title: 257864010001_1_1_SALS1

description: Sample 18

source_name: patients with clear SALS diagnosis

tag: Sex

tag: age at death (in years)

value: Sporadic Amyotrophic Lateral Sclerosis

value: medium term survival up to 6 yrs

value: caucasian

value: leg onset

tag: smoker or non smoker

tag: alchool use or not

value: abuse of acohol

tag: other pathologies

value: period of alcohol abuse as well as depression period in the past. Suffered stomach ache

tag: therapy used

value: theolair retard, temesta, lactulose, codeine, zantac, regla, tranxene, euphiline, morfine hcl

tag: vaccination boost


title: adjacent tissues-2P

status: Public on Dec 31 2018

type: RNA

city: NanJing

first: Zhengdong

last: Zhang

address: 101 Longmian Avenue

department: Department of Environmental Genomics, School of Public Health

country: China

institute: Nanjing Medical University

description: Gene expression of lncRNA and mRNA in gastric cancer adjacent tissues

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing: Data was extracted using Agilent Feature Extraction software.Normalization was performed using the Agilent GeneSpring GX v11.5.1.

molecule: total RNA

organism: Homo sapiens

source_name: gastric tumor adjacent tissues-2P

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: The total RNA was extracted from fresh tissues and cells using TRIzol reagent (Invitrogen, CA, USA). The quantity of RNA was assessed by NanoDrop ND-2000, and the RNA integrity was tested by standard denaturing agarose gel electrophoresis. RNA from the 5 paired tissues was used for microarray analysis by Arraystar Human lncRNA microarray V2.0 (Agilent, USA).

treatment_protocol: None of the patients received radiotherapy and chemotherapy before the surgery.

tag: tissue

value: gastric tissue

tag: gender

value: male


title: MGAS7912

type: SRA

city: Houston

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

country: USA

institute: Houston Methodist Research Institute

library_source: transcriptomic

data_processing:
Multiplexed SE libraries were sequenced on an Illumina NextSeq 500 instrument. Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.
RNAtag-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 and NOISeq-sim (NOISeq package) running in R version 3.4.0. Differentially expressed genes were identified in each of the 441 strains compared to a common reference strain (MGAS28737).
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina)
Resultant RNAs were tagged and pooled, reverse transcribed to cDNA, tagged a second time, pooled into superpools and sequenced

treatment_protocol: At the desired growth stage, early-stationary (OD 600nm 1.65), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: 257864010009_2_1_SALS1

type: genomic

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

description: Sample 19

hyb_protocol: After probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65°C with rotation for 24 hr.

scan_protocol: After two washing steps, arrays were scanned at 3 µm resolution using an Agilent G4900DA SureScan Microarray Scanner System.

data_processing:
aCGH image data were processed using Agilent’s Feature Extraction software to assess the array spot quality as well as check signal and background intensity statistics in default setting.Feature extracted raw data was normalized, analyzed and visualized using Agilent CytoGenomics v. 4.0.3.12 and Genomic Workbench v. 7.0.4.0 software (Agilent Technologies, Santa Clara, CA, USA). Briefly, after filtering for saturated and non-uniform probes, data were normalized by GC correction with a window size of 2 kb and Diploid Peak Centralization. The Centralization Normalization Algorithm with a threshold of 6.0 and a bin size of 10 was also used for detecting aberrant regions or regions of constant CNVs. Aberrations were detected by the Aberration Detection Method II algorithm (ADM-2), with a sensitivity threshold of 6.0 and moving average window of 2Mb, which permits to identify all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score. For chromosome X, only females were used and for chromosome Y only males were used.  An aberration filter was applied for identifying copy number alterations, changes were considered as true positive events with a minimum log2ratio test/control of ±0.5 and a minimum of 3 consecutive probes. Positive statistical score meant amplification, while negative score indicated deletion. Human reference sequence hg19 assembly was used to define the genomic coordinates of detected CNVs.
Normalized log2ratio (Cy5/Cy3) representing test/reference. Changes were considered as true positive events with a minimum log2ratio test/control of ±0.5 and a minimum of 3 consecutive probes.

molecule: genomic DNA

label_protocol: DNA test and a reference of the same sex (Euro Reference, Agilent Technologies, Santa Clara, CA), both at the concentration of 500 ng, were double digested with RsaI and AluI for 2 hours at 37°C. After heat inactivation of the enzymes at 65°C for 20 min, each digested sample was labeled by random priming by using the genomic DNA Enzymatic Labelling Kit (Agilent Technologies, Santa Clara, CA) for 2 hours using Cy5-dUTP for patient DNAs and Cy3-dUTP for reference DNAs. Labeled products were column purified by using the SureTag DNA Labeling Kit Purification Columns (Agilent Technologies, Santa Clara, CA).

extract_protocol: DNA extractions from frozen brain tissues and whole-blood samples were performed using standard procedures.Individual slices of 10 μm were produced from tissue samples at -20°C by a Leica CM1510S cryostat (Leica Microsystems) and stored at -80°C until further processing. Two slices per sample were stained by hematoxylin/eosin staining (Bio Optica) and for Nissl substance (with a microfiltered solution of cresyl violet, Sigma-Aldrich), respectively, to assess integrity of cellular and tissue morphology. Ten adjacent slices per sample were pooled and dissolved in SE buffer (750 m NaCl (pH 8), 250 m EDTA, 1% SDS) containing Proteinase K for DNA isolation. The extracted genomic DNA was quantified by ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and assessed for quality by microcapillary electrophoresis on 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: disease state

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

tag: occupation (job)

value: Plummer, intensive contact with copper and PVC-glue

value: smoker

value: more than moderate (3 /d men, 2/d women, elderly)

value: recidive sinusitis, suffered frequent colds

value: Participated in the n-acetylcysteine trial. Further medication Normison and Laxantia.

tag: familial anamnesis

source_name: Euro Reference, Agilent Technologies


title: ume6 YPD+10% serum 3

city: San Francisco

first: Suzanne

middle: M

last: Noble

state: CA

address: 513 Parnassus Ave., Box 0414

institute: UCSF

description: cells harvested at 5 hours

data_processing:
Real time base calling on Illumina HiSeq 4000
kallisto to align reads to genome with parameters: --plaintext --bias --single --rf-stranded -l $AvgLibSize -s $SD (AvgLibSize and SD pulled from BioAnalyzer traces)
extract estimated counts and tpms from abundances.tsv files
tpms and estimated counts = 0 replaced with 1, transcripts filtered to included only those with values greater than 10 in at least one sample
limma/voom with genotype.environment as factor to produce log base 2 fold changes and adj. p values from estimated counts
tpms were used for heat map generation
Genome_build: C. albicans SC5314 Assembly 21
Supplementary_files_format_and_content: excel files containing 1. fold changes and adjusted p-values and 2. tpms

molecule: polyA RNA

organism: Candida albicans

source_name: In vitro culture

extract_protocol:
Acid phenol chloroform extraction 4 times, phenol chloroform isoamyl extraction 4 times, additional cleanup using RNA SPRI bead mix
NEB Ultra Directional mRNA-seq

tag: strain (c. albicans/mus musculus)

tag: growth condition

value: YPD+10% serum

tag: time point

value: 5 hours


title: Mother_P037

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description: DNA extracted from peripheral venous blood of the mother.

