title: Blood_822910

value: whole blood


title: Blood_822911

status: Public on Dec 31 2020

type: RNA

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

country: United Kingdom

institute: GSK

hyb_protocol: Labelled cDNA was hybridized onto HG-U133  GeneChip oligonucleotide arrays (Affymetrix).

scan_protocol: Standard protocols

data_processing: Data were analysed in R/Bioconductor, normalised by RMA  Data were analysed in R/Bioconductor, normalised by RMA  dadasdaData were analysed in R/Bioconductor, normalised by RMA  asdasdasData were analysed in R/Bioconductor, normalised by RMA

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole Blood from COPD subject

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

extract_protocol: WT-Ovation Pico RNA Amplification System (NuGen).

treatment_protocol: intranasal

tag: patient diagnosis

value: COPD

tag: tissue

tag: treatment

value: All Placebo

tag: visit

value: V3 DAY 12

tag: Sex

value: F

tag: subject

tag: rin

tag: investigatorcountry

value: DENMARK


title: Blood_822913

value: V6 DAY 84


title: Blood_822912

value: V4 DAY 28


title: Blood_822662

value: M

value: CANADA


title: Blood_822663


title: Blood_822916


title: CTRL5_0_Nuclear_1

type: SRA

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to hg38 ribosomal RNA using bowtie v1.1.2 with parameters -q -p 8 -v 0. Unmapped reads were finally mapped to hg38 whole genome using STAR.
For differential gene and transcript expression analysis we ran Kallisto and Sleuth. Kallisto was used to 1) build a transcript index from the GenCode hg38 release Homo sapiens transcriptome (-k 31), 2) pseudo-align the RNA-seq reads to the transcriptome and 3) quantify transcript abundances (-b 100  -s 50 --rf-stranded). We next identified differentially expressed transcripts and genes with Sleuth, a companion program that uses Kallisto results to differentiate between true biological expression differences and variation resulting from sources of experimental noise.
Genome_build: hg38
Supplementary_files_format_and_content: Relative transcript abundance and transcript per million as obtained from Kallisto software.

source_name: iPSC

growth_protocol: Dermal fibroblasts were cultured in OptiMEM +10% FCS medium. The following episomal plasmids were transfected for iPSC generation: pCXLE hOct4 shp53, pCXLE hSK and pCXLE hUL (Addgene), as previously reported [15].Details of the lines used in thus study are reported in Supplementary table 1. Two of the control lines used (control 2 and control 3) are commercially available and were purchased from Coriell (cat. number ND41866*C ) and ThermoFisher Scientific (cat. number A18945) respectively. Induced PSCs were maintained on Geltrex (Life Technologies) with Essential 8 Medium media (Life Technologies) and passaged using EDTA (Life Technologies, 0.5mM).All cell cultures were maintained at 37°Cand 5% carbon dioxide.

extract_protocol:
Biochemical subcellular fractionation was achieved for all cell stages using the Ambion PARIS kit (ThermoFisher Scientific) cell fractionation buffer, following the manufacturer's general protocol, and an 8M Urea Nuclear Lysis Buffer prepared in house. Initially, cells were washed once using ice-cold PBS. Cytosolic fraction was then obtained by lysing cells directly in ice-cold cell fractionation buffer (ThermoFisher Scientific) for 3-15 minutes, thus disrupting plasma membranes, whilst leaving nuclear membranes intact. Lysates were then centrifuged for 3 minutes at 500 x g at 4C. The supernatant was then collected, further centrifuged at maximum speed in a bench centrifuge at 4C for 1 minute, and the resulting supernatant was then processed as cytosolic fraction. Nuclear pellets from the first centrifugation step were gently washed once with cell fractionation buffer and then lysed on ice for 30 minutes in 8M Urea Nuclear Lysis Buffer, containing 50mM Tris-HCL (pH 8), 100mM NaCl, 0.1% SDS, and 1mM DTT. The resulting nuclear fraction was then homogenised using a QIAshredder (QIAGEN) to shred chromatin and reduce viscosity, before being further processed for RNA extraction.  Both lysis buffers were supplemented with 0.1 U/µl RiboLock RNase Inhibitor (ThermoFisher Scientific) and HALT Protease Inhibitor Complex (ThermoFisher Scientific).
Total RNA was extracted from cells using the Maxwell RSC simplyRNA cells kit (Promega), that includes DNase treatment, according to manufacturer’s instructions.
500ng total RNA input was used with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®, with NEBNext® Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: Motor neuron (MN) differentiation was carried out using an adapted version of a previously published protocol (Hall et al., 2017). Briefly, iPSCs were first differentiated to neuroepithelium by plating on Geltrex-coated plates to 100% confluency in chemically defined medium consisting of DMEM/F12 Glutamax, Neurobasal, L-Glutamine, N2 supplement, non essential amino acids, B27 supplement, β-mercaptoethanol (all from Life Technologies) and insulin (Sigma). Treatment with small molecules from day 0-7 was as follows: 1µM Dorsomorphin (Millipore), 2µM SB431542 (Tocris Bioscience), and 3.3µM CHIR99021 (Miltenyi Biotec). Starting from day 8, the neuroepithelial layer was patterned for 7 days with 0.5µM retinoic acid and 1µM Purmorphamine. At day 14 pMN precursors were treated with 0.1µM Purmorphamine for a further 4 days before being terminally differentiated in 0.1 µM Compound E (Enzo Life Sciences) to promote cell cycle exit.

tag: cell line id

tag: genotype

value: Wildtype

tag: fraction

value: Nuclear

tag: days of differentiation

tag: round of sequencing

value: round 1


title: CTRL5_0_Cytoplasmic_2

value: Cytoplasmic


title: CTRL5_0_Cytoplasmic_1


title: CTRL5_35_Nuclear_2

source_name: Electrically active MNs


title: CTRL5_35_Nuclear_1


title: CTRL4_22_Cytoplasmic_2

source_name: Immature MNs


title: CTRL5_22_Nuclear_1


title: CTRL5_35_Cytoplasmic_1


title: CTRL5_22_Nuclear_2


title: Blood_822661

value: SCREENING


title: CTRL5_35_Cytoplasmic_2


title: CTRL4_14_Nuclear_2


title: CTRL4_22_Cytoplasmic_1


title: Blood_822655


title: Blood_822659

value: All NEMI


title: Blood_822658


title: Blood_822660


title: Blood_822657


title: Blood_822653


title: Blood_822652


title: CTRL4_14_Nuclear_1


title: Blood_822654


title: Blood_822650


title: Blood_822651


title: CTRL4_14_Cytoplasmic_2


title: Blood_822649


title: Blood_822656


title: Blood_822648


title: CTRL4_14_Cytoplasmic_1


title: CTRL4_7_Nuclear_2


title: CTRL4_7_Nuclear_1


title: CTRL4_7_Cytoplasmic_2


title: CTRL4_7_Cytoplasmic_1


title: CTRL4_3_Nuclear_2


title: CTRL4_3_Cytoplasmic_2


title: CTRL4_3_Nuclear_1


title: CTRL4_3_Cytoplasmic_1


title: CTRL4_0_Nuclear_2


title: CTRL4_0_Nuclear_1


title: CTRL4_35_Nuclear_2


title: CTRL4_0_Cytoplasmic_1


title: Blood_822647


title: Blood_822640


title: Blood_822643


title: Blood_822636


title: Blood_822637


title: Blood_822638


title: Blood_822644


title: Blood_822646


title: Blood_822642


title: Blood_822641


title: Blood_822645


title: Blood_822639


title: Blood_822634


title: Blood_822633


title: CTRL4_22_Nuclear_2


title: CTRL4_35_Cytoplasmic_1


title: CTRL4_0_Cytoplasmic_2


title: MUT1_0_Cytoplasmic_2

value: VCP R155C


title: CTRL4_35_Nuclear_1


title: CTRL4_35_Cytoplasmic_2


title: CTRL4_22_Nuclear_1


title: CTRL3_22_Cytoplasmic_2


title: CTRL3_22_Cytoplasmic_1


title: CTRL3_14_Nuclear_2


title: Blood_822631

value: whole blood


title: CTRL3_14_Nuclear_1


title: CTRL3_14_Cytoplasmic_2


title: CTRL3_14_Cytoplasmic_1


title: CTRL3_7_Nuclear_2


title: CTRL3_7_Nuclear_1


title: CTRL3_7_Cytoplasmic_1


title: CTRL3_7_Cytoplasmic_2


title: Blood_822632

value: COPD


title: Blood_822635


title: Blood_822628


title: CTRL3_3_Nuclear_2


title: CTRL3_3_Nuclear_1


title: Blood_822630


title: Blood_822627


title: Blood_822625

value: All Placebo


title: Blood_822629


title: CTRL3_3_Cytoplasmic_2


title: Blood_822626


title: Blood_822622


title: Blood_822621


title: Blood_822624


title: Blood_822623

value: V3 DAY 12


title: Blood_822617

value: F


title: Blood_822618


title: Blood_822620


title: CTRL3_0_Nuclear_1


title: CTRL3_3_Cytoplasmic_1


title: CTRL3_0_Cytoplasmic_2


title: Blood_822616


title: CTRL3_0_Nuclear_2


title: CTRL3_0_Cytoplasmic_1


title: CTRL3_35_Nuclear_1


title: Blood_822615


title: CTRL3_35_Cytoplasmic_2


title: CTRL3_22_Nuclear_2


title: CTRL3_22_Nuclear_1


title: CTRL1_22_Cytoplasmic_2


title: Blood_822614


title: CTRL1_22_Cytoplasmic_1


title: CTRL3_35_Nuclear_2


title: Blood_822619


title: Blood_822613


title: Blood_822606


title: Blood_822612


title: Blood_822611


title: Blood_822608


title: Blood_822610


title: Blood_822609


title: Blood_822603


title: CTRL3_35_Cytoplasmic_1


title: Blood_822604


title: CTRL1_14_Cytoplasmic_1


title: Blood_822607


title: CTRL5_3_Cytoplasmic_1


title: CTRL1_7_Nuclear_2


title: CTRL1_7_Nuclear_1


title: CTRL1_7_Cytoplasmic_2


title: Blood_822601


title: Blood_822598


title: Blood_822599


title: CTRL1_7_Cytoplasmic_1


title: Blood_822600


title: CTRL1_14_Nuclear_2


title: Blood_822605


title: CTRL1_14_Cytoplasmic_2


title: CTRL1_3_Nuclear_2


title: CTRL1_3_Cytoplasmic_2


title: CTRL1_0_Nuclear_2


title: CTRL1_3_Nuclear_1


title: CTRL1_0_Cytoplasmic_2


title: CTRL1_0_Nuclear_1


title: CTRL1_3_Cytoplasmic_1


title: Blood_553480


title: CTRL1_35_Nuclear_1


title: Blood_822602


title: CTRL1_35_Cytoplasmic_2


title: Blood_553476


title: Blood_553472


title: Blood_553474


title: Blood_553473


title: Blood_553478


title: CTRL1_35_Nuclear_2


title: Blood_553477


title: CTRL1_22_Nuclear_2


title: Blood_553479


title: CTRL1_35_Cytoplasmic_1


title: CTRL1_22_Nuclear_1


title: Blood_553471


title: Blood_553475


title: Blood_553470


title: CTRL1_0_Cytoplasmic_1


title: Blood_553467


title: Blood_553468


title: MUT4_14_Nuclear

value: VCP R191Q


title: Blood_553466

value: V6 DAY 84


title: Blood_553465


title: Blood_553463


title: Blood_553464


title: Blood_553461

value: V4 DAY 28


title: Blood_553469


title: MUT4_14_Cytoplasmic


title: MUT4_7_Nuclear


title: MUT4_22_Cytoplasmic


title: MUT4_0_Nuclear


title: Blood_553458


title: MUT4_0_Cytoplasmic


title: Blood_553460


title: MUT3_22_Cytoplasmic


title: Blood_553457


title: MUT4_35_Nuclear


title: MUT4_22_Nuclear


title: MUT4_7_Cytoplasmic


title: MUT3_14_Nuclear


title: MUT3_14_Cytoplasmic


title: MUT4_3_Cytoplasmic


title: Blood_553462

value: M


title: Blood_553455

value: CANADA


title: Blood_553456


title: MUT3_7_Cytoplasmic


title: Blood_515652


title: MUT4_35_Cytoplasmic


title: Blood_515653


title: Blood_515654

value: No Treatment


title: Blood_553459


title: Blood_515571


title: MUT3_3_Nuclear

value: Nuclear


title: MUT4_3_Nuclear

value: round 1


title: CTRL1_14_Nuclear_1

value: Wildtype


title: Blood_515651

value: SCREENING


title: Blood_515570


title: MUT3_0_Nuclear


title: MUT3_3_Cytoplasmic

value: Cytoplasmic


title: Blood_515572

value: All NEMI


title: Blood_515568

value: whole blood


title: MUT3_7_Nuclear


title: Blood_515569

value: COPD


title: MUT3_0_Cytoplasmic


title: MUT3_35_Nuclear


title: seedings under scutellarin treatment, biological rep3

city: Kunming

first: Xudong

last: Zhang

state: Yunnan

address: 132# Lanhei Road, Heilongtan

country: China

institute: Kunming Institute of Botany, Chinese Academy of Sciences

description:
BH2010234_2_100uM3
Gene expression data from Arabidopsis thaliana seedings treated with 100 μM scutellarin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis ATH1 Array. 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 with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Alexa Fluor 546

