ChIP and for validation of ChIP-Seq, ChIP DNA was analyzed via qPCR using SYBR Green PCR Master Mix and the LightCycler 480. Primer sequences are available upon request.
For ChIP-Seq, 30 µl of ChIP DNA were used to generate blunt-ended DNA using reagents supplied with the Epicenter DNA EndRepair kit (Epicenter Biotechnologies) according to the manufacturer’s instructions. The end-repaired DNA was purified using the Quiaquick PCR purification kit. Using Klenow Fragment (3` to 5` exo-, NEB) “A” bases were added to the DNA. The DNA was purified using the MinElute kit. T4 DNA ligase (NEB) was used for ligation of Illumina/Solexa adapters to the DNA fragments. The adaptor-ligated DNA was purified with the MinElute kit. The DNA fragments were subjected to 18 cycles of PCR using the Illumina/Solexa primers 1.0 and 2.0 to generate the ChIP-Seq libraries. The ChIP-Seq libraries were purified with the MinElute kit.   Samples were sequenced on the Illumina Hiseq2000 platform for 50 cycles, and raw sequencing data were processed using the CASAVA_v1.8.2 software to generating fastq files. Sequencing reads were aligned to the mouse genome (mm9) using Bowtie v0.12.7 (Langmead et al., 2009). Reads were kept if they aligned with 2 errors or less and did not align to more than one location in the genome. A 25 bp density coverage map was created by extending each read for 100 bp to account for average library fragment length and mapping the number of reads per 25 bp bin using igvtools (Thorvaldsdottir et al., 2013). Values in each sample were normalized to fpkm values by calculating the fraction of mapped reads per bin in one million total reads.   For comparative analysis of promoter regions, the number of aligned reads in the area surrounding the transcriptional start site (+/- 3kb) of each gene was used.

value: lymph node purified CD4 T cells


title: t_HFD_wt_3

source_name: Tumour from control, biological rep 3

tag: gender

value: female


title: t_HFD_wt_1

source_name: Tumour from control, biological rep 1


title: t_HFD_ko_1

description: Gene expression data from colitis-associated colon tumour from 17 weeks old IL-6Radelta/KO mouse

source_name: Tumour from IL-6Ra deficent, biological rep 1


title: t_HFD_ko_3

source_name: Tumour from IL-6Ra deficent, biological rep 3


title: CD4T_Ezh1 [RNA-seq]

description: mRNA-seq

tag: strain


title: CD4T_WT [RNA-seq]

description: mRNA-seq

tag: genotype

value: WT


title: CD4T_WT [ChIP-seq]

description: H3K27me3 ChIP-seq


title: CD4T_Ezh1 [ChIP-seq]

description: H3K27me3 ChIP-seq


title: t_HFD_ko_2

source_name: Tumour from IL-6Ra deficent, biological rep 2


title: CD4T_Ezh12 [ChIP-seq]

description: H3K27me3 ChIP-seq


title: ESC_WT_3


title: CD4T_Ezh2 [ChIP-seq]

description: H3K27me3 ChIP-seq


title: CD4T_Ezh12 [RNA-seq]

description: mRNA-seq


title: RNASEQ_TOT_RNA_DOX_DAY7_rep1

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

description: ribodepleted RNA

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (ChIPseq, ATAC-seq): BWA
alignment (RNAseq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: RNA-seq was performed in RMG-1 clone in ARID1A-KD condition  (doxyclicline inducible KD [7 days])

growth_protocol: RMG-1 cells were maintained in DMEM/F12 50/50 medium (Corning) supplemented with 10% (v/v) of TET-free fetal bovine serum (Clontech) or super calf serum (GEMcell) and 2 mM of L-glutamine (Corning).

extract_protocol: NEBNext Ultra Directional Strand specific RNA-Seq  Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: Doxycicline (2ug/ml, 72 hours) was used to induced the knock-down of ARID1A with a TET-inducible shRNA.


title: DOX_NO_FP_rep3

source_name: RNAPII was profiled in RMG-1 clone in ARID1A-KD condition

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

value: Custom, rabbit polyclonal, raised against N terminus of RNAPII


title: CTRL_NO_FP_rep3

source_name: RNAPII was profiled in RMG-1 clone in ARID1A-WT condition


title: RNASEQ_TOT_RNA_DOX_DAY7_rep2

description: ribodepleted RNA


title: 3T3L1_BRD4_D0_EXP2

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: ChIP-sequencing of BRD4 in 3T3L1 on day 0 of differentiation

data_processing:
For all samples reads were aligned to their indicated build using bowtie2 with parameters -k 1
MACS1.4 with p-value = 1e-9 and default parameters was sued to call peaks and generate wiggles
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Preadipocyte

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with calf serum. 48 hours post-confluence, cells were differentiated with insulin, dexamethasone and IBMX.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Vehicle or JQ1 (500 nM) was included on day 0 of differentiation.