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG).
Image data was analyzed using Genomestudio with genotyping module (Illumina).

label: Cy5, Cy3

source_name: Peripheral blood

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

extract_protocol: A total of 9 mL of peripheral venous blood from parents and 4 mL of umbilical cord blood were collected into ethylenediaminetetraacetic acid-containing tubes (BD Vacutainer, Becton, Dickinson and Co) for DNA extraction. DNA was isolated from blood and the placental tissue using PureLink® Genomic DNA Kit (Invitrogen, Life Technologies™) according to manufacturer’s protocol. DNA samples were eluted with 200 µL of PureLink® Genomic Elution Buffer (10 mM Tris-HCl, pH 9.0, 0.1 mM EDTA) and stored at -20 °C until analysis. NanoDrop 2000 (Thermo Fisher Scientific Inc.) was used to assess DNA concentration and purity.

treatment_protocol: Full-thickness placental blocks of around 1 cm were taken from the placenta and stored at -80 °C for subsequent DNA extraction. The maturity and health of the term placenta were confirmed by histological examination.

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: Natural

value: Peripheral blood

tag: birthweight at delivery

value: AGA


title: 257864010008_1_2_SALS1

description: Sample 15

tag: Sex

value: female

tag: age at death (in years)

value: Sporadic Amyotrophic Lateral Sclerosis

value: medium term survival up to 6 yrs

value: caucasian

value: trunk onset

value: Employed in agricultural machinery factory. Sportive type. Suffered a severe fall on her buttocks while skating on ice.

tag: smoker or non smoker

value: non smoker

tag: alchool use or not

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

tag: other pathologies

value: diverticulosis since 2nd WW. Benign mammay cyst. Uterus myoma. Melanoma right leg

tag: therapy used

value: Salazopyrin when needed

tag: vaccination boost


title: MGAS7922

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: gastric tumor-2Ca

description: Gene expression of lncRNA and mRNA in gastric cancer

source_name: gastric tumor-2Ca

tag: tissue

value: gastric tissue

tag: gender

value: male


title: Father_P037

description: DNA extracted from peripheral venous blood of the father.

value: multi cells

value: Natural

value: Peripheral blood


title: ume6 YPD+10% serum 2

description: cells harvested at 5 hours

tag: strain (c. albicans/mus musculus)

tag: growth condition

value: YPD+10% serum

tag: time point

value: 5 hours


title: Umbilicalcord_P037

description: DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood

tag: dna sample

tag: quartet

tag: conception method

value: Cord blood

value: AGA


title: MGAS7906


title: ume6 YPD+10% serum 1

description: cells harvested at 5 hours


title: ume6 YPD isolate 3

description: cells harvested at OD = 1

value: YPD

value: ~4.5 hours


title: Placenta_P037

description: DNA extracted from placenta tissue.

source_name: Placenta tissue

value: Placenta tissue

tag: birthweight at delivery


title: gastric tumor-12Ca

source_name: gastric tumor-12Ca


title: 257864010009_1_1_SALS1

description: Sample 13

tag: Sex

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

value: medium term survival up to 6 yrs

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

tag: location of onset

value: arm onset

tag: occupation (job)

tag: smoker or non smoker

value: non smoker

value: abstinent

value: Participated in the n-acetylcysteine trial

tag: familial anamnesis


title: MGAS7891

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: 257864010001_1_4_SALS1

description: Sample 12

value: male

value: long term survival more than 6 yrs

tag: alchool use or not

tag: other pathologies

tag: therapy used

value: rilutek

tag: vaccination boost


title: Mother_P035

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: Natural

tag: tissue

value: Peripheral blood

tag: birthweight at delivery

value: AGA


title: 257864010004_1_4_Control

description: Sample 10

source_name: control individual

tag: Sex

tag: age at death (in years)

tag: disease state

value: Control

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race


title: 257864010008_2_4_SALS1

description: Sample 11

value: Sporadic Amyotrophic Lateral Sclerosis

tag: location of onset

tag: occupation (job)

value: technical architecture head civil servant

tag: smoker or non smoker

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

value: (1989) Anamnesis of Chronic aspecific respiratory disease, hypertsension and adipositas. Uncinate fits (temporal epilepsy). In 1988 Salmonella typhimu

value: Hypertension medication (tagamet, inhibin, trasolan, isoptin). Participated in the Acetyl cyst. trial

tag: familial anamnesis


title: 257864010007_2_1_Control

description: Sample 9

value: caucasian

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: ume6 YPD isolate 2

description: cells harvested at OD = 1

tag: strain (c. albicans/mus musculus)

tag: growth condition

value: YPD

tag: time point

value: ~4.5 hours


title: Father_P035

tag: dna sample

tag: quartet

tag: conception method

tag: tissue

tag: birthweight at delivery


title: MGAS7886

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: ume6 YPD isolate 1

description: cells harvested at OD = 1


title: Umbilicalcord_P035

value: Cord blood


title: Placenta_P035

description: DNA extracted from placenta tissue.

value: multi cells

value: Placenta tissue


title: MGAS7890


title: WT YPD+10% serum 3

description: cells harvested at 5 hours

value: YPD+10% serum

value: 5 hours


title: MGAS7878


title: Mother_P030

value: Natural

value: Peripheral blood

value: AGA


title: MGAS7893


title: Father_P030


title: WT YPD+10% serum 2

description: cells harvested at 5 hours


title: WT YPD+10% serum 1

description: cells harvested at 5 hours


title: MGAS7869


title: 257864010009_2_4_Control

description: Sample 8

tag: Sex

value: male

tag: age at death (in years)

tag: disease state

value: Control

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

tag: occupation (job)

tag: smoker or non smoker


title: 257864010001_1_2_Control

description: Sample 6

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost

tag: familial anamnesis


title: 257864010008_2_1_Control

description: Sample 7


title: MGAS7872

tag: subclade

tag: site of isolation

value: upper respiratory tract isolate


title: 257864010007_1_2_Control

description: Sample 5

tag: Sex

value: caucasian


title: WT YPD isolate 3

description: cells harvested at OD = 1

tag: strain (c. albicans/mus musculus)

tag: growth condition

value: YPD

tag: time point


title: MGAS7867

tag: growth phase


title: MGAS7865


title: Placenta_P030

description: DNA extracted from placenta tissue.

tag: dna sample

tag: quartet

tag: conception method

tag: tissue

tag: birthweight at delivery


title: WT YPD isolate 2

description: cells harvested at OD = 1

value: ~4.5 hours


title: 257864010008_2_2_Control

description: Sample 4

value: female

tag: age at death (in years)

tag: disease state

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not


title: Umbilicalcord_P030


title: WT YPD isolate 1

description: cells harvested at OD = 1

tag: strain (c. albicans/mus musculus)

tag: growth condition

tag: time point


title: colorectal cancer HCT/neg3

status: Public on Dec 30 2018

city: Kamakura

first: Atsuko

last: Mizoguchi

state: Kanagawa

department: New Frontiers Research Laboratories

country: Japan

institute: Toray Industries, Inc.