organism: Arabidopsis thaliana

source_name: Arabidopsis seedings under scutellarin treatment

label_protocol: Alexa Fluor 546 labeled cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Surface-sterilized A. thaliana seeds were placed on filter paper with 1% DMSO as a mock treatment or with 100 μM scutellarin in 1% DMSO. The seeds were treated at 4C in the dark for 2 days for homogeneous germination and then moved to a growth chamber with conditions of 25C, 120 μmol m−2 s−1 fluorescent lighting, 60% relative humidity, and a 12/12-h photoperiod.

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

treatment_protocol: Seedings were under DMSO and scutellarin treatment for 10 days respectively.

tag: ecotype background

value: Columbia

tag: age

value: seedings growing on filter paper

value: 100 μM scutellarin


title: MUT3_35_Cytoplasmic

value: VCP R191Q


title: seedings under scutellarin treatment, biological rep1

description:
BH2010234_2_100uM1
Gene expression data from Arabidopsis thaliana seedings treated with 100 μM scutellarin


title: Blood_515565

value: All Placebo


title: MUT3_22_Nuclear


title: seedings under scutellarin treatment, biological rep2

description:
BH2010234_2_100uM2
Gene expression data from Arabidopsis thaliana seedings treated with 100 μM scutellarin


title: seedings under mock treatment, biological rep3

description:
BH2010234_2_CK3
Gene expression data from Arabidopsis thaliana seedings treated with DMSO

source_name: Arabidopsis seedings under mock treatment

value: DMSO


title: seedings under mock treatment, biological rep1

description:
BH2010234_2_CK1
Gene expression data from Arabidopsis thaliana seedings treated with DMSO


title: Blood_515566

value: V3 DAY 12

value: M


title: Blood_515562

value: CANADA


title: MUT2_14_Cytoplasmic

value: VCP R155C


title: Blood_515567


title: MUT2_22_Cytoplasmic

value: round 1


title: Blood_515563


title: MUT2_3_Nuclear

value: Nuclear


title: seedings under mock treatment, biological rep2

description:
BH2010234_2_CK2
Gene expression data from Arabidopsis thaliana seedings treated with DMSO


title: MUT2_7_Nuclear


title: MUT2_3_Cytoplasmic


title: MUT2_0_Cytoplasmic


title: MUT2_0_Nuclear


title: MUT2_7_Cytoplasmic


title: MUT2_14_Nuclear


title: Blood_515559

value: V4 DAY 28

value: F


title: Blood_515557

value: V6 DAY 84


title: Blood_515558

value: whole blood


title: Blood_515564

value: COPD

value: All NEMI


title: Blood_515561


title: Blood_515556


title: Blood_515560


title: MUT2_35_Cytoplasmic

value: Cytoplasmic


title: MUT2_35_Nuclear


title: HepG2_PATZ1 ChIP-Seq

city: Singapore

first: Zhen Long

last: Ng

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2.
Data were filtered using the following specifications: PCR duplication
Peaks were called using Partek 6.6 software with an average fragment size of 300bps and 0.05 as the cutoff p-value of Mann-Whitney U test for separation of forward and reverse reads in a peak
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

source_name: HepG2 cells

growth_protocol: HepG2 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) High Glucose (GE Healthcare) supplemented with 10% heat inactivated fetal bovine serum (FBS; GE Healthcare). The cells were cultured in a 500 cm square dish with 10 mL of medium and maintained at 5% CO2 at 37°C in a humidified incubator.

extract_protocol:
HepG2 cell lysates were subjected to cell and nuclear lysis followed by sonication to obtain the input DNA. Chromatin immunoprecipitation was then performed with anti-PATZ1 antibody to obtain PATZ1 ChIP-DNA.
ChIP-DNA library was generated by Illumina ChIP Library Prep Kit (Illumina, San Diego, CA).

tag: cell line

tag: cell type

value: liver cancer cells

tag: genotype/variation

value: wild type

tag: chip antibody

value: anti-PATZ1 (sc-292109; Santa Cruz)


title: Blood_515554

tag: patient diagnosis

tag: tissue

tag: treatment

value: No Treatment

value: SCREENING


title: Blood_515555

tag: visit

tag: Sex

tag: subject


title: Blood_515534

value: All Placebo

tag: rin

tag: investigatorcountry


title: MUT1_22_Cytoplasmic

tag: cell line id

tag: genotype

tag: fraction


title: MUT2_22_Nuclear

tag: days of differentiation

tag: round of sequencing


title: Blood_515535

value: CANADA


title: Blood_515532

value: M


title: Blood_515533


title: HepG2_Input DNA

tag: cell line


title: MUT1_14_Cytoplasmic

value: VCP R155C

value: round 1


title: MUT1_14_Nuclear

value: Nuclear


title: MUT1_7_Nuclear


title: MUT1_7_Cytoplasmic


title: MUT1_3_Cytoplasmic


title: MUT1_3_Nuclear


title: MUT1_0_Nuclear


title: Blood_515531

value: V3 DAY 12


title: Blood_515529

value: V4 DAY 28

value: F


title: Blood_515528

value: COPD

value: whole blood


title: 14-043_6 hr_mod TBI/NS (14-043-CB)

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

hyb_protocol: cRNA was hybridized to a whole rat genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2505C-US09493743 Images were quantified using Agilent Feature Extraction (FE) Software

data_processing:
Agilent Feature Extraction Software (v 10.7.) was used for background subtraction and Statistical analyses were performed using GraphPad® version 5.0 software (GraphPad Software, Inc., La Jolla, CA). Experimental results were expressed as mean ± SEM.  Two-way ANOVA was computed to understand the impact of the two co-factors, mild vs. moderate TBI, and time course. Unpaired t-tests were used to evaluate the shift in phenotypic endpoints (cut-off criteria p<0.1, p<0.05, and p<0.01).
Transcriptomic data was Lowess normalized log10 ratio (test/reference). DEG were selected by moderated t-test p<0.05. A fold change based cut-off was introduced to refine the gene sets.

organism: Rattus norvegicus

source_name: Cerebellum

label_protocol: Total RNA (200ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

extract_protocol: Total RNA extracted using Trizol (Invitrogen, Thermo Fisher Scientific, Waltham, MA) following manufacturer's instructions

tag: strain

value: Wistar Han

tag: gender

value: Male

tag: age

value: 6 Weeks

tag: condition

value: mod TBI/NS

tag: time

value: 6 hrs post injury

value: Cerebellum

source_name: Agilent's Universal Rat Reference RNA composed of total RNA from 14 rat cell lines

value: Unknown

tag: sample type

value: Reference


title: MUT1_35_Nuclear


title: 14-042_6 hr_mod TBI/NS (14-042-CB)

tag: tissue


title: 14-067_6 hr_mod TBI/NS (14-067-CB)


title: 14-065_6 hr_mod TBI/NS (14-065-CB)


title: MUT1_0_Cytoplasmic

value: Cytoplasmic


title: 14-066_6 hr_mod TBI/NS (14-066-CB)


title: Blood_515530

tag: patient diagnosis

tag: treatment

value: All NEMI

tag: visit

tag: Sex

value: CANADA


title: MUT1_35_Cytoplasmic

tag: cell line id

value: VCP R155C

value: round 1


title: MUT1_22_Nuclear

tag: genotype

value: Nuclear


title: SKBR3_ATO_0H

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

institute: Fujian Maternity and Child Health Hospital

description: Gene expression data from ATO treated SKBR3 cells

hyb_protocol: Fragmented and biotin-labeled cRNA was hybridized to affymetrix human U133 plus 2.0 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000

data_processing: Raw data were normalized by RMA algorithm

label: biotin

source_name: breast cancer cell line SKBR3

label_protocol: 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was used to synthesize biotin-labeled cRNA with the IVT kit (Affymetrix, USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.

growth_protocol: Breast cancer SKBR3, MCF7, colon cancer SW620, HCT116 and lung cancer H1299, A549 cells were cultured on plates in 10% FBS.

extract_protocol: Cellular RNA was isolated by Tri-Reagent using the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: Breast cancer SKBR3, MCF7, colon cancer SW620, HCT116 and lung cancer H1299, A549 cells were treated with ATO 5μM for 0, 6, 12, 24 and 36 hours. TP53 wild type MCF7, HCT116 and A549 cells were treated with the combination of ATO and TP53 inhibitor PFTα at 6h, 12h, 24h and 36 hours

tag: time point

tag: disease

value: breast cancer

tag: agent

value: ATO


title: SKBR3_ATO_36h

tag: cell line


title: 14-121_6 hr_mod TBI/NS (14-121-CB)

tag: strain


title: SKBR3_ATO_24h


title: SKBR3_ATO_12h


title: 14-115_48 hr_mild TBI/NS (14-115-CB)

tag: gender

value: mild TBI/NS

value: 48 hrs post injury


title: CTRL5_22_Cytoplasmic

value: Wildtype

tag: fraction

tag: days of differentiation

tag: round of sequencing


title: 14-123_6 hr_mod TBI/NS (14-123-CB)

value: Wistar Han

value: Male

tag: age

value: 6 Weeks

tag: condition

tag: time

tag: sample type


title: 14-089_48 hr_mod TBI/NS (14-089-CB)

value: mod TBI/NS

tag: tissue

value: Cerebellum


title: 14-077_48 hr_mod TBI/NS (14-077-CB)

value: Unknown

value: Reference


title: MCF7_ATO_PFTα_36H

description: Gene expression data from ATO and PFTα treated MCF7 cells

source_name: breast cancer cell line MCF7

value: ATO and PFTalpha


title: 14-122_6 hr_mod TBI/NS (14-122-CB)

value: 6 hrs post injury


title: MCF7_ATO_PFTα_12H


title: MCF7_ATO_PFTα_24H


title: SKBR3_ATO_6h


title: 14-090_48 hr_mod TBI/NS (14-090-CB)


title: 14-078_48 hr_mod TBI/NS (14-078-CB)


title: MCF7_ATO_PFTα_6H


title: CTRL5_14_Nuclear


title: CTRL5_14_Cytoplasmic

value: Cytoplasmic


title: CTRL5_7_Nuclear

value: round 1


title: CTRL5_7_Cytoplasmic


title: 14-091_48 hr_mod TBI/NS (14-091-CB)


title: CTRL5_3_Cytoplasmic


title: MCF7_ATO_36H

description: Gene expression data from ATO treated MCF7 cells


title: LPS_NNK_Fvbn_6

city: Pittsburgh

first: Chia-Hsin

last: Liu

state: PA

address: 130 Desoto Street, GSPH-A419

institute: University of Pittsburgh

hyb_protocol: After precipitation, purification, and quantification, 1.25µg labeled samples were hybridized according to the supplier‚ as protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high-resolution laser microarray scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were then normalized by third quantiles and log 2 transformation (Partek Genomics Suite, St Louis, Missouri).