tag: chip target

tag: antibody vendor/catalog

value: Bethyl A301-985A

tag: agent

value: Vehicle

tag: time point

value: day 0 of differentiation


title: 3T3L1_BRD4_D2_EXP2

description: ChIP-sequencing of BRD4 in 3T3L1 on day 2 of differentiation

tag: cell line

value: day 2 of differentiation


title: 3T3L1_WCE_D0_EXP2

description: ChIP-sequencing of input samples in 3T3L1 on day 0 of differentiation


title: 3T3L1_WCE_D2_JQ1_EXP2

description: ChIP-sequencing of input samples in 3T3L1 on day 2 of differentiation in the presence of JQ1


title: 3T3L1_POL2_D0_EXP2

description: ChIP-sequencing of RNA Pol2 in 3T3L1 on day 0 of differentiation

value: RNA Pol2

value: Santa Cruz SC-899


title: 3T3L1_BRD4_D2_JQ1_EXP2

description: ChIP-sequencing of BRD4 in 3T3L1 on day 2 of differentiation in the presence of JQ1


title: 3T3L1_POL2_D2_JQ1_EXP2

description: ChIP-sequencing of RNA Pol2 in 3T3L1 on day 2 of differentiation in the presence of JQ1


title: 3T3L1_POL2_D2_EXP2

description: ChIP-sequencing of RNA Pol2 in 3T3L1 on day 2 of differentiation


title: 3T3L1_WCE_D2_EXP2

description: ChIP-sequencing of input samples in 3T3L1 on day 2 of differentiation


title: CTRL_FP_rep3

source_name: RNAPII was profiled in RMG-1 clone in ARID1A-WT condition after a treatment with Flavopiridol for 2 hours

tag: chip antibody


title: DOX_FP_rep3

source_name: RNAPII was profiled in RMG-1 clone in ARID1A-KD condition after a treatment with Flavopiridol for 2 hours


title: H98_42: Carotid artery_Control 01

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

description: H98_42: H98_42: Carotid artery_Control 01

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). Next, microarrays were washed 30 seconds in acetonitrile and 30 seconds in Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using R statistical software. Raw values of all probes on all arrays were normalized against a virtual median chip (median raw intensity per row) using a locally weighted scattered plot smoother analysis (LOWESS). Values for replicate probes were averaged. The data were filtered to remove probes with low intensity values.

source_name: Control carotid artery

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using the Low Input QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Macherey Nagel NucleoSpin columns. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed using an Agilent 2200 TapeStation system.

value: Control carotid artery

value: male


title: control, experiment 2

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

description: Gene expression data from established neuroblastoma cell line

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized on Human Exon 1.0ST Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using the RMA algorithm with Affymetrix Expression Console

source_name: SHSY5Y cells, control, exp2

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol

growth_protocol: SHSY5Y cells were grown under standard conditions

extract_protocol: RNA was isolated using GeneMatrix Universal RNA Kit (roboklon, Berlin, Germany)

treatment_protocol: Cells were treated for 24 hrs with 0, 100, or 200 µM cobalt chloride

value: neuroblastoma cell line


title: 200 µM, experiment 1

description: Gene expression data from established neuroblastoma cell line after treatment with cobalt chloride

source_name: SHSY5Y cells, 200µM CoCl2, exp1


description: H97_18: H97_18: Infra-popliteal artery_Control 12

source_name: Control infra-popliteal artery

value: Control infra-popliteal artery


title: H91_111: Femoral artery_12

description: H91_111: H91_111: Femoral artery_12

source_name: Atherosclerotic femoral artery

value: Atherosclerotic femoral artery


title: H96_31: Carotid artery_Control 16

description: H96_31: H96_31: Carotid artery_Control 16


title: GroupB_290 Untreated prelimbic cortex

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix GeneChip® Mouse Genome 430 2.0 Array for 16hrs at 45oC.

scan_protocol: GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). Scanning was done using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: CEL files were preprocessed with RMA method provided by affy package, and called differentially expressed genes using limma package in R.

source_name: Prelimbic cortex isolated from control male mice (postnatal day 90).

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® 3’ IVT PLUS Reagent Kit User Manual, Affymetrix).

extract_protocol: Total RNA was extracted from punched samples of the mPFC using a RNeasy kit (Qiagen) followed by cDNA synthesis using a Quantitect Reverse Transcription kit (Qiagen).

value: Prelimbic cortex

tag: treatment

value: untreated


title: H79_89: Carotid artery_Control 10

description: H79_89: H79_89: Carotid artery_Control 10


title: GroupB_270 Untreated prelimbic cortex


title: 100 µM, experiment 2

source_name: SHSY5Y cells, 100µM CoCl2, exp2


title: control, experiment 1

source_name: SHSY5Y cells, control, exp1