description:
HCT/neg3
mRNA

hyb_protocol: Hybridized for 16h at 37C with rotary shake (250rpm). Hybridization buffer and washing protocol were followed by the protocol of the 3D-Gene® mRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.

source_name: HCT116 cells

label_protocol: cDNA and Amino Allyl aRNA were synthesized by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

extract_protocol: Total RNA was extracted using miRNeasy mini kit (Qiagen) and RNA extraction reagent from liquid sample kit (Toray Industries, Inc.) in accordance with the manufacturer's instructions.

tag: cell line

tag: cell type

value: colorectal cancer cell line

tag: treatment

value: miRNA-negative control


title: colorectal cancer HCT/neg2

description:
HCT/neg2
mRNA


title: colorectal cancer HCT/neg1

description:
HCT/neg1
mRNA


title: 257864010004_1_2_Control

description: Sample 2

tag: Sex

tag: other pathologies

tag: therapy used

tag: vaccination boost

tag: familial anamnesis


title: colorectal cancer HCT/mock2

description:
HCT/mock2
mRNA

value: mock


title: colorectal cancer HCT/8073_1

description:
HCT/8073_1
mRNA

value: miR-8073 mimic


title: colorectal cancer HCT/mock1

description:
HCT/mock1
mRNA


title: SPT15WT_Rep 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 600ng of labeled cRNA were hybridized on the array (AMADID: 16333) using the Agilent Gene Expression Hybridization kit (Part Number 5190-0404) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift method normalization method .Gene based analysis was performed.

organism: Saccharomyces cerevisiae

source_name: yeast strain expressing spt15WT gene at 1.5 OD replicate 2

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Yeast cells  constitutively expressing either SPT15WT or spt15_A101T were grown in SD minimal media containing appropriate amino acids and harvested in mid exponential phase at 1.5OD 600

extract_protocol: Total RNA was extracted from yeast strains using Qiagen RNeasy Mini RNA isolation kit with DNAse treatment (Catalogue no. 74104).

treatment_protocol: yeast cell pellet harvested and washed with PBS and resuspended in RNA later till RNA extraction

tag: genotype/variation

value: expressing spt15WT


title: colorectal cancer HCT/8073_2

description:
HCT/8073_2
mRNA


title: tumor_obese_HMB_supplemented_replicate 4

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Mouse Gene 2.1 ST Array Strips using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment 3.0.0. RMA was used to normalize the data and fit log2 transformed expression values

label: biotin

organism: Mus musculus

source_name: subcutanious Panc02 tumor

label_protocol: Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 250 ng total RNA (GeneAtlas™ WT Expression Kit User Manual P/N 702935 Rev. 3)

extract_protocol: Total RNA was extracted by RNeasy Kit  (Qiagen) from homogenized tumor samples. RNA quality was checked using an Agilent bioanalyzer. RNA was subsequently hybridized to the Affymetrix Mouse Gene 2.1 ST 24-Array plate.

tag: strain

value: Male

tag: diet induced obesity

value: obesity (diet induced)

tag: hmb supplementation

value: HMB supplemented


title: spt15_A101T_Rep 2

source_name: yeast strain expressing spt15_A101T gene at 1.5 OD replicate 2

value: expressing spt15_A101T


title: colorectal cancer HCT/8073_3

description:
HCT/8073_3
mRNA


title: 257864010001_2_3_Control

description: Sample 3

tag: age at death (in years)

tag: disease state

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

tag: occupation (job)

tag: smoker or non smoker


title: tumor_control_HMB_supplemented_replicate 2

tag: Sex

value: non-obese control


title: 257864010004_2_4_Control

description: Sample 1

value: male

tag: alchool use or not

tag: other pathologies

tag: therapy used


title: tumor_obese_unsupplemented_replicate 3

value: un-supplemented control


title: tumor_obese_unsupplemented_replicate 2


title: tumor_obese_HMB_supplemented_replicate 2


title: tumor_obese_HMB_supplemented_replicate 1


title: tumor_obese_unsupplemented_replicate 1


title: tumor_control_HMB_supplemented_replicate 3


title: tumor_obese_HMB_supplemented_replicate 3


title: tumor_control_HMB_supplemented_replicate 1


title: tumor_control_unsupplemented_replicate 2


title: tumor_control_unsupplemented_replicate 3


title: gm_10ng_rep2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

library_source: genomic

data_processing:
MeDIP sequencing reads were mapped to the human genome (hg19) or mouse genome (mm10) using Bowtie2 (v2.2.5)
Peaks of each MeDIP sample were called against input by MACS (v2.1.0)
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: bigWig files were generated by MACS

growth_protocol: GM12878 cells were obtained from Coriell Institute for Medical Research. GM12878 cells were cultured in RPMI 1640 (Invitrogen, Carlsbad, CA, USA) with 15% fetal bovine serum, 100 U penicillin, 100mg streptomycin/ml (Invitrogen) at 37°C in a humidified incubator containing 5% CO2. Cells were sub-cultured every two to three days to maintain exponential growth.

extract_protocol:
Hemizygous transgenic female mice (FVB-Tg(C3-1-TAg)cJeg/JegJ, Jackson Laboratory) were used in this study. Mice were euthanized at age of 6, 16, 23 weeks by exposing mice to 100% carbon dioxide at 1 – 2 l/min for 5 min followed by cervical dislocation. Mice were sprayed with 70% ethanol on the ventral side. Skin on the ventral side was cut through, pulled away from mouse body, and pinned down to expose mammary glands. Mammary tumors were identified and cut off. The size and weight of a tumor were recorded.Genomic DNA from GM12878 cells was extracted from 106 cells using Blood & Cell Culture DNA Mini Kit (Qiagen). Mouse genomic DNA was extracted from mouse mammary tissues using DNeasy Blood & Tissue Kit (Qiagen). Extracted genomic DNA was sonicated with a Covaris E220 sonicator for 180 s with 10 % duty cycle, 50 peak incident power and 200 cycles per burst. The concentration of sonicated DNA was quantified using a Qubit 2.0 fluorometer with dsDNA HS Assay kit (Q32851, Life Technologies). Different sample sizes (0.5~100 ng) were aliquoted and diluted with MeDIP buffer to generate a final volume of 50 µl for microfluidic MeDIP. 0.5 ng, 5 ng, 10 ng, or 100 ng of the sonicated sample was used as the input. Sonicated DNA samples were freshly denatured into single strand DNA (ssDNA) under 95℃ for 15 min and put on ice for 5 min before microfluidic MeDIP.
Sequencing libraries were prepared by DNA SMART™ ChIP-Seq kit (634865, Clontech). This kit generates sequencing libraries from low-input ssDNA MeDIP samples (100 pg - 10 ng) without using ligation. Sequencing libraries were amplified by PCR using primers containing Illumina adapters. The libraries were purified using Ampure XP beads (A63880, Beckman Coulter). The library fragment size was determined using high sensitivity DNA analysis kit (5067-4626, Agilent) on an Agilent 2200 TapeStation. Sonicated DNA for MeDIP had average fragment size around 200 bp. After library preparation, the average peak size shifted to 350 bp as library construction added about 150 bp adaptor (75 bp on each end) to the MeDIP DNA. KAPA library quantification kit (KK4809, Kapa Biosystems) was used to determine effective library concentrations. The final concentrations of libraries submitted for sequencing were ~8 nM. The libraries were sequenced on an Illumina HiSeq 4000 with single-end 50 nt read. Typically 15-20 million reads were generated per library.