organism: Mus musculus

source_name: Lung tissue

label_protocol: Total RNA labeling was performed with the single color Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Animals were euthanized one week after the last treatment. Total mRNA was isolated from the lung tissue using TRIzol method.

treatment_protocol: Seven-week-old female FVB/N mice were exposed with NNK (3mg/mouse, intraperitoneal injection biweekly for first 4 weeks), LPS (5ug/mouse, intranasal instillation weekly for 16 weeks), or combined NNK and LPS.

value: FVB/NJ

tag: teatment

value: NNK/LPS

value: Lung

tag: teatment regimen

value: semi-weekly for 4 weeks/weekly treatment for 16 weeks


title: 14-113_48 hr_mod TBI/NS (14-113-CB)

value: 48 hrs post injury


title: 14-079_48 hr_mod TBI/NS (14-079-CB)


title: MCF7_ATO_24H

value: breast cancer

value: ATO


title: LPS_NNK_Fvbn_2


title: LPS_NNK_Fvbn_3


title: CTRL5_3_Nuclear

tag: cell line id

tag: genotype

value: Wildtype

value: Nuclear


title: CTRL5_0_Cytoplasmic


title: 14-102_14 day_mod TBI/NS (14-102-CB)

value: Wistar Han

value: Male

value: 6 Weeks

value: mod TBI/NS

value: 14 days post injury


title: NNK_Fvbn_2

value: NNK

value: semi-weekly for 4 weeks


title: NNK_Fvbn_5


title: 14-103_14 day_mod TBI/NS (14-103-CB)

value: Cerebellum

value: Unknown

value: Reference


title: MCF7_ATO_12H

tag: time point

tag: disease


title: 14-053_14 day_mod TBI/NS (14-053-CB)


title: 14-101_14 day_mod TBI/NS (14-101-CB)


title: SW620_ATO_36H

description: Gene expression data from ATO treated SW620 cells

source_name: colon cancer cell line SW620

value: colon cancer

tag: agent

tag: cell line


title: CTRL5_0_Nuclear

value: round 1


title: MCF7_ATO_0H


title: MCF7_ATO_6H


title: SW620_ATO_24H


title: CTRL5_35_Nuclear


title: SW620_ATO_12H


title: CTRL5_22_Nuclear


title: LPS_Fvbn_6

tag: strain

value: FVB/NJ

value: LPS

value: Lung

value: weekly treatment for 16 weeks


title: NNK_Fvbn_3


title: LPS_Fvbn_1


title: 14-055_14 day_mod TBI/NS (14-055-CB)

tag: gender


title: CTRL4_22_Cytoplasmic

value: Wildtype

tag: fraction

value: Cytoplasmic

tag: days of differentiation


title: CTRL4_14_Nuclear

value: Nuclear

tag: round of sequencing


title: PBS_Fvbn_3

value: PBS


title: CTRL4_14_Cytoplasmic


title: SW620_ATO_0H

value: ATO


title: SW620_ATO_6H


title: 14-031_14 day_mod TBI/NS (14-031-CB)

value: Wistar Han

value: Male

tag: age

value: 6 Weeks

tag: condition

value: mod TBI/NS

value: 14 days post injury


title: LPS_Fvbn_5


title: CTRL4_7_Cytoplasmic


title: HCT116_ATO_PFTα_6H

description: Gene expression data from ATO and PFTα treated HCT116 cells

source_name: colon cancer cell line HCT116

value: ATO and PFTalpha


title: CTRL4_3_Nuclear


title: 14-124_6 hr_mild TBI/NS (14-124-CB)

value: mild TBI/NS

tag: time

value: 6 hrs post injury

value: Cerebellum

value: Unknown

tag: sample type

value: Reference


title: 14-030_14 day_mod TBI/NS (14-030-CB)

tag: tissue


title: 14-054_14 day_mod TBI/NS (14-054-CB)


title: 14-126_6 hr_mild TBI/NS (14-126-CB)


title: PBS_Fvbn_2

value: FVB/NJ

tag: teatment

value: Lung

tag: teatment regimen

value: weekly treatment for 16 weeks


title: 14-070_6 hr_mild TBI/NS (14-070-CB)


title: 14-069_6 hr_mild TBI/NS (14-069-CB)


title: HCT116_ATO_PFTα_12H

value: colon cancer


title: HCT116_ATO_PFTα_24H


title: HCT116_ATO_36H

description: Gene expression data from ATO treated HCT116 cells


title: CTRL5_35_Cytoplasmic

tag: cell line id

tag: genotype

value: Wildtype

value: Cytoplasmic

value: round 1


title: 14-125_6 hr_mild TBI/NS (14-125-CB)

value: Wistar Han

value: Male


title: HCT116_ATO_24H

tag: time point

tag: disease

value: ATO


title: HCT116_ATO_12H

tag: agent

tag: cell line


title: CTRL4_3_Cytoplasmic


title: CTRL4_7_Nuclear

value: Nuclear


title: CTRL4_0_Nuclear


title: CTRL4_0_Cytoplasmic


title: CTRL4_35_Nuclear


title: CTRL4_35_Cytoplasmic


title: HCT116_ATO_6H


title: 14-046_6 hr_mild TBI/NS (14-046-CB)

tag: strain

tag: gender

value: 6 Weeks


title: H1299_ATO_36H.

description: Gene expression data from ATO treated H1299 cells

source_name: lung cancer cell line H1299

value: lung cancer


title: HCT116_ATO_0H


title: 14-094_48 hr_mild TBI/NS (14-094-CB)

value: mild TBI/NS

value: 48 hrs post injury


title: CTRL3_22_Cytoplasmic

tag: fraction

tag: days of differentiation


title: 14-080_48 hr_mild TBI/NS (14-080-CB)

tag: age

value: Cerebellum

value: Unknown


title: CTRL3_14_Cytoplasmic

tag: round of sequencing


title: 14-068_6 hr_mild TBI/NS (14-068-CB)

tag: condition

tag: time

value: 6 hrs post injury

value: Reference


title: CTRL4_22_Nuclear


title: CTRL3_7_Nuclear


title: CTRL3_7_Cytoplasmic


title: CTRL3_14_Nuclear


title: H1299_ATO_6H


title: PBS_Fvbn_1

value: FVB/NJ

value: PBS

tag: tissue

value: Lung

value: weekly treatment for 16 weeks


title: 14-092_48 hr_mild TBI/NS (14-092-CB)

tag: sample type


title: H1299_ATO_12H.


title: A549_ATO_PFTα_36H

description: Gene expression data from ATO and PFTα treated A549 cells

source_name: lung cancer cell line A549

value: ATO and PFTalpha


title: 14-082_48 hr_mild TBI/NS (14-082-CB)

value: Wistar Han


title: A549_ATO_PFTα_24H


title: 14-057_14 day_mild TBI/NS (14-057-CB)

value: Male

value: 14 days post injury


title: H1299_ATO_0H

value: ATO


title: 14-033_14 day_mild TBI/NS (14-033-CB)

value: 6 Weeks


title: A549_ATO_PFTα_12H

value: lung cancer


title: A549_ATO_PFTα_6H


title: 14-106_14 day_mild TBI/NS (14-106-CB)

value: mild TBI/NS


title: CTRL3_3_Cytoplasmic

value: Wildtype

value: Cytoplasmic

value: round 1


title: 14-093_48 hr_mild TBI/NS (14-093-CB)

value: 48 hrs post injury

value: Cerebellum

value: Unknown


title: 14-081_48 hr_mild TBI/NS (14-081-CB)

value: Reference


title: CTRL3_3_Nuclear

value: Nuclear


title: H1299_ATO_24H.


title: 14-034_14 day_mild TBI/NS (14-034-CB)


title: A549_ATO_36H

description: Gene expression data from ATO treated A549 cells


title: 14-105_14 day_mild TBI/NS (14-105-CB)


title: CTRL3_0_Nuclear


title: CTRL3_0_Cytoplasmic


title: CTRL3_35_Nuclear


title: CTRL3_35_Cytoplasmic


title: CTRL3_22_Nuclear


title: 14-058_14 day_mild TBI/NS (14-058-CB)


title: 14-066_6 hr_mod TBI/NS (14-066-HC)

source_name: Hippocampus

value: mod TBI/NS

value: 6 hrs post injury

value: Hippocampus


title: A549_ATO_12H


title: A549_ATO_24H


title: CTRL1_14_Nuclear


title: CTRL1_14_Cytoplasmic


title: A549_ATO_6H


title: A549_ATO_0H


title: CTRL1_7_Cytoplasmic


title: CTRL1_22_Cytoplasmic


title: 14-065_6 hr_mod TBI/NS (14-065-HC)

value: Wistar Han

value: Male


title: 14-121_6 hr_mod TBI/NS (14-121-HC)


title: 14-041_6 hr_mod TBI/NS (14-041-HC)


title: 14-122_6 hr_mod TBI/NS (14-122-HC)


title: 14-042_6 hr_mod TBI/NS (14-042-HC)


title: CTRL1_3_Nuclear


title: LWX_Cancer tissue

city: Changsha

first: Xiangping

last: Song

state: Hunan

address: 87 Xiangya Road

institute: Xiangya Hospital

description: Gene expression

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, 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 to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Cancer tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

tag: location

value: Rectum

tag: tumor stage

value: TNM III

value: Female


title: WCX_Non-cancerous tissue

description: Gene expression

source_name: Non-cancerous tissue


title: WCX_Cancer tissue

description: Gene expression


title: CTRL1_3_Cytoplasmic

tag: cell line id

tag: genotype


title: 14-067_6 hr_mod TBI/NS (14-067-HC)

value: 6 Weeks


title: 14-123_6 hr_mod TBI/NS (14-123-HC)


title: WHF_Cancer tissue

description: Gene expression


title: CTRL1_0_Nuclear

source_name: iPSC

value: Wildtype


title: 14-079_48 hr_mod TBI/NS (14-079-HC)


title: CTRL1_35_Nuclear

source_name: Electrically active MNs


title: CTRL1_35_Cytoplasmic

value: Cytoplasmic


title: LWX_Non-cancerous tissue

description: Gene expression


title: CTRL1_22_Nuclear

source_name: Immature MNs

value: round 1


title: T_cell_scRNA-seq

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

data_processing:
Raw reads were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline (Early access), which included filtering by reads quality, annotating reads, annotating molecules, determining putative cells and generating single-cell expression matrix. Briefly speaking, Read pairs with low sequencing quality (too long, too short, low sequencing score or with high single nucleotide frequency) were firstly removed in the reads quality filtering step
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence, meanwhile the quality-filtered R2 reads were mapped to Genome Reference Consortium Human Build 37(GRCh37) using STAR (verison 2.5.2b) in reads annotation step. Further adjustment were performed with the recursive substitution error correction (RSEC) and distribution-based error correction (DBEC) algorithms to remove artifact molecules due to amplification bias in molecules annotation step.
putative cells information were combined together with RSEC/DBEC-adjusted molecules to generate a single-cell expression matrix. The pipeline output provided raw gene expression matrices corrected by RSEC and DBEC algorithms. Among all the matrices, UMI counts per cell corrected by DBEC algorithm were later used in the clustering analysis.
Raw gene expression matrices from two cartridges were read into R (version 3.6.0) separately and converted to Seurat objects using the Seurat R package (version 3.0.1). CCA integration were performed with Seurat R package between two batches.