tag: cell line


title: gm_100ng_rep1


title: gm_5ng_input


title: colonic epithelial HC3_SH6YF29_Cell2

description: miRNA

hyb_protocol: Hybridization buffer and washing protocol were attached in the 3D-Gene® miRNA oligo chip kit.

source_name: HCoEpic exosome

label_protocol: miRNA was labeled by labeling kit in the 3D-Gene® miRNA oligo chip kit.

value: HCoEpic

tag: cell type

value: normal colonic epithelial cell line

tag: fraction

value: exosome


title: colonic epithelial HC2_SH6YF29_Cell1

description: miRNA

source_name: HCoEpic supernatant

value: supernatant


title: gm_0.5ng_rep1


title: gm_100ng_rep2


title: gm_5ng_rep2


title: gm_0.5ng_rep2


title: gm_10ng_rep1


title: colonic epithelial HC1_SH6YF24_Cell4

description: miRNA

source_name: HCoEpic cell

value: cell content


title: SPT15WT_Rep 1

source_name: yeast strain expressing spt15WT gene at 1.5 OD replicate 1

tag: genotype/variation


title: spt15_A101T_Rep 1

source_name: yeast strain expressing spt15_A101T gene at 1.5 OD replicate 1


title: colorectal cancer H6_SH6YF24_Cell3

description: miRNA

source_name: HCT116 exosome

value: colorectal cancer cell line


title: colorectal cancer H3_SH68Q44_Cell4

description: miRNA


title: colorectal cancer H5_SH6YF24_Cell2

description: miRNA

source_name: HCT116 supernatant


title: colorectal cancer H4_SH6YF24_Cell1

description: miRNA

source_name: HCT116 cell


title: colorectal cancer H2_SH68Q44_Cell3

description: miRNA


title: tumor_control_unsupplemented_replicate 1

tag: strain

tag: diet induced obesity

tag: hmb supplementation


title: gm_5ng_rep1


title: colorectal cancer H1_SH68Q44_Cell1

description: miRNA


title: ControlBMDM_LPSstimulated_rep6

city: Oxford

first: Laurienne

last: Edgar

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were controlled for quality and trimmed of any remaining adapters with Trim Galore (v.1.8) and FastQC (v.0.11.3).
Reads were then aligned to the mouse genome (Mm10) with Bowtie (v.2.2.6) in "--sensitive-local" mode.
Aligned reads were filtered to remove low quality matches (MAPQ <= 10) or reads mapping to mitochondrial sequences. On average, 16 million uniquely mapped reads (13.4-24.6 million representing 60% of total) were retained per sample.
Alignment start positions were shifted in a strand-aware manner (+4bp, -5bp) prior to peak calling with MACS2 (v.2.1.1) with the following settings: --nomodel --extsize 147 -q 0.01 -m 5 50 -s 50 --call-summits.
Differentially bound regions were identified using DiffBind (v.2.4.8, 59,60) with peak centering (summits=100) and edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: unique.bam files show aligned reads that have been filtered to removed low quality matches (MAPQ <= 10) or reads mapping to mitochondrial sequences.
Supplementary_files_format_and_content: peaks.narrowPeak files generated using peak calling with MACS2 (v.2.1.1) and containing  peak (regions of enrichment) information.

source_name: Bone Marrow Derived Macrophage

extract_protocol:
Nuclei from 50,000 cells per replicate were isolated and lysed (10 mmol/L Tris-Cl (pH 7.4), 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.05% NP-40) on ice.
Isolated nuclei were put through transposition reaction using Tn5 transposase and TD buffer (Illumina, USA) and DNA purified with MinElute PCR Purification Kit (Qiagen). Library amplification (NEBNext High Fidelity 2x PCR master mix, New England Biolabs, USA) was performed using cutom Nextera primers, followed by SPRI size selection to exclude fragments larger than 1,200 bp. Libraries were sequenced using the Illumina HiSeq 3000/4000 platform and the 50-bp single-read configuration.

treatment_protocol: IL-1β samples were cultured for 6hrs. Baseline cells were immediately lysed.

value: Bone Marrow Derived Macrophage

tag: mouse phenotype

value: Wild-type control

tag: treatment

tag: mouse sex

tag: stimulation

value: 100 ng/mL LPS + 10 ng/mL IFNγ


title: DiabeticBMDM_LPSstimulated_rep4

value: Diabetic

value: Streptozotocin (STZ) induction of diabetes


title: DiabeticBMDM_LPSstimulated_rep6

value: Male


title: ControlBMDM_LPSstimulated_rep5


title: ControlBMDM_LPSstimulated_rep3


title: DiabeticBMDM_LPSstimulated_rep3


title: ControlBMDM_LPSstimulated_rep2


title: ControlBMDM_LPSstimulated_rep1


title: DiabeticBMDM_LPSstimulated_rep5


title: ControlBMDM_LPSstimulated_rep4


title: WT_B.plsY_1

city: Coventry

first: Emma

middle: L

last: Denham

address: Gibbet Hill Road

department: Warwick Medical School

institute: University of Warwick

description: Wild type parent strain with B.plsY in overexpression plasmid_rep1

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol:
The strains listed were grown in Luria Bertani broth O.D. 600nm 1.0, at which point subtilin was added to a final concentration of 1%.  The cells were grown for a further two hours at which point the cells were harvested for RNA isolation.
The complete description of the growth protocols can be found in Zweers et al., to be submitted

extract_protocol: Total RNA was isolated by the method described by Eymann et al. (PMID: 11948165) with minor modifications. The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.

tag: genotype

value: B. subtilis 168 amyE::spaRK pNS8910::B.plsY


title: sigW_B.plsY_3

description: sigW mutant with B.plsY in overexpression plasmid_rep3

value: B. subtilis sigW mutant amyE::spaRK pNS8910::B.plsY


title: sigW_B.plsY_2

description: sigW mutant with B.plsY in overexpression plasmid_rep2


title: DiabeticBMDM_LPSstimulated_rep2


title: cssRS_B.plsY_1

description: cssRS mutant with B.plsY in overexpression plasmid_rep1

value: B. subtilis cssRS mutant amyE::spaRK pNS8910::B.plsY


title: sigW_B.plsY_1

description: sigW mutant with B.plsY in overexpression plasmid_rep1


title: WT_B.plsY_3

description: Wild type parent strain with B.plsY in overexpression plasmid_rep3


title: WT_B.plsY_2

description: Wild type parent strain with B.plsY in overexpression plasmid_rep2


title: cssRS_B.plsY_2

description: cssRS mutant with B.plsY in overexpression plasmid_rep2


title: cssRS_B.plsY_3

description: cssRS mutant with B.plsY in overexpression plasmid_rep3


title: DiabeticBMDM_LPSstimulated_rep1


title: WT_empty_2

description: Wild type parent strain with empty overexpression plasmid_rep2

value: B. subtilis 168 amyE::spaRK pNZ8910


title: WT_empty_3

description: Wild type parent strain with empty overexpression plasmid_rep3


title: ControlBMDM_unstimulated_rep6

value: Unstimulated


title: ControlBMDM_unstimulated_rep5


title: DiabeticBMDM_unstimulated_rep6


title: ControlBMDM_unstimulated_rep4


title: ControlBMDM_unstimulated_rep3


title: WT_empty_1

description: Wild type parent strain with empty overexpression plasmid_rep1


title: DiabeticBMDM_unstimulated_rep5


title: 7307 -  Treg-2 M24hr

city: St. Louis

first: Guangyong

last: Peng

state: MO

address: 1100 S Grand Blvd.

department: Internal Medicine

institute: Saint Louis University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Normalization was accomplished in six steps -- self-normalization uses information contained within the array itself (normalization ID) followed by additional outlier removal, background estimation, rotational estimation, shear estimation, and scaling estimation.

source_name: Human PBMC

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays. The labeled RNA was hybridized to the array and later stained with fluorescently labeled anti-biotin antibody.

growth_protocol: Human naturally occurring Treg cells were isolated from PBMCs of healthy donors and and cultured in RPMI1640 with 10% huam AB serum.

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

treatment_protocol: Regulatory T cells were treated with or without Poly-G3 for 0 and 24 hours.

tag: cell

value: human naturally occuring Treg cells


title: 7306 -  Treg-1 G24hr

description: replicate 1


title: 7308 -  Treg-2 G24hr

description: replicate 2


title: 7303 -  Treg-1 ohr

description: replicate 1

value: untreated


title: ControlBMDM_unstimulated_rep2


title: 7304 -  Treg-2 ohr

description: replicate 2


title: 7305 -  Treg-1 M24hr

description: replicate 1


title: pDCvsGF: pDC

city: Fukuoka

first: Takao

last: Fukuda

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku,

department: Faculty of dental science

institute: Kyushu University

hyb_protocol: RNA fragmentation and hybridization were preformed using the Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instructions. 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. The fragmentation mixture was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash buffer 2 (Agilent) according to the manufacturer's instructions.

scan_protocol: The arrays were then scanned using the Agilent DNA Microarray Scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Dental pulp

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit, one color (Agilent) according to the manufacturer's instructions.

extract_protocol: The total RNA was isolated from cells using QIAshredder Cat No 79654 and RNeasy Mini Kit Cat No 74104, with DNase treatment.

tag: tissue

value: dental pulp cells


title: mouse_10ng_23wk_input

value: mammary tissue/tumor

tag: tumor stage

value: 23 week


title: DiabeticBMDM_unstimulated_rep4


title: DiabeticBMDM_unstimulated_rep1


title: pDCvsGF: GF

source_name: Gingiva

value: gingival tissue-derived fibroblasts


title: Blood_CKDu Stage 5_rep 3

city: Kandy

first: Dhammika

last: Magana-Arachchi

state: Central

address: Hantana Road

department: Cell Biology

country: Sri Lanka

institute: National Institute of Fundamental Studies

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0).

label: Biotinylated cRNA

source_name: Peripheral whole blood, Stage 5 CKDu, male pool

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: RNA was extracted from peripheral whole blood using Qiazol lysis reagent (Qiagen, Netherlands) and column purified using PAXgene spin columns (Qiagen, Netherlands)

value: blood

tag: diagnosis

value: CKDu

tag: Stage

value: Stage 5

tag: gender

tag: occupation

value: Farming


title: DiabeticBMDM_unstimulated_rep3

tag: cell type

value: Bone Marrow Derived Macrophage

value: Diabetic

value: Streptozotocin (STZ) induction of diabetes


title: Blood_Girandurukotte Healthy_rep 2

source_name: Peripheral whole blood, Girandurukotte Healthy, male pool

value: Healthy

value: Girandurukotte Healthy

value: Male

value: Non-Farming


title: ControlBMDM_unstimulated_rep1

value: Wild-type control

value: Unstimulated


title: mouse_10ng_23wk_rep2


title: mouse_10ng_23wk_rep1


title: Blood_Girandurukotte Healthy_rep 3


title: Blood_CKDu Stage 2_rep 2

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: Peripheral whole blood, Stage 2 CKDu, male pool

value: Stage 2


title: Blood_CKDu Stage 5_rep 2


title: mouse_10ng_16wk_input

value: mammary tissue/tumor

value: 16 week


title: Blood_CKDu Stage 3_rep 2

source_name: Peripheral whole blood, Stage 3 CKDu, male pool

value: Stage 3


title: Blood_Girandurukotte Healthy_rep 1

value: blood


title: Blood_CKDu Stage 3_rep 3

value: CKDu


title: DiabeticBMDM_unstimulated_rep2


title: mouse_10ng_16wk_rep2


title: Blood_CKDu Stage 3_rep 1


title: Blood_CKDu Stage 2_rep 3


title: Blood_CKDu Stage 5_rep 1

value: Stage 5


title: mouse_10ng_6wk_input

value: 6 week


title: mouse_10ng_16wk_rep1


title: Blood_CKDu Stage 2_rep 1

value: Farming


title: mouse_10ng_6wk_rep2


title: Pt_youngshoot_salt_rep3

city: Sapporo

first: Chiaki

last: Hori

state: Hokkaido

address: Kita13, Nishi8

department: Research Faculty of Engineering

institute: Hokkaido University

description: a week with 100 mM NaCl

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40˚C on GeneChip Poplar Genome Array.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Quality control (RMA normalization) was carried out using the R packages affy.

label: Biotin

organism: Populus trichocarpa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip 3'IVT Expression kit, Affymetrix).

growth_protocol: The soil-grown poplars for one month were treated with stresses for a week as below. After one week, young shoot tissues (top 3 cm) were harvested, immediately frozen in liquid nitrogen, and stored at – 80 ˚C.

extract_protocol: Total RNA was isolated from sampled organs using Plant RNA Isolation Reagent (Invitrogen), and then purified using an RNeasy Mini Kit (QIAGEN).

treatment_protocol: In water-sufficient condition, poplars were well watered with 250 ml tap water (3 times/week).For the drought stress treatment, the water supply was suspended. For salt stress treatment, plants were irrigated with 200 ml of 100 mM NaCl solutions (3 times/week)

value: young shoot


title: Pt_youngshoot_salt_rep1

description: a week with 100 mM NaCl


title: Pt_youngshoot_drought_rep1

description: a week with deficient water


title: Pt_youngshoot_salt_rep2

description: a week with 100 mM NaCl


title: NIK overexpression αTC1-6 cells

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   F  PKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  Per  Kilobase  of  transcript  sequence  per   Millions  base  pairs  sequenced  ,  considers  the  effect  of  sequencing  depth  and  gene  length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression  levels (  Tr  apnell, Cole, et al., 2010  )
Genome_build: Ensemble_GRCm38.90
Supplementary_files_format_and_content: abundance measurements

source_name: NIK overexpression αTC1-6 cells

growth_protocol: αTC1-6 cells were cultured at 37 °C in 5% CO2 in DMEM supplemented with 100 units ml−1 penicillin, 100 units ml−1 streptomycin, and 10% FBS.