source_name: T cells that were electroplated with PX458-BCL11B at day 0 (2263 cells), day 5 (1565 cells), day 10 (498 cells), day 15 (204 cells), and day 20 (418 cells)

growth_protocol: T cells that were electroplated with PX458-BCL11B at day 0 , day 5 , day 10 , day 15 , and day 20 in T551 H3 medium with  supplemented 5% heat-inactivated fetal bovine serum (FBS), 500 U/ml recombinant human IL-2, 10 mM HEPES, 2 mM glutamine and 1% penicillin/streptomycin.

extract_protocol:
Targeted single-cell RNA-Seq analysis was conducted using the BD Rhapsody Single-Cell AnalysisSystem (BD Biosciences,USA), following the manufacture’s protocol. Briefly, double strand cDNA were firstly generated from Microbeads-captured single cell transcriptome following several steps including reverse transcription, second strand synthesis, end preparation, adapter ligation and whole transcriptome amplification. Then final cDNA library were generated from double strand full length cDNA by random priming amplification with BD Rhapsody cDNA Kit (BD Biosciences, 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, 633774).
Based on BD Rhapsody system Whole transcriptome analysis alpha protocol for single cell whole transcriptome analysis, Microbeads-captured single cell transcriptome were generated into cDNA library containing Cell label and UMI information. Briefly, double strand cDNA were firstly generated from Microbeads-captured single cell transcriptome following several steps including reverse transcription, second strand synthesis, end preparation, adapter ligation and whole transcriptome amplification. Then final cDNA library were generated from double strand full length cDNA by random priming amplification with BD Rhapsody cDNA Kit (BD Biosciences, 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, 633774).

tag: cell type

value: T cells


title: 14-090_48 hr_mod TBI/NS (14-090-HC)

value: 48 hrs post injury


title: HZL_Cancer tissue

description: Gene expression

value: Sigmoid


title: CTRL1_0_Cytoplasmic


title: WHF_Non-cancerous tissue

description: Gene expression


title: LJB_Cancer tissue

description: Gene expression


title: LJB_Non-cancerous tissue

description: Gene expression


title: GSX_Non-cancerous tissue

description: Gene expression


title: 14-002_48 hr_mod TBI/NS (14-002-HC)

value: Unknown

value: Reference


title: 14-009_48 hr_mod TBI/NS (14-009-HC)

value: mod TBI/NS


title: HCT116_ATO_PFTα_36H

tag: time point

tag: disease

value: colon cancer

tag: agent

value: ATO and PFTalpha


title: 14-089_48 hr_mod TBI/NS (14-089-HC)

tag: strain

value: Wistar Han

tag: gender

value: Hippocampus


title: GSX_Cancer tissue

description: Gene expression

value: Rectum

value: Male


title: 14-113_48 hr_mod TBI/NS (14-113-HC)


title: 14-091_48 hr_mod TBI/NS (14-091-HC)


title: 14-078_48 hr_mod TBI/NS (14-078-HC)


title: 14-010_48 hr_mod TBI/NS (14-010-HC)


title: 14-017_14 day_mod TBI/NS (14-017-HC)

value: 14 days post injury


title: 14-001_48 hr_mod TBI/NS (14-001-HC)

value: 6 Weeks


title: 14-114_48 hr_mod TBI/NS (14-114-HC)


title: 14-053_14 day_mod TBI/NS (14-053-HC)


title: 14-019_14 day_mod TBI/NS (14-019-HC)


title: HZL_Non-cancerous tissue

description: Gene expression


title: 14-045_6 hr_mild TBI/NS (14-045-CB)

value: mild TBI/NS

value: 6 hrs post injury

value: Cerebellum


title: 14-043_6 hr_mod TBI/NS (14-043-HC)


title: 14-018_14 day_mod TBI/NS (14-018-HC)


title: 14-045_6 hr_mild TBI/NS (14-045-HC)


title: 14-069_6 hr_mild TBI/NS (14-069-HC)


title: 14-102_14 day_mod TBI/NS (14-102-HC)


title: 14-070_6 hr_mild TBI/NS (14-070-HC)


title: 14-126_6 hr_mild TBI/NS (14-126-HC)


title: 14-125_6 hr_mild TBI/NS (14-125-HC)


title: 14-101_14 day_mod TBI/NS (14-101-HC)


title: 14-055_14 day_mod TBI/NS (14-055-HC)


title: 14-054_14 day_mod TBI/NS (14-054-HC)


title: 14-031_14 day_mod TBI/NS (14-031-HC)


title: 14-030_14 day_mod TBI/NS (14-030-HC)


title: 14-012_48 hr_mild TBI/NS (14-012-HC)


title: 14-068_6 hr_mild TBI/NS (14-068-HC)


title: 14-003_48 hr_mild TBI/NS (14-003-HC)


title: 14-046_6 hr_mild TBI/NS (14-046-HC)


title: 14-011_48 hr_mild TBI/NS (14-011-HC)


title: CTRL1_7_Nuclear

value: Wildtype

tag: fraction

value: Nuclear

tag: days of differentiation

value: round 1


title: 14-082_48 hr_mild TBI/NS (14-082-HC)

tag: age

value: 48 hrs post injury

value: Unknown


title: 14-092_48 hr_mild TBI/NS (14-092-HC)

tag: condition

value: Reference


title: 14-124_6 hr_mild TBI/NS (14-124-HC)

tag: time


title: 14-081_48 hr_mild TBI/NS (14-081-HC)

tag: tissue


title: 14-093_48 hr_mild TBI/NS (14-093-HC)

tag: sample type


title: 14-080_48 hr_mild TBI/NS (14-080-HC)


title: 14-029_6 hr_mild TBI/NS (14-029-HC)


title: 14-115_48 hr_mild TBI/NS (14-115-HC)


title: H3K4me2 of Hst1 & Hos2 double deleted cells dataset 2

type: genomic

city: Taipei

first: Gan-Guang

last: Liou

state: Taiwan

address: Institute of Molecular Biology, Academia Sinica., 128 Sec. 2, Academia Rd, Nankang,

country: Taiwan

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

scan_protocol: The protocol for scanning one-color NimbleGen arrays with a GenePix 4000B Scanner and associated software Genepix6.0. (NimbleGen_ChIP_Users_Guide_v3p1)

data_processing: Images were aligned and quantified using NimbleScan software  (V2.4) (Roche NimbleGen) which produced .pair reports of raw data and converted to ratio of Cy5 vs cy3

organism: Saccharomyces cerevisiae

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

extract_protocol: TAP tag-antibody (for Snt1), PolII-antibody and H3K4me2 antibody individually coupled resins were incubated with cell lysate at 4°C overnight. Beads were then washed once with cell lysis buffer (50 mM Hepes-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and protease inhibitors), twice with 50 mM Hepes-KOH pH 7.5, 250 mM NaCl, 1 mM EDTA, 0.25% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS, and protease inhibitors, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, and 1 mM EDTA, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl and 1 mM EDTA, and once with TE (10 mM Tris-HCl pH 8.0 and 1 mM EDTA pH 8.0) at room temperature. Beads were eluted by incubating with 100 μl of 50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS at 65°C for 15 minutes. Elute was transferred to a fresh tube and pooled with a final bead wash of 150 μl TE with 0.67% SDS. For input DNA, 200 μl TE with 1% SDS was added to 50 μl cell lysate extract. To reverse the cross-links, all samples were incubated at 65°C overnight, combined with 250 μl TE, 5 μg glycogen, and 100 mg proteinase K, and incubated at 37°C for 2 h. After adding 55 μl of 4 M LiCl, samples were extracted once with phenol/chloroform and once with chloroform. The remaining associated DNA was precipitated by the addition of 400 mM LiCl, and 2 volumes of ethanol, washed with 75% ethanol, air dried, and resuspended in 50 μl TE with RNase A (20 mg/ml for input DNA and 2 mg/ml for affinity-precipitated DNA) and incubated at 37°C for 1 hour

tag: wild-type, hst1 deleted, hos2 deleted or hst1 & hos2 double deleted strain

source_name: input DNA


title: H3K4me2 of Hos2 deleted cells dataset 2

institute: Institute of Molecular Biology, Academia Sinica.

value: H3K4me2 of Hos2 deleted cells


title: H3K4me2 of Hst1 deleted cells dataset 2

value: H3K4me2 of Hst1 deleted cells


title: 14-004_48 hr_mild TBI/NS (14-004-HC)

value: Wistar Han


title: 14-094_48 hr_mild TBI/NS (14-094-HC)

value: Hippocampus


title: 14-034_14 day_mild TBI/NS (14-034-HC)


title: PolII of Hst1 & Hos2 double deleted cells dataset 2

source_name: PolII


title: 14-105_14 day_mild TBI/NS (14-105-HC)

source_name: Agilent's Universal Rat Reference RNA composed of total RNA from 14 rat cell lines


title: 14-058_14 day_mild TBI/NS (14-058-HC)


title: 14-057_14 day_mild TBI/NS (14-057-HC)


title: PolII of Hst1 deleted cells dataset 2

value: PolII of Hst1 deleted cells


title: PolII of Hos2 deleted cells dataset 2

value: PolII of Hos2 deleted cells


title: PolII of wild-type cells dataset 2

value: PolII of wild-type cells


title: H3K4me2 of Hst1 & Hos2 double deleted cells

extract_protocol: TAP tag-antibody (for Set3), PolII-antibody and H3K4me2 antibody individually coupled resins were incubated with cell lysate at 4°C overnight. Beads were then washed once with cell lysis buffer (50 mM Hepes-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and protease inhibitors), twice with 50 mM Hepes-KOH pH 7.5, 250 mM NaCl, 1 mM EDTA, 0.25% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS, and protease inhibitors, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, and 1 mM EDTA, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl and 1 mM EDTA, and once with TE (10 mM Tris-HCl pH 8.0 and 1 mM EDTA pH 8.0) at room temperature. Beads were eluted by incubating with 100 μl of 50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS at 65°C for 15 minutes. Elute was transferred to a fresh tube and pooled with a final bead wash of 150 μl TE with 0.67% SDS. For input DNA, 200 μl TE with 1% SDS was added to 50 μl cell lysate extract. To reverse the cross-links, all samples were incubated at 65°C overnight, combined with 250 μl TE, 5 μg glycogen, and 100 mg proteinase K, and incubated at 37°C for 2 h. After adding 55 μl of 4 M LiCl, samples were extracted once with phenol/chloroform and once with chloroform. The remaining associated DNA was precipitated by the addition of 400 mM LiCl, and 2 volumes of ethanol, washed with 75% ethanol, air dried, and resuspended in 50 μl TE with RNase A (20 mg/ml for input DNA and 2 mg/ml for affinity-precipitated DNA) and incubated at 37°C for 1 hour


title: 14-056_14 day_mild TBI/NS (14-056-HC)

value: Male

value: 6 Weeks

value: 14 days post injury


title: 14-033_14 day_mild TBI/NS (14-033-HC)

value: mild TBI/NS


title: 14-106_14 day_mild TBI/NS (14-106-HC)


title: Snt1 of Hos2 deleted cells

value: Snt1 of Hos2 deleted cells


title: H3K4me2 of wild-type cells dataset 2

value: H3K4me2 of wild-type cells


title: 14-020_14 day_mild TBI/NS (14-020-HC)


title: Snt1 of Hst1 deleted cells

value: Snt1 of Hst1 deleted cells


title: 14-022_14 day_mild TBI/NS (14-022-HC)


title: Snt1 of wild-type cells

value: Snt1 of wild-type cells


title: BTXA3

city: Beijing

first: Mao

last: Qianying

address: No. 22 Zhong Guan Cun South Street, Haidian District,

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: submandibular gland

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: The submandibular glands of rat are preserved at -80 degrees Celsius.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: submandibular gland

value: male

tag: treatment

value: BTXA

value: SD


title: BTXA5


title: H3K4me2 of wild-type cells


title: 14-032_14 day_mild TBI/NS (14-032-HC)

value: Wistar Han

value: Unknown

value: Reference


title: Snt1 of Hst1 & Hos2 double deleted cells


title: H3K4me2 of Hos2 deleted cells

value: H3K4me2 of Hos2 deleted cells


title: H3K4me2 of Hst1 deleted cells

value: H3K4me2 of Hst1 deleted cells


title: Ctrl4

value: control


title: BTXA1


title: Ctrl3


title: Ctrl1


title: PolII of Hst1 deleted cells

value: PolII of Hst1 deleted cells


title: Uninfected SP-R210L(DN) RAW Cells 2

city: Hershey

first: Zissis

last: Chroneos

address: 500 University Drive

department: Pediatrics

institute: Penn State College of Medicine

description:
processed data file:
DNRNA_InfvUninf.csv

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were aligned to the mm10 reference genome using hisat2. Abundance for each gene was obtained using featureCounts function available in Rsubread R package. The raw count data from 3 independent replicates were analyzed using DESeq2 to obtain differentially expressed genes with p-value <0.05
Genome_build: mm10
Supplementary_files_format_and_content: Procesed Deseq results providing differentially expressed genes with p-value <0.05 between cell type  are in the correspondingly labeled CSV file. Deseq results comparing infected samples without filtereing are in the correspondingly labeled CSV file.