extract_protocol:
Total RNAs were extracted usingTriPure Isolation Reagent (Roche, Mannheim, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: αTC1-6 cells were infected with β-Gal, NIK, and NIK (KA) adenovirus for 16 h

value: alpha TC1-6 cells

tag: genotype/variation

value: NIK overexpression


title: β-Gal control αTC1-6 cells

source_name: β-Gal control αTC1-6 cells

value: beta-gal control


title: NIK(KA)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.  FPKM, expected  number  of  Fragments  Per  Kilobase  of  transcript  sequence  per Millions  base  pairs  sequenced,  considers  the  effect  of  sequencing  depth  and  gene  length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010)
Genome_build: Ensemble_GRCm38.90

source_name: NIK(KA) overexpression aTC1-6 cells

value: NIK(KA) overexpression


title: Pt_youngshoot_drought_rep3

description: a week with deficient water


title: mouse_10ng_6wk_rep1

tag: strain


title: hda6 hda9

city: guangzhou

first: Liang

middle: Bing

last: Yuan

state: Guangdong

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Life of Science

institute: Sun Yat-Sen University

data_processing:
tophat v2.1.1; cufflinks v2.2.1; cuffmerge; cuffdiff
Genome_build: Tair 10
Supplementary_files_format_and_content: counts and FPKM

organism: Arabidopsis thaliana

source_name: 4 DAP silique

growth_protocol: Seedlings were grown in growth rooms with 16-h light/8-h dark cycles at 22℃.

extract_protocol:
Total RNA was isolated from about 100 milligrams of 4 days after pollination  using the RNAprep pure Plant Kit (Tiangen) according to supplier’s instruction.
RAN libaries

tag: developmental stage

value: 4 days after pollination

value: silique

tag: age


title: delta-pdtaS - Glucose H

description: Gene expression profile at mid-log phase (O.D. 0.6)

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Custom M.smeg GXP_8X15k Array designed by Genotypic Technology Private Limited. (AMADID: 020791). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

organism: Mycolicibacterium smegmatis

source_name: Duplicate cultures grown in 7H9 + Glucose

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Cultures were grown in 7H9 medium supplemented with 0.2% glycerol or glucose and 0.025% tyloxapol at 37°C in a shaking incubator

extract_protocol: RNA extraction was carried out using Rneasy Mini Kit from Quiagen (cat. #/ID: 74106) according to manufacturer's recommendation

treatment_protocol: Mid log phase cells were used for RNA extraction

tag: strain/genotype

value: pdtaS (MSMEG_1918) knockout


title: delta-pdtaS - Glucose G


title: WT-Glucose E

value: MC2155 wildtype


title: Blood_Healthy_rep3

source_name: Peripheral whole blood, healthy, male

value: Healthy

value: Male

value: Other


title: Pt_youngshoot_drought_rep2

description: a week with deficient water


title: delta-pdtaS - Glycerol D

source_name: Duplicate cultures grown in 7H9 + Glycerol


title: Blood_CKDu Stage 4_rep 2

source_name: Peripheral whole blood, Stage 4 CKDu, male

value: blood

value: Stage 4


title: OA 3

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue Biology Department

department: Biology

institute: Wesleyan University

data_processing:
FASTQC on each of the 6 raw fastq files
Bowtie2 alignment using the D. sechellia reference genome available at the time of analysis (Drosophila_sechellia.GCA_000005215.1.dna.toplevel.fa)
Cuffdiff for quantification and differential expression analysis using the D. sechellia reference genome available at the time of analysis (Drosophila_sechellia.GCA_000005215.1.dna.toplevel.fa) and gene file available at the time of analysis (Drosophila_sechellia.GCA_000005215.1.34.gff3) with geometric library normalization
Genome_build: Drosophila_sechellia.GCA_000005215.1.dna.toplevel.fa
Supplementary_files_format_and_content: Tab-delimited Cuffdiff output in text format

organism: Drosophila sechellia

source_name: Whole larvae

growth_protocol: Flies were reared on cornmeal medium using a 16:8 light:dark cycle at 20 degrees Celsius

extract_protocol:
Total RNA was extracted from whole larvae using Promega SV Total RNA Isolation System
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were exposed to 0.2% octanoic acid mixed into instant Drosophila food or control food for a period of 24 hours

tag: treatment

value: food containing 0.2% octanoic acid

value: Whole larvae


title: OA 2


title: OA 1


title: Pt_youngshoot_control_rep3

description: a week with sufficient water


title: Blood_Healthy_rep1


title: Blood_Healthy_rep2


title: Blood_CKDu Stage 4_rep 3

value: CKDu

value: Farming


title: Control 3

value: control food


title: Blood_CKDu Stage 4_rep 1


title: Pt_youngshoot_control_rep2

description: a week with sufficient water

value: young shoot


title: GFvsDP-1: GF

data_processing: The scanned images were analyzed with Feature Extraction Software10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

value: gingival tissue-derived fibroblasts


title: Pt_youngshoot_control_rep1

description: a week with sufficient water


title: Control 2


title: GFvsDP-1: DP-1

source_name: Dental pulp cell line

value: immortalized dental pulp cells


title: 22RV1-miR-421-C-2

hyb_protocol: 300ng of Cy3 labeled sample and 300ng of Cy5 labeled sample were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1

data_processing: Data Analysis was performed using Genespring GX Software using LOWESS normalization.(Gene based analysis was performed).

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies). Then  the samples  were labeled using Agilent Quick-Amp labeling Kit (p/n:5190-0444).  Five hundred nanograms each of the samples were incubated with reverse transcription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP(Agilent) and Cy5-CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA from each condition were isolated using Qaigen miRNeasy mini Kit (Cat: 217004) according to the manufacturer protocol.

treatment_protocol: SPINK1 positive prostate cancer stable 22RV1 cells were generated by transfection with lentiviral pLemiR-338-5p, pLemiR-421 and control pLemiR-RFP vectors. Transfected cells were cultured in RPMI medium supplimented with 10% Fetal Bowine Serum (FBS), 5% Penicillin Streptomycin (penstrep) and puromycin (1µg/mL).

tag: cell line

tag: miRNA overexpression

value: control

value: SPINK1 positive prostate cancer cells


title: 22RV1-miR-421-C-1


title: hda6

value: 4 days after pollination

value: silique


title: WT-Glucose F

value: MC2155 wildtype


title: delta-pdtaS - Glycerol C

value: pdtaS (MSMEG_1918) knockout


title: hda9


title: WT-Glycerol B


title: Control 1


title: WT


title: 22RV1-miR-421-Pool


title: 22RV1-miR-338-5p-C-3


title: Vector2

status: Public on Dec 29 2018

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: HEK293T cell expressing vector only

data_processing:
Illumina BaseSpace used for base calling
Sequenced reads were trimmed for adaptor sequence, and aligned to the human genome using TopHat (v1.1.0)
Aligned .BAM files were processed in Partek Flow and normalized to Reads Per Kilobase of gene per Million Reads (RPKM) and saved as tab-delimited text files.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: HEK293T cells

growth_protocol: HEK293T cells were plated at a density of 40-60,000 cells per well in triplicate on uncoated plastic in DMEM.