source_name: Modified RAW264.7 RAW Cell Line

growth_protocol: RAW264.7 cells were stably transfected with empty for SP-R210ct pTriex-2-Neo vectors and selected using 600ug/mL neomycin sulfate to generate WT and SP-R210L(DN) RAW264.7 cells, respectively. SP-R210KO cells were generated using CRISPR/Cas9.  Guide RNA sequences targeting exons 5, 6, 12, and 14 were designed using crispr.mit.edu and gRNA oligonucleotides were ligated into the LRG hU6-sgRNA- EFS-GFP-P2A vector.  RAW 264.7 macrophages were transduced with a Cas9 containing lentivirus and selected using blasticidin to generate a stable Cas9 expressing cell line. Stable Cas9 RAW264.7 cells were transfected with a pooled library of ligated gRNA vectors. Transfected GFP+ cells were isolated by flow activated cell sorting into 96-well plates to culture individual clones.  SP-R210-deficient cells were identified by Western blot analysis. 1E6 cells of each of WT, SP-R210L(DN) and SP-R210KO cells were plated for each sample.

extract_protocol:
RNA was isolated from 1,000,000 cells per sample using the RNA-Bee protocol. Briefly, plated cells were washed with PBS and 0.5 mL of RNA-Bee Isolation Reagent was added to the cells, lysed with repeated pipetting, and transferred to a microcentrifuge tube followed by the addition of 0.1 mL of chloroform was added and mixed by shaking for 15-30 seconds. Homogenate was centrifuged at 12,000xg for 15 minutes at 4oC. The aqueous phase was retained and mixed with 0.5 mL ice-cold isopropanol and placed at -20oC for 3 hours. Samples were then centrifuged at 12,000 x g for 15 minutes at 4oC and supernatant was discarded. Precipitated RNA was washed with 1 mL ice-cold 75% ethanol twice, and then allowed to air dry for 15-30 minutes at 4oC. RNA was dissolved in 25 uL RNAse, DNAse-free deionized water.
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique index sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). .
Pooled libraries were diluted and then denatured using the Illumina protocol. The denatured libraries were loaded onto a TruSeq v2 Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe or onto a S1 flow cell on an Illumina NovaSeq 6000 and run for 2X50 cycles according to the manufacturer's instructions.

treatment_protocol: Infected cells were infected with MOI 2 of PR8 influenza A virus for 2 hours in infection media (1:1 DMEM/PBS), after which virus-containing media was removed and replaced with DMEM with 10% FBS. Infection was allowed to porceed for 22 hour for a total 24 hour infection period. Control cells had media replaced with infection media for 2 hours, after which 10% FBS containing DMEM was replaced for the remainder of the time.

tag: sp-r210 isoform expression

value: RAW264.7 cells with SP-R210ct pTriex-2-Neo vector

tag: iav infection

value: Uninfected


title: Infected WT RAW Cells 2

description:
processed data file:
WTRNA_InfvUninf.csv
WTRNAvDNRNA_Inf.csv

value: WT RAW 264.7 cells with empty pTriex-2-Neo vector

value: PR8 IAV Infected, MOI2


title: Ctrl2


title: Infected WT RAW Cells 1


title: Infected SP-R210L(DN) RAW Cells 2

description:
processed data file:
DNRNA_InfvUninf.csv
WTRNAvDNRNA_Inf.csv


title: mOct4-rescued ZHBTC4 clone 2

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

description: Gene expression after establishing POUV rescue-cell line

hyb_protocol: Fragmentation was performed on 600 ng of cRNA from each sample  and the fragmented cRNA was then hybridized to Agilent Mouse 8X60K slides (Grid_GenomicBuild: mm9:NCBI37:Jul2007) for 17h at 65 ºC. Processed slides were then washed with Agilent wash buffers

scan_protocol: scanned on an Agilent Scanner (Agilent Technologies, G2600D SG12524268)

data_processing: The data were analyzed using the NIA Array Analysis Tool (http://lgsun.grc.nia.nih.gov/ANOVA/bin/login.cgi)

source_name: ZHBTc4, mOct4, with tetracycline, with Puromycin, clone 2

label_protocol: High quality total RNA (RNA integrity number = 10) was labeled with Cyanine 3 CTP and purified using Qiagen’s RNeasy Mini Spin Columns. The quantity of purified Cy3 labelled cRNA was measured using aNanodrop spectrophotometer.

growth_protocol: ESC were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma)  containing 0.1 mM non-essential amino acids (Sigma), 2 mM L-glutamine (Invitrogen), 1.0 mM sodium pyruvate (Invitrogen), 0.1 mM β –mercaptoethanol (Sigma), 10% Fetal Bovine Serum (FBS, Invitrogen) and LIF (homemade). The flasks/dishes (Corning) for ESC culture were coated with 0.1% gelatin in PBS.

extract_protocol: RNA preparations were performed using the RNeasyTM Mini Kit (Qiagen)

treatment_protocol: Ten million ZHBTc4 ESCs were electroporated with 100 μg of linearized pCAG-IP-POUV plasmid (Gene Pulser Xcell™ Electroporation Systems at 0.8 kV, 10 μF, 0.4 mm cuvette). One million electroporated cells were then plated into gelatinized 100 mm culture dishes containing ESC medium with and without tetracycline (Sigma) (Tc, 2 μg/mL). At day 2 post electroporation, the medium was replaced with ESC medium supplemented with 1 μg/mL puromycin (Sigma) (with and without Tc) to select the cells expressing transfected POUV genes and the medium was changed every other day thereafter. At day 9 post electroporation, the resulting ESC colonies were fixed and stained for alkaline phosphatase activity and several colonies were picked for expansion to generate stable lines.

tag: cell line

tag: cell type

value: mouse embryonic stem cells


title: Uninfected WT RAW Cells 1

description:
processed data file:
WTRNA_InfvUninf.csv


title: Set3 of Hst1 deleted cells

value: Set3 of Hst1 deleted cells


title: Uninfected SP-R210L(DN) RAW Cells 1


title: SP-R210L(DN) H3K27me3 ChIP

description:
DN_H3K27me3
DN_H3K27me3ChIP

data_processing:
FASTQ sequences were aligned to the mm10 genome using the mem function of the bwa package. Peaks were identified from the bed files using the callpeaks function of MACS2 (v2.1.0). Peak annotation and identification of overlapping peaks was done via ChIPpeakAnno (v3.14) using the UCSC mm10 annotated genome.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files are provided for each respective sample

growth_protocol: RAW264.7 cells were stably transfected with empty for SP-R210ct pTriex-2-Neo vectors and selected using 600ug/mL neomycin sulfate to generate WT and SP-R210L(DN) RAW264.7 cells, respectively. Five plates of WT and SP-R210L(DN) RAW 264.7 macrophages were cultured at density of 1E7 for each sample.

extract_protocol:
Cells were removed from plaates and cross-linked with 1% formaldehyde for 10 minutes. Nuclei were extracted from cell pellets via 10 minute incubation via incubation in L1 lysis buffer (50mM Hepes KOH, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, pH7.5) and L2 lysis buffer (200 mM NaCl, 1mM EDTA, 0.5mM EGTA, 10mM Tris, pH8.0). Pelleted nuclei was resuspended in 5 mL of L3 buffer (1mM EDTA, 0.5mM EGTA, 10mM Tris, 1x protease inhibitor) and DNA from nuclei was fragmented using the Bioruptor sonicator for 30 min (30s pulses, 30s pauses in between for 10 min, run 3 times). 25 uL of sheared DNA was aliquoted to run as input DNA. anti-PU.1 antibody , anti-H3K4me3,  anti-H3K9me3 , or anti-H3K27me3 bound Goat-anti-rabbit IgG Dynabeads  were incubated with 500 uL chromatin in TE buffer (with 0.1% deoxycholate, 1% Triton X-100) overnight . Protein/DNA complexes were washed and captured with a Magnetic Particle Concentrator. DNA-protein crosslink was reversed via incubation at 65oC overnight and then  treated with 1 mg/mL proteinase K for 2 hours at 37oC. DNA was extracted using phenol and chloroform extraction and precipitated using 100% EtOH. The dried DNA pellet was reconstituted in 50 uL H2O treated with 330ug/mL of RNase A for 2 hours at 37oC and then recovered using the QIAquick PCR Purification kit
ChIP-seq libraries were created using Kapa HyperPrep Kit (Roche Sequencing and Life Science). The unique dual index sequences (NEXTFLEX® Unique Dual Index Barcodes, BioO Scientific) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
Pooled libraries were diluted and then denatured using the Illumina protocol. The denatured libraries were loaded onto a TruSeq v2 Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe.

treatment_protocol: Infected cells were infected with MOI 1 of PR8 influenza A virus for 2 hours in infection media (1:1 DMEM/PBS), after which virus-containing media was removed and replaced with DMEM with 10% FBS. Infection was allowed to porceed for 22 hour for a total 24 hour infection period. Control cells had media replaced with infection media for 2 hours, after which 10% FBS containing DMEM was replaced for the remainder of the time.