extract_protocol:
Cells were lightly trypsinzed and centrifuged to remove media. Total RNA was purified using the RNeasy mini kit (Qiagen). The quality of total RNA was validated by Bioanalyzer (Agilent Technologies).
Approximately 1 µg of RNA per sample was used to construct the cDNA sequencing library using TruSeq stranded mRNA library prep kit (Illumina), followed by quantitation using KAPA library quantification kit for Illumina platforms (Kapa Biosystems).

treatment_protocol: Cells were grown to 60% confluency and transfected with indicated vector or vector containing indicated insert for 24 hours.

value: human embryonic kidney 293T cells

value: vector only

tag: treatment time

value: 24 hours


title: Vector1

description: HEK293T cell expressing vector only


title: Wildtype1

description: HEK293T cell overexpressing wildtype ANT1

value: wildtype ANT1


title: Vector3

description: HEK293T cell expressing vector only


title: Wildtype3


title: Triple2

description: HEK293T cell expressing triple mutant ANT1 (A90D, L98P, A114P)

value: triple mutant ANT1 (A90D, L98P, A114P)


title: Triple1


title: Triple3


title: WT-Glycerol A


title: Quad1

description: HEK293T cell expressing quadruple mutant ANT1 (A90D, L98P, A114P, A123D)


title: 22RV1-miR-338-5p-C-2


title: MeRIP_ko_IP1

city: Bethesda

first: Chuanyuan

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

description:
MeRIP-Seq
MeRIP-Seq

data_processing:
The fastq file was mapped by STAR software
Low mapping quality read was filtered by SAMtools software
For MeRIP-Seq data, peak file was generated by MACS2 software
Genome_build: mm9
Supplementary_files_format_and_content: The Ribo-Seq bigwig file was generated by bamComverage in deepTools software with -bs=1 and --normalizeUsing BPM. The MeRIP-Seq bigwig file was generated by makeUCSCfile in HOMER software with -style rnaseq, -strand both, -norm 1e7, -tbp 5, -bigWig and -fsize 1e20.

source_name: BMDCs

extract_protocol:
For Ribo-Seq：5x10e6 DCs were treated with 100 μg/ml cycloheximide (CHX) for 7 min. The cells were then harvested by the cell lifter. The cell suspension was spun at 400g for 5 min and the cell pellet was washed twice with 5 ml cold PBS with CHX (100 μg/ml). 200 μl lysis buffer (10 mM Tris, pH 7.4, 150 mM KCl, 5 mM MgCl2, 100 μg/ml CHX, 0.5% Triton-X-100, freshly add 1:100 protease inhibitor, 40 U/ml SUPERasin) was added to the cell pellet and lysed on ice for 15 min with rotating; For m6A-Seq: Total RNA was isolated from DCs. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen).
For Ribo-Seq：10% clarified lysate was saved as INPUT and the rest lysate was separated through a 5ml 10%-50% sucrose gradient and centrifuged at 4°C for 2 h at 28,000 r.p.m. Fractions were collected separately and analyzed by Qubit™ RNA HS Assay Kit (Invitrogen). The fractions corresponding to ribosomes were combined and concentrated on Amicon-Ultra 100K columns (Millipore). 2 A260 units of ribosome fractions were digested with 60U RNase I (Ambion) at room temperature for 30 min. RNA was extracted by RNA Clean&Concentrate (Zymo) and ribosomal RNA were deleted prior to size selection. RNA fragments (26-32nt) were isolated by 15% denaturing Urea-PAGE gel. RNA was eluted from gel in elution buffer (300 mM sodium acetate pH 5.2, 1 mM EDTA) followed by phenol-chloroform extract and ethanol precipitation. RNA fragments were dephosphorylated and prepared into libraries by SMARTer® smRNA-Seq Kit (Clontech); For m6A-Seq: RNA samples were fragmented into ~100-nucleotide-long fragments with sonication. Fragmented RNA (100ng mRNA or 5µg total RNA) was performed m6A-IP following EpiMark N6-methyladenosine enrichment kit (NEB E1610S) protocol. RNA was enriched through RNA Clean&Concentration-5 (Zymo Research) and used for library generation with SMARTer Stranded Total RNA-Seq Kit (Takara).

value: BMDC

tag: genotype

tag: sample type


title: MeRIP_wt_IP2

description:
MeRIP-Seq
MeRIP-Seq

value: wt


title: MeRIP_ko_IP2

description:
MeRIP-Seq
MeRIP-Seq


title: Quad2

value: quadruple mutant ANT1 (A90D, L98P, A114P, A123D)


title: MeRIP_wt_IP1

description:
MeRIP-Seq
MeRIP-Seq


title: MeRIP_ko_input2

description:
MeRIP-Seq
MeRIP-Seq


title: MeRIP_ko_input1

description:
MeRIP-Seq
MeRIP-Seq


title: MeRIP_wt_input2

description:
MeRIP-Seq
MeRIP-Seq


title: Wildtype2


title: 22RV1-miR-338-5p-C-1


title: Ribo_ko_polysome2

description: Ribo-Seq

data_processing:
Library strategy: Ribo-Seq
The fastq file was mapped by STAR software
Low mapping quality read was filtered by SAMtools software
For MeRIP-Seq data, peak file was generated by MACS2 software
Genome_build: mm9
Supplementary_files_format_and_content: The Ribo-Seq bigwig file was generated by bamComverage in deepTools software with -bs=1 and --normalizeUsing BPM. The MeRIP-Seq bigwig file was generated by makeUCSCfile in HOMER software with -style rnaseq, -strand both, -norm 1e7, -tbp 5, -bigWig and -fsize 1e20.

value: Ribo


title: MeRIP_wt_input1

description:
MeRIP-Seq
MeRIP-Seq


title: KO_ribo_input_1

description: library strategy: Ribo-Seq

data_processing:
The fastq file was mapped by STAR software
Low mapping quality read was filtered by SAMtools software
For MeRIP-Seq data, peak file was generated by MACS2 software
For RIP-Seq data, peak file was generated by Piranha software
Genome_build: mm9
Supplementary_files_format_and_content: The MeRIP-Seq, RIP-Seq and Ribo-Seq bigwig file was generated by bamComverage in deepTools software with -bs=1 and --normalizeUsing BPM.