tag: cell line background

value: RAW264.7 RAW

tag: chip antibody

value: anti-H3K27me3-bound Goat-anti-rabbit IgG Dynabeads

tag: chip antibody source

value: Abcam Cat #ab8580


title: LcPOU5F3-rescued ZHBTc4 clone 1

source_name: ZHBTc4, coelacanth POU5F3, with tetracycline, with Puromycin, clone 1


title: SP-R210L(DN) H3K9me3 ChIP

description:
DN_H3K9me3
DN_H3K9me3ChIP

value: anti-H3K9me3-bound Goat-anti-rabbit IgG Dynabeads

value: Abcam Cat #ab8898


title: 14-104_14 day_mild TBI/NS (14-104-HC)

tag: strain

value: Wistar Han

tag: gender

value: Male

value: 6 Weeks

value: mild TBI/NS

value: 14 days post injury

value: Hippocampus

value: Unknown


title: LcPOU5F3-rescued ZHBTc4 clone 2

source_name: ZHBTc4, coelacanth POU5F3, with tetracycline, with Puromycin, clone 2


title: mOct4-rescued ZHBTC4 clone 1

source_name: ZHBTc4, mOct4, with tetracycline, with Puromycin, clone 1


title: PolII of Hst1 & Hos2 double deleted cells


title: Set3 of Hst1 & Hos2 double deleted cells


title: PolII of Hos2 deleted cells

value: PolII of Hos2 deleted cells


title: Uninfected WT RAW Cells 2

value: WT RAW 264.7 cells with empty pTriex-2-Neo vector

value: Uninfected


title: Set3 of wild-type cells

value: Set3 of wild-type cells


title: Set3 of Hos2 deleted cells

value: Set3 of Hos2 deleted cells


title: PolII of wild-type cells

value: PolII of wild-type cells


title: WT_H3ChIPinput

value: RAW264.7 RAW


title: SP-R210L(DN) H3K4me3 ChIP

description:
DN_H3K4me3
DN_H3K4me3ChIP

value: RAW264.7 cells with SP-R210ct pTriex-2-Neo vector

value: anti-H3K4me3-bound Goat-anti-rabbit IgG Dynabeads

value: Sigma Aldrich Cat #07-449


title: DN_H3ChIPinput


title: WT H3K27me3 ChIP

description:
WT_H3K27me3
WT_H3K27me3ChIP

value: anti-H3K27me3-bound Goat-anti-rabbit IgG Dynabeads

value: Abcam Cat #ab8580


title: WT H3K9me3 ChIP

description:
WT_H3K9me3
WT_H3K9me3ChIP

value: anti-H3K9me3-bound Goat-anti-rabbit IgG Dynabeads

value: Abcam Cat #ab8898


title: DN_ChIPinput_inf1

value: PR8 IAV Infected, MOI 1


title: DN_ChIPinput_inf2


title: Infected SP-R210L(DN) Cells PU.1 ChIP 2

description:
DNInf_ChIP_PU1_2
DN_PU1ChIP_inf2

value: anti-PU.1 antibody-bound Goat-anti-rabbit IgG Dynabeads

value: Invitrogen Cat #MA5-15064, clone E.388.3


title: WT H3K4me3 ChIP

description:
WT_H3K4me3
WT_H3K4me3ChIP


title: BTXA2

value: submandibular gland

value: male

value: BTXA

value: SD


title: WT_ChIPinput_inf1

value: WT RAW 264.7 cells with empty pTriex-2-Neo vector


title: Infected WT RAW Cells PU.1 ChIP 2

description:
WT_Inf_ChIP_PU1_2
WT_PU1ChIP_inf2


title: S3_RRBS

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

department: Biological Sciences

institute: Florida State University

description:
tissue punch
S4_CTATAC

data_processing:
Base-calling was performed by CASAVA.  Resulting sequencing reads were demultiplexed using bcl2fastq_v1.8.4.
Sequenced reads were trimmed for adapter sequences, low-quality base-calls (< 20;phred 33), and too short reads (< 20 bases), and an artifact of RRBS library preparation (if captured during sequencing); then, the resulting trimmed reads were mapped to a bisulfite converted rn6 genome using Bismark_v0.19.0 with parameters: --directional -q --score-min L,0,-0.2 -p 2 --reorder --ignore-quals
Binary alignment mapping files were sorted using samtools and were processed using methylKit_v1.4.1 with the following parameters: mincov=10 minqual=20 read.context="CpG"
Proccessed files in methylKit were assessed for differential methylation using getMethDiff() with the following parameters: difference=15, qvalue=0.05, type="all"
Genome_build: rn6
Supplementary_files_format_and_content: For processed files, they are in .wig format and each sample has an individual .wig file.  This format is a tab-delimited file with the following columns: chromosome, start position, end position, methylation percent.  Methylation percent refers to number of methylated Cytosine calls / total number of cytosine calls.

source_name: Stress Biological Replicate 3

extract_protocol:
Genomic DNA was isolated using the ZR-Duet DNA/RNA MiniPrep kit (cat. D7001) from Zymo Research Corp.  This kit is suitable for extraction of DNA and RNA molecules from a wide range of sources using trade-marked Clear-Spin column technology.
Libraries were prepared according to Diagenodes Premium RRBS Sequencing Kit (cat. C02030032).  Briefly, genomic DNA was digested using MspI, restriction fragment ends were filled in to produce a 3`-"A" base for ligation of Illumina Sequencing Adapters, and size selection using AMPure XP beads.  After size selection, samples were pooled and PCR-amplified for 25 cycles, and subsequently generated amplicons were treated with a Bisulfite Conversion Reagent.  Following Bisulfite Conversion, further PCR amplification of 15 cycles was performed to enrich the library, and after amplification, AMPure XP Beads were used to remove remaining primer oligos and any library fragments digested as a result of Bisulfite Conversion.

treatment_protocol: prolonged unpredictable stress, two stressors per day including: restraint (4hr), forced swim (15C, 5min), elevated platform (30min), tilted cage with wet bedding on orbital shaking (45o angle, 100 cycle/min. 1hr)

value: Sprague Dawley

tag: Sex

value: pre-frontal cortex

value: 3-5 wks (juvenile adolescent)


title: Infected WT RAW Cells PU.1 ChIP 1

description:
WT_Inf_ChIP_PU1_1
WT_PU1ChIP_inf1

value: RAW264.7 RAW


title: DN_ChIPinput_uninf2

value: RAW264.7 cells with SP-R210ct pTriex-2-Neo vector

value: Uninfected


title: S2_RRBS

description:
tissue punch
S3_CTAGCT

source_name: Stress Biological Replicate 2

tag: age


title: C4_RRBS

description:
tissue punch
C7_CCAACA

source_name: Control Biological Replicate 4


title: S1_RRBS

description:
tissue punch
S2_CGGAAT

source_name: Stress Biological Replicate 1


title: C3_RRBS

description:
tissue punch
C5_CATTTT

source_name: Control Biological Replicate 3


title: C1_RRBS

description:
tissue punch
C1_CAGGCG

source_name: Control Biological Replicate 1


title: DN_ChIPinput_uninf1


title: SP-R210L(DN) Cells PU.1 ChIP 2

description:
DNUninf_ChIP_PU1_2
DN_PU1ChIP_uninf2


title: WT_ChIPinput_uninf2


title: SP-R210L(DN) Cells PU.1 ChIP 1

description:
DNUninf_ChIP_PU1_1
DN_PU1ChIP_uninf1


title: WT_ChIPinput_uninf1


title: Infected SP-R210L(DN) Cells PU.1 ChIP 1

description:
DNInf_ChIP_PU1_1
DN_PU1ChIP_inf1


title: mRNA-seq Rep2

city: Tokorozawa

first: Hiroaki

last: Sako

country: Japan

institute: Waseda University

data_processing:
Adapter sequences were removed with Cutadapt
rRNA contmaination was removed from sequenced reads with Bowtie
Sequences were aligned to non-overlapped transcript sequences with Bowtie
Genome_build: mm10 and hg19 (reporter sequence was replaced with CFTR in hg19)
Supplementary_files_format_and_content: txt, raw counts

source_name: gastrocnemius

growth_protocol: DMEM high glucose with 10% FBS, streptomycin, and penicillin

extract_protocol:
Both skeletal muscle and cells were lysed with polysome lysis buffer
TruSeq Ribo Profile (Mammalian) Kit (illumina) was used with some modifications. For mRNA-Seq, ploA mRNA was purified before library construction.

value: 9 week old

tag: genotype/variation

value: WT


title: mRNA-seq Rep3


title: Ribosome profiling Rep2

data_processing:
Library strategy: Ribo-seq
Adapter sequences were removed with Cutadapt
rRNA contmaination was removed from sequenced reads with Bowtie
Sequences were aligned to non-overlapped transcript sequences with Bowtie
Genome_build: mm10 and hg19 (reporter sequence was replaced with CFTR in hg19)
Supplementary_files_format_and_content: txt, raw counts


title: mRNA-seq Rep1


title: Ribosome profiling Rep3


title: S4_RRBS

description:
tissue punch
S5_CTCAGA

source_name: Stress Biological Replicate 4


title: WT_ChIPinput_inf2


title: C2_RRBS

description:
tissue punch
C2_CATGGC

source_name: Control Biological Replicate 2


title: Ribosome profiling Rep1


title: WT RAW Cells PU.1 ChIP 2

description:
WTUninf_ChIP_PU1_2
WT_PU1ChIP_uninf2


title: WT RAW Cells PU.1 ChIP 1

description:
WTUninf_ChIP_PU1_1
WT_PU1ChIP_uninf1


title: w303vsby4743-2

city: Torino

first: Irene

last: Stefanini

address: via Accademia Albertina

country: Italy

institute: University of Turin

description: Arsenic-sensitive strain

hyb_protocol: Hybridization took place at 65 °C for 16 h.

scan_protocol: Fluorescent DNA bound to the microarray was detected with a GenePix 4000B microarray scanner (Axon Instruments), using the GenePixPro6.1 software package to quantify microarray fluorescence.

data_processing: Data were normalized using the limma R package and DEGs (Differentially Expressed Genes) were identified with the RankProduct R package

label_protocol: The genomic DNA extracted was concentrated using the filter Microcon YM-30 (Millipore) and fragmented by sonication. The labeling of the DNA was performed, at 37°C for 2 hours, using the BioPrime DNA labeling Sytem (Invitrogen, Life Technologies), but using 100mM dNTP set (Invitrogen, Life Technologies) instead of the biotinilated nucleotides present in the kit, as well as the fluorescent nucleotides Cy3-dCTP and Cy5-dCTP of Amersham, GE Healthcare. Once finished the reaction, the DNA was purified with the Microcon YM-30 and the appropriate pairs of samples labeled with the different fluorochromes were combined in a single eppendorf in 450µL of TE (Tris-EDTA), pH 8.0 (Sigma-Aldrich). We used Human cot-1 DNA (Invitrogen, Life Technologies) to block non-specific hybridization, and Yeast tRNA (Invitrogen, Life Technologies) as coprecipitant.

growth_protocol: strains were grown in YPD (1% Yeast Extract, 2% Peptone, 2% glucose) overnight at 30€™C in shaking.

extract_protocol: genomic DNA was extracted from over-night strains cultures with the phenol-chloroform protocol. DNA quality was checked through gel electrophoresis and photometric measurement.

source_name: laboratory


title: 4T1_1_ENMD_1.25uM_2

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

data_processing:
Quality of the raw reads data for each sample was first evaluated using FastQC (version 0.11.3). RNA-seq data were mapped to the reference genome (hg38 and mm10) using Bowtie/TopHat. The reads were counted with HTSeq, and the differential expression between experimental groups was quantified using DESeq2 (Fold change > 2 and P value < 0.05)
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: .txt and counts

growth_protocol: 2×10e5 MDA-MB-231 cells were plated in a 6-well plate for 24 h and then treated with ENMD-2076 at 2.5 or 5 µmol/L(or TAK901 at 1 or 2 µmol/L) for 24 h. 1 × 105 4T1 cells were plated in a 6-well plate for 24 h and then treated with ENMD-2076 at 1 or 2 µmol/L(or TAK901 at 1 or 2 µmol/L) for 24 h

extract_protocol:
total RNA was isolated using TRIzol (Invitrogen).
The libraries were constructed by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on HiSeq 2500 sequencing system (Illumina)


title: 4T1_1_ENMD_1.25uM_1


title: sk1vsby4743-2

description: Arsenic-sensitive strain


title: sk1vsby4743-1

description: Arsenic-sensitive strain


title: sgu90vsby4743-2

description: Arsenic-resistant strain

source_name: Wine grape


title: sgu90vsby4743-1

description: Arsenic-resistant strain


title: 4T1_2_ENMD_2.5uM_2


title: sgu407vsby4743-2

description: Arsenic-sensitive strain


title: sgu407vsby4743-1

description: Arsenic-sensitive strain


title: 4T1_2_ENMD_2.5uM_1


title: w303vsby4743-1

description: Arsenic-sensitive strain


title: SG60vsby4743-2

description: Arsenic-resistant strain


title: sgu406vsby4743-2

description: Arsenic-sensitive strain


title: 9_miRsup

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Huh7 human hepatoma cells

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

growth_protocol: Huh7 cells were grown in DMEM with 10% FBS and Pen-Strep. Cells were seeded in 6-well plates in DMEM without antibiotics for the transfection experiments. 24h post seeding, cells were transfected.

extract_protocol: 48h post transfection, cells were trypsinized and harvested, and total RNA was extracted. miRNA expression was validated by qPCR before sending the samples for gene expression profiling.

treatment_protocol: Huh7 cells were transiently transfected with scramble control or miRNA mimic to see the effect on global gene expression.

value: human hepatoma


title: SG60vsby4743-1

description: Arsenic-resistant strain


title: sgu114vsby4743-1

description: Arsenic-resistant strain


title: 7_control


title: sgu406vsby4743-1

description: Arsenic-sensitive strain


title: 10_miRsup


title: m57vsby4743-2

description: Arsenic-sensitive strain


title: 8_control


title: sgu114vsby4743-2

description: Arsenic-resistant strain


title: 2_control


title: LcPOU5F1-rescued ZHBTc4 clone 4

source_name: ZHBTc4, coelacanth POU5F1, with tetracycline, with Puromycin, clone 4

value: mouse embryonic stem cells


title: 3_miRsup


title: 4_miRsup


title: m57vsby4743-1

description: Arsenic-sensitive strain


title: Patient 12 A14

city: seongnam

first: Kyunggi

last: Cho

address: yatap 59

department: neurosurgery

country: South Korea

institute: CHA bundang medical center

description:
A14
750 mRNA
Log2 normalized counts

hyb_protocol: 5μL (100-300ng) of each RNA sample was mixed with 8μL of the Master Mix (reporter codeSet and hybridization buffer). 2μL of the capture probeSet was added; the solution was mixed and spun down. It was placed in a 65°C thermocycler (Bio-Rad Laboratories Inc, Hercules, California, USA) for 16 hours (maximum hybridization time should not exceed 48 hours).

scan_protocol: The samples were transferred to the preparation station (NanoString Technologies, Seattle, WA) with prepared nCounter Master Kit and a cartridge. The samples binding to the cartridge. The preparation station 12 lanes per run in approximately 2.5 to 3 hours. The cartridges were transferred to the Digital Analyzer (NanoString Technologies, Seattle, WA) for analysis. Cartridges were then scanned on the Digital Analyzer at 555 fields of view.

data_processing: To quantify gene expression values, first normalization step was analyzed by geNormalgorithm in nCounter Advanced Analysis ver2.0.115.

label: NanoString Oligonucleotide Probe

source_name: Recurrent GBM

label_protocol: The RNA samples were run on the NanoString nCounter Analysis System (NanoStringTechnologies, Inc., WA, USA) according to the manufacturer's directions.

growth_protocol: Not available.

extract_protocol: RNA was extracted from tumor tissues of patients with recurrent GBM prior to AKC treatment.

treatment_protocol: Not available.

tag: diagnosis

value: Recurrent glioblastoma

value: Glioblastoma tumor

value: Male

tag: os

value: Alive

tag: os time (month)

tag: pfs

value: Not progression

tag: fps time (month)

tag: outcome

value: Durable response


title: Patient 11 A12

description:
A12
750 mRNA
Log2 normalized counts

tag: tissue

value: Female

value: Dead

value: Progression

value: Poor response


title: 1014gamma1svsby4743-1

description: Arsenic-sensitive strain


title: m28vsby4743-1

description: Arsenic-sensitive strain


title: em93vsby4743-1

description: Arsenic-sensitive strain


title: Patient 09 A10

description:
A10
750 mRNA
Log2 normalized counts


title: 1014gamma1svsby4743-2

description: Arsenic-sensitive strain


title: Patient 10 A11

description:
A11
750 mRNA
Log2 normalized counts


title: 1_control

tag: cell line


title: em93vsby4743-2

description: Arsenic-sensitive strain


title: Patient 06 A06

description:
A06
750 mRNA
Log2 normalized counts


title: Patient 07 A07

description:
A07
750 mRNA
Log2 normalized counts


title: Patient 08 A08

description:
A08
750 mRNA
Log2 normalized counts


title: Patient 04 A04

description:
A04
750 mRNA
Log2 normalized counts


title: Patient 03 A03

description:
A03
750 mRNA
Log2 normalized counts


title: Patient 05 A05

description:
A05
750 mRNA
Log2 normalized counts


title: SC_Y-50049_28h

city: Peoria

first: Z Lewis

state: IL

address: 1815 N University

institute: USDA-ARS

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 28h.
Y-50049(28h)

hyb_protocol: Hybridization was performed based on Hegde et al. (2000, BioTechniques 29:548-562) with modifications using TECAN HS 4800 Hybridization station (TECAN, Research Triangle Park, NC USA).

scan_protocol: Microarray slides were scanned using a GenePix 4000B scanner. A pre-scan control mini-array was used to adjust PMT Gain against Cy3 and Cy5 channels and the ratios of signal intensities between Cy3 and Cy5 were balanced to 1.0 using the calibration control as described by Liu and Slininger (2007). Each spot was individually examined and adjusted. Invalid spot was flagged as necessary.

data_processing:
Median of foreground signal intensity subtracted by background for each dye channel was used for analysis. Raw data for each slide were normalized based on spike-in control gene CAB (CtrlGm_5), and the normalized data were analyzed using GeneSpring GX 10.0. Expression values less than 50 in 1 of 26 samples were filtered out from probesets, then as subject of Hierarchical clustering analysis and 2-way ANOVA analysis (p≤0.05). Significant differential expressions were defined by at least 3-fold changes at each time point separately.
Normalized log2 ratio representing test/reference.

source_name: Yeast RNA, furfural and HMF untreated, 0min

label_protocol: 15 μg of total RNA was used for each sample labeling reaction in a total volume of 30 μl. RNA probe together with incorporated RNA controls was labeled using an indirect dUTP Cy3 or Cy5 dye as described by Liu and Slininger (2007, J. Microbiol Methods 68:486-496).

growth_protocol: The yeast strains were maintained and cultured on YM medium (0.3% yeast extract, 0.3% malt extract, 0.5% peptone, 2% glucose). Culture inocula were prepared using freshly grown cells harvested at logarithmic growth phase after incubation with agitation of 250 rpm at 30˚C for 16 h. Pre-culture cells were incubated on YM medium to 0.03 0f OD600 in a fleaker fermentation system at 30˚C with agitation.

extract_protocol: Total RNA was extracted by hot phenol method and further purified using RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: Furfural and HMF were added into the culture after 6-h pre-culture at a final concentration of 20 mM each. The time point of the furfural-HMF treatment was designated as 0 h.

tag: treatment

value: furfural and HMF untreated, 0min

source_name: Yeast RNA, furfural and HMF treated, 28h

value: Y-50049 (adapted tolerant industrial yeast)


title: m28vsby4743-2

description: Arsenic-sensitive strain


title: LcPOU5F1-rescued ZHBTc4 clone 5

source_name: ZHBTc4, coelacanth POU5F1, with tetracycline, with Puromycin, clone 5

tag: cell type


title: Patient 02 A02

description:
A02
750 mRNA
Log2 normalized counts


title: Patient 01 A01

description:
A01
750 mRNA
Log2 normalized counts


title: SC_Y-50049_24h

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 24h.
Y-50049(24h)

source_name: Yeast RNA, furfural and HMF treated, 24h


title: Infected SP-R210L(DN) RAW Cells 1

source_name: Modified RAW264.7 RAW Cell Line

tag: sp-r210 isoform expression

value: RAW264.7 cells with SP-R210ct pTriex-2-Neo vector

tag: iav infection

value: PR8 IAV Infected, MOI2


title: hpr1Δ_37C_15

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

description:
hpr1_37C_15min
BY4741 hpr1Δ
ssDNA

hyb_protocol: In each experiment a G1 control sample and an S phase sample (released into S phase at 37C for 10, 15, 20 and 25 min) were paired and the DNA cohybridized to Agilent G4493A Yeast Whole Genome ChIP-on-Chip 4x44k microarrays.

scan_protocol: Scanned on an Agilent G2565B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization. Chromosome coordinates (kb) for each probe were extracted.

label_protocol: Agarose-embedded chromosomal DNA samples were differentially labeled for ssDNA by random-primed DNA synthesis by Klenow (Exo-), with Cy5- or Cy3-conjugated dUTP. All procedures were performed as previously described (Feng et al., G3 (Bethesda) 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554).

growth_protocol: Cells grown exponentially at 30°C were synchronized in G1 by 3 µM α factor. Fifteen minutes prior to the release into S phase by 0.3 mg/ml pronase addition, half of the cells were shifted to 37°C and used for ssDNA mapping. As control (for flow cytometry analysis) the other half of the culture were maintained at 30°C and released into S phase at 30°C. Following the release into S phase, cells were sampled at 10, 15, 20 and 25 min and subjected to ssDNA labeling.

extract_protocol: ssDNA-labeled chromosomal DNA was extracted from agarose plugs by beta-agarase digestion and sonicated in a Bioruptor to reduce DNA fragment size to an average of 500 bp.

tag: strain

value: BY4741 hpr1<delta>

tag: growth phase

value: G1 control

value: S

tag: time point

value: 15 min post shift to 37C


title: SC_Y-50049_18h

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 18h.
Y-50049(18h)

source_name: Yeast RNA, furfural and HMF treated, 18h


title: SC_Y-50049_8h_rep2

description:
Biological replicate 2 of 2.  Furfural and HMF (20mM each) treated, harvested at 8h.
Y-50049(8h)-II

source_name: Yeast RNA, furfural and HMF treated, 8h


title: hpr1Δ_37C_25

description:
hpr1_37C_25min
BY4741 hpr1Δ
ssDNA

value: 25 min post shift to 37C


title: 2_min_after_exercise_9

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35), also 5’-guanine was clipped.
Reads were aligned using STAR (v2.7.0a) with mismatch rate threshold 0.06
rRNA reads and reads from mitochondrial genome excluded using split_bam.py script (RSEQC) with combined annotation (RefSeq and Ensembl rRNA genes and mt genome). Only uniquely mapped reads were used for further analysis.
TSS tag clusters were identified using DPI (Decomposition-based peak identification) for unique mapped filtered reads (50 samples)
TSS tag clusters were annotated using consistently Ensembl (GRCh38.101), Refseq (08/15/2020) and Cufflinks-based annotation (stranded RNA-Seq data, GSE120862).
Genome_build: GRCh38.p13 primary assembly genome
Supplementary_files_format_and_content: Robust DPI TSS clusters (.bed file) and its annotation (tab-delimited .txt)

source_name: muscle vastus lateralis

extract_protocol:
RNA was extracted from the frozen samples (~20 mg) using an RNeasy mini kit (Qiagen, Germany) with DNase I treatment (Fermentas, Lithuania). The RNA concentration and integrity were evaluated in a fluorimeter (Qubit 3.0; Thermo Scientific) and by capillary electrophoresis (Bioanalyzer 2100, Agilent, USA), respectively; all samples were at least 7 in RIN.
Libraries were constructed from 2.5-3 mg of RNA according to nAnT-iCAGE (non-Amplified non-Tagging Illumina Cap Analysis of Gene Expression) protocol  using nAnT-iCAGE Library Preparation kit (DNAform, Japan) and SuperScript III Reverse Transcriptase (Invitrogen, USA). The concentration of the obtained libraries was measured on a Qubit 3.0 fluorimeter (Thermo Scintific, USA); the quality of the libraries was checked using an Agilent Bioanalyzer 2100 (Agilent Technologies, USA). The libraries were then validated using real-time PCR (KAPA Library Quantification Kits Illumina, KAPA Biosystems, South Africa) and sequenced

treatment_protocol: Amateur endurance-trained athletes (10 long distance runners, cyclists and cross country skiers, median age, 32 years [interquartile range, 30–36 years]; weight, 75 kg [71–78 kg]; V’O2max/kg [maximal pulmonary O2 consumption rate], 58 ml/min/kg [54–60 ml/min/kg of body mass]) were involved in our study. An intermittent exercise induces greater molecular response compare to a continuous exercise with the same average power. Hence, each subject carried out an intermittent exercise (60 min, [3 min, 50% LT4 [power at lactate threshold at 4 mmol/l] + 2 min, 100% LT4]  12) on a cycle ergometer (Ergoselect 200, Ergoline, Germany) 2 h after a standardized breakfast (3582 kJ; 22 g protein, 154 g carbohydrates and 16 g fat). The LT as well as V’O2max – markers of aerobic performance, were evaluated in a preliminary test session in the incremental cycling test till exhaustion using a Biosen C line analyzer (EKF Diagnostics, Germany) and a medical gas mass-spectrometer AMIS 2000 with a mixing chamber (Innovision, Denmark), as describe elsewhere. Subjects ate a standardized lunch (3714 kJ; 45 g protein, 183 g carbohydrates and 27 g fat) 1 h 15 min after an intermittent exercise. Biopsy samples were taken under local anesthesia (2 mL 2% lidocaine) using a Bergstrome needle with aspiration from the m. vastus lateralis prior to, 2 min, 1 h, 3 h, and 6 h after an intermittent exercise (1st, 2d, and 3d from the one leg, 4st and 5st from another leg) (Figure 1). The muscle samples were quickly blotted with gauze to remove superficial blood, frozen in liquid nitrogen, and stored at -80°C until required.

value: skeletal muscle

tag: individual

value: + 2 min after exercise

tag: training status

value: endurance trained amateur athlete

tag: Sex

value: male

tag: age

tag: weight

tag: height

tag: bmi


title: HPR1_37C_20

description:
WT_37C_20min
ssDNA

value: 20 min post shift to 37C


title: hpr1Δ_37C_20

description:
hpr1_37C_20min
BY4741 hpr1Δ
ssDNA


title: hpr1Δ_37C_10

description:
hpr1_37C_10min
BY4741 hpr1Δ
ssDNA

value: 10 min post shift to 37C


title: 2_min_after_exercise_8


title: 2_min_after_exercise_10


title: SC_Y-50049_2h_rep1

description:
Biological replicate 1 of 2.  Furfural and HMF (20mM each) treated, harvested at 2h.
Y-50049(2h)-I

source_name: Yeast RNA, furfural and HMF treated, 2h


title: SC_Y-50049_8h_rep1

description:
Biological replicate 1 of 2.  Furfural and HMF (20mM each) treated, harvested at 8h.
Y-50049(8h)-I


title: SC_Y-50049_2h_rep2

description:
Biological replicate 2 of 2.  Furfural and HMF (20mM each) treated, harvested at 2h.
Y-50049(2h)-II


title: 2_min_after_exercise_7


title: HPR1_37C_25

description:
WT_37C_25min
ssDNA


title: SC_Y-50049_1h_rep2

description:
Biological replicate 2 of 2.  Furfural and HMF (20mM each) treated, harvested at 1h.
Y-50049(1h)-II

source_name: Yeast RNA, furfural and HMF treated, 1h


title: 2_min_after_exercise_6


title: 2_min_after_exercise_4


title: 2_min_after_exercise_5


title: 2_min_after_exercise_3


title: HPR1_37C_15

description:
WT_37C_15min
ssDNA


title: 2_min_after_exercise_2


title: SC_Y-50049_1h_rep1

description:
Biological replicate 1 of 2.  Furfural and HMF (20mM each) treated, harvested at 1h.
Y-50049(1h)-I


title: SC_Y-50049_30min_rep1

description:
Biological replicate 1 of 2.  Furfural and HMF (20mM each) treated, harvested at 30min.
Y-50049(0.5h)-I

source_name: Yeast RNA, furfural and HMF treated, 30min


title: SC_Y-50049_30min_rep2

description:
Biological replicate 2 of 2.  Furfural and HMF (20mM each) treated, harvested at 30min.
Y-50049(0.5h)-II


title: 2_min_after_exercise_1


title: SC_Y-50049_10min_rep2

description:
Biological replicate 2 of 2.  Furfural and HMF (20mM each) treated, harvested at 10min.
Y-50049(0.2h)-II

source_name: Yeast RNA, furfural and HMF treated, 10min


title: SC_Y-50049_10min_rep1

description:
Biological replicate 1 of 2.  Furfural and HMF (20mM each) treated, harvested at 10min.
Y-50049(0.2h)-I


title: HPR1_37C_10

description:
WT_37C_10min
ssDNA


title: SC_Y-50049_0min_rep2

description:
Biological replicate 2 of 2. None treated control, harvested at 0min.
Y-50049(0h)-II

source_name: Yeast RNA, furfural and HMF treated, 0min


title: SC_Y-50049_0min_rep1

description:
Biological replicate 1 of 2. None treated control, harvested at 0min.
Y-50049(0h)-I


title: HeLa miRNA

first: Xiaowo

address: Qinghuayuan, Haidian

institute: Tsinghua University

data_processing:
TopHat (2.1.1)
Cufflinks (2.2.1)
miRDeep2 (0.1.2)
Genome_build: RNA: hg38
Genome_build: miRNA: hg19
Supplementary_files_format_and_content: isoforms.fpkm_tracking, FPKMs of RNAs
Supplementary_files_format_and_content: miRNA.count, counts of miRNAs

source_name: HeLa cell line

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA was enriched by Oligo(dT), ligated with adapters, and then sequenced by NovaSeq 6000 (Illumina).
Small RNA was isolated by PEG8000, ligated with adapters, and then sequenced by Hiseq2500 (Illumina)

value: HeLa


title: SC_Y-12632_8h

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 8h.
Y-12632(8h)


title: SC_Y-12632_2h_rep1

description:
Biological replicate 1 of 2.  Furfural and HMF (20mM each) treated, harvested at 2h.
Y-12632(2h)-I


title: SC_Y-12632_2h_rep2

description:
Biological replicate 2 of 2.  Furfural and HMF (20mM each) treated, harvested at 2h.
Y-12632(2h)-II


title: SC_Y-12632_28h

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 28h.
Y-12632(28h)


title: SC_Y-12632_1h

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 1h.
Y-12632(1h)


title: SC_Y-12632_30min_rep2

description:
Biological replicate 2 of 2.  Furfural and HMF (20mM each) treated, harvested at 30min.
Y-12632(0.5h)-II


title: SC_Y-12632_24h

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 24h.
Y-12632(24h)


title: SC_Y-12632_30min_rep1

description:
Biological replicate 1 of 2.  Furfural and HMF (20mM each) treated, harvested at 30min.
Y-12632(0.5h)-I


title: SC_Y-12632_10min

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 10min.
Y-12632(0.2h)


title: sgDROSHA mRNA-seq Rep1

description: non-clonal

tag: genotype/variation

value: DROSHA KO


title: sgDROSHA mRNA-seq Rep2

description: non-clonal


title: SC_Y-12632_0min

description:
No biological replicate. None treated control, harvested at 0min.
Y-12632(0h)

value: furfural and HMF untreated, 0min


title: NTC mRNA-seq Rep2

description: non-clonal

value: WT


title: Tumor T19 polysome-associated mRNA

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA sequencing reads were aligned to mm10 using HISAT2 (D. Kim, B. Langmead, S. L. Salzberg, HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357-360 (2015)) and reads mapping to multiple locations in the genome were discarded.
Gene expression was quantified as described using default settings (D. Ramskold, E. T. Wang, C. B. Burge, R. Sandberg, An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5, e1000598 (2009).) and RefSeq gene definitions (N. R. Coordinators, Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46, D8-D13 (2018).).
Only genes with <4 missing data points were included.
Raw counts were TMM normalized (M. D. Robinson, A. Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11, R25 (2010)) and log2 transformed using Voom (M. E. Ritchie et al., limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43, e47 (2015).) in R 3.5.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RNA sequencing counts and TMM-log2 normalized data

source_name: CD11b+F4/80+Ly6G- macrophages

growth_protocol: PyMT cells were injected into the fourth inguinal mammary gland of anesthetized female FVB mice (5-7 weeks old). Mice with tumors of different sizes were sacrificed by cervical dislocation and the excised tumor was weighed prior to dissociation. Animals were purchased from Charles River Laboratory.

extract_protocol:
Polysome-profiling was performed  using macrophages isolated from 13 tumors ranging in size. Sorting of Møs from tumors was performed on a FACSJazz (BD Biosciences) flow sorter and gating the CD11b positive, F4/80 positive and Ly6G negative cell population. Sorted cells were kept in ice-cold PBS supplemented with 2% FBS and 100 μg/mL cycloheximide. For sorted TAMs, a fraction (~10%) of the obtained cell population was lysed in TRIzol reagent (ThermoFisher Scientific) and used for RNA sequencing with total RNA as input. Remaining cells were lysed in a hypotonic lysis buffer, as described and and lysates were  applied onto a 5%-50% (w/v) sucrose gradient, fractionated, and fractions corresponding to mRNA associated with 3 or more ribosomes were collected in TRIzol reagent for subsequent RNA extraction. Such pooled samples were used for RNA sequencing of efficiently translated polysome-associated mRNA.
SmartSeq2 sequencing libraries were prepared

tag: rna source

value: polysome-associated mRNA

tag: tumor weight

value: Tumor-associated macrophages (TAMs)

tag: experimental batch


title: Tumor ER3 polysome-associated mRNA

treatment_protocol: Mice with tumors of different sizes were sacrificed by cervical dislocation and the excised tumor was weighed prior to dissociation.

tag: cell type


title: Tumor LR3 polysome-associated mRNA


title: Tumor T22 polysome-associated mRNA


title: Tumor ER2 polysome-associated mRNA


title: Tumor LR2 polysome-associated mRNA


title: NTC mRNA-seq Rep1

description: non-clonal


title: Tumor T16 polysome-associated mRNA


title: Tumor ER1 polysome-associated mRNA


title: sgDROSHA Ribosome profiling Rep2

description: non-clonal


title: NTC Ribosome profiling Rep2

description: non-clonal


title: SC_Y-12632_18h

description:
No biological replicate. Furfural and HMF (20mM each) treated, harvested at 18h.
Y-12632(18h)

tag: treatment


title: Tumor T4 polysome-associated mRNA


title: Tumor LR1 polysome-associated mRNA


title: sgDROSHA Ribosome profiling Rep1

description: non-clonal


title: Tumor T3 polysome-associated mRNA


title: NTC Ribosome profiling Rep1

description: non-clonal


title: Tumor T2 polysome-associated mRNA


title: Tumor LR3 total mRNA

value: total mRNA


title: Tumor LR2 total mRNA


title: Tumor LR1 total mRNA


title: Tumor ER2 total mRNA


title: Tumor ER3 total mRNA


title: Tumor T22 total mRNA


title: Tumor ER1 total mRNA


title: Tumor T19 total mRNA


title: Tumor T15 polysome-associated mRNA


title: Tumor T16 total mRNA


title: Tumor T3 total mRNA


title: Tumor T4 total mRNA


title: Wild type oocyte rep2

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing:
sequence data were process by trim-galore
Clean data were mapped  to mm10 using Bismark
Methylation levels of CpG sites were extracted using Bismark suite
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, the forth column contains the methylation level

source_name: Wild Type Oocyte

growth_protocol: Briefly, MII oocytes without granulosa cells attachment (20 oocytes from five mice) were collected.

extract_protocol:
The oocytes were lysed in buffer containing 0.5 µl proteinase K for 1 h at 37°C. DNA was converted by the EZ DNA Methylation-Gold kit (Zymo Reserch) according to the instructions.
Then the converted DNA was subjected to library construction. The purified libraries were assessed for quality using High-Sensitivity DNA chips on the Agilent Bioanalyzer 2100 and StepOnePlus RealTime PCR System.
The libraries were sequenced on one lane of an Illumina HiSeq 2500 for 140-bp paired-end sequencing.

value: wild type


title: Wild type oocyte rep1


title: D257A ooycte rep3

source_name: D257A treated oocyte

value: D257A treated


title: Wild type oocyte rep3