source_name: Flt3L-DC, Ribo_INPUT

extract_protocol:
For Ribo-Seq：5x10e6Flt3L-DCs were treated with 100 μg/ml cycloheximide (CHX) for 7 min. The cells were then harvested by the cell lifter. The cell suspension was spun at 400g for 5 min and the cell pellet was washed twice with 5 ml cold PBS with CHX (100 μg/ml). 200 μl lysis buffer (10 mM Tris, pH 7.4, 150 mM KCl, 5 mM MgCl2, 100 μg/ml CHX, 0.5% Triton-X-100, freshly add 1:100 protease inhibitor, 40 U/ml SUPERasin) was added to the cell pellet and lysed on ice for 15 min with rotating; For m6A-Seq: Total RNA was isolated from DCs. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). For RIP-seq: 20 million Flt3L-DCs were harvested and co-cultured with necrotic B16-OVA overnight. DCs were then purified and pelleted by centrifuge for 5 min. Cells were washed twice with cold PBS and the cell pellet was re-suspended with 2 volumes of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/mL RNase inhibitor). Lysate was incubated on ice for 5 min and centrifuged for 15 min to clear the lysate. 1/10 volume of cell lysate was saved as input and total RNA was extracted by Trizol. The rest of cell lysate was incubated with 5μg anti-YTHDF1 (Proteintech) at 4°C overnight with gentle rotation followed by incubation with 40μl protein G beads for 1 hour at 4°C. The beads were then washed five times with 1 mL ice-cold washing buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/mL RNase inhibitor). The IP complex was resuspended in 400μl 1xProteinase K and digested with 2 mg Proteinase K at 55°C for 1 hour. RNA was then extracted by RNA isolation kit (Zymo).
For Ribo-Seq：10% clarified lysate was saved as INPUT and the rest lysate was separated through a 5ml 10%-50% sucrose gradient and centrifuged at 4°C for 2 h at 28,000 r.p.m. Fractions were collected separately and analyzed by Qubit™ RNA HS Assay Kit (Invitrogen). The fractions corresponding to ribosomes were combined and concentrated on Amicon-Ultra 100K columns (Millipore). 2 A260 units of ribosome fractions were digested with 60U RNase I (Ambion) at room temperature for 30 min. RNA was extracted by RNA Clean&Concentrate (Zymo) and ribosomal RNA were deleted prior to size selection. RNA fragments (26-32nt) were isolated by 15% denaturing Urea-PAGE gel. RNA was eluted from gel in elution buffer (300 mM sodium acetate pH 5.2, 1 mM EDTA) followed by phenol-chloroform extract and ethanol precipitation. RNA fragments were dephosphorylated and prepared into libraries by SMARTer® smRNA-Seq Kit (Clontech); For m6A-Seq: RNA samples were fragmented into ~100-nucleotide-long fragments with sonication. Fragmented RNA (100ng mRNA or 5g total RNA) was performed m6A-IP following EpiMark N6-methyladenosine enrichment kit (NEB E1610S) protocol. RNA was enriched through RNA Clean&Concentration-5 (Zymo Research) and used for library generation with SMARTer Stranded Total RNA-Seq Kit (Takara). For RIP-Seq: Input and IP RNA of each sample were used to generate the library using SMARTer stranded Total RNA-Seq Kit (Takara).


title: KO_ribo_input_2

description: library strategy: Ribo-Seq


title: WT_ribo_input_2

description: library strategy: Ribo-Seq


title: Ribo_ko_polysome1

description: Ribo-Seq


title: WT_ribo_input_1

description: library strategy: Ribo-Seq


title: Quad3


title: KO_ribo_2

description: library strategy: Ribo-Seq

source_name: Flt3L-DC, Ribo


title: Ribo_wt_polysome2

description: Ribo-Seq


title: Ribo_wt_polysome1

description: Ribo-Seq


title: KO_ribo_1

description: library strategy: Ribo-Seq


title: WT_ribo_2

description: library strategy: Ribo-Seq


title: WT_ribo_1

description: library strategy: Ribo-Seq


title: WT_rip_input_2

source_name: Flt3L-DC, RIP_INPUT


title: WT_rip_ip_2

source_name: Flt3L-DC, RIP_IP


title: Ribo_ko_monosome1

description: Ribo-Seq


title: WT_rip_ip_1


title: Ribo_wt_monosome2

description: Ribo-Seq


title: WT_m6a_input_2

description: library strategy: meRIP-Seq

source_name: Flt3L-DC, m6A_INPUT


title: ko_m6a_input_1

description: library strategy: meRIP-Seq


title: ko_m6a_input_2

description: library strategy: meRIP-Seq


title: Ribo_ko_input2

description: Ribo-Seq


title: Ribo_wt_monosome1

description: Ribo-Seq


title: ko_m6a_ip_2

description: library strategy: meRIP-Seq

source_name: Flt3L-DC, m6A_IP


title: ko_m6a_ip_1

description: library strategy: meRIP-Seq


title: Ribo_ko_input1

description: Ribo-Seq


title: WT_m6a_ip_2

description: library strategy: meRIP-Seq


title: WT_m6a_ip_1

description: library strategy: meRIP-Seq


title: Ribo_wt_input2

description: Ribo-Seq


title: Ribo_wt_input1

description: Ribo-Seq


title: Ribo_ko_monosome2

description: Ribo-Seq


title: 330_T

city: Columbia

first: Susheel Bhanu

last: Busi

address: 4011 Discovery Drive

institute: UNIVERSITY OF MISSOURI - COLUMBIA

data_processing:
Sequence read alignment was done using Tophat v2.0.12
To remove adaptors and low-quality reads, Trimmomatic v.0.32 was used with standard settings
Aligned to the Rat genome (Rnor_6.0) (download from: ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Rattus_norvegicus/NCBI/RGSC_v3.4/Rattus_norvegicus_NCBI_RGSC_v3.4.tar.gz on May 24th, 2017
Aligned reads were sorted with SAMtools v1.3 followed by HTSeq v0.9.1 analysis
DESeq2 v1.18.1. in R v.3.4 was then used to differential gene expression
Genome_build: Rat genome (Rnor_6.0)
Supplementary_files_format_and_content: gene abundance measurements

organism: Rattus norvegicus

source_name: Colonic adenoma

growth_protocol: All rats were fed Labdiet 5058 with access to ad libitum water. Tumor arise due to spontaneous mutations as a consequence of the Apc gene mutation

extract_protocol:
Lysates were clarified from sonicated normal epithelium and tumor tissues. RNA was extracted using the Qiagen Allprep DNA/RNA kit and eluted into double-distilled RNAse-free water.
Total RNA was used for poly-A selection and Illumina TruSeq paired-end library preparation following manufacturer’s protocols

tag: gut microbiota (gm) profile

tag: concentration

value: 1 microg


title: 341_T


title: 045_T


title: 331_T


title: 049_T


title: 853_T


title: 518_N

source_name: Colonic normal epithelium


title: 87_N


title: 517_N


title: 547_N


title: 777_N


title: 045_N


title: 330_N


title: WT_rip_input_1


title: Aged_PQ_rep1

city: Ames

first: Kerui

last: Huang

state: IA

address: 2437 Pammel Drive

department: Genetics and Genomics

institute: Iowa State University

data_processing:
Base calls performed by Illumina HiSeq 3000 Real-Time Analysis software RTA2
Galaxy-Tophat2: Mapping the reads against a reference genome
Galaxy-Cufflinks: Reconstructing Transcripts
Galaxy-Cuffmerge: Merge together several Cufflinks assemblies
Galaxy-Cuffdiff: Finding significantly differentially expressed genes based on Cuffmerge
Genome_build: Aug. 2014 (BDGP R6 + ISO1 MT/dm6)
Supplementary_files_format_and_content: Average FPKM values for treatment groups, each group contains three replicates, significant changes are indicated as "yes" or "no"

organism: Drosophila melanogaster

source_name: Oenocyte

growth_protocol: Flies were maintained at 25°C, 40% relative humidity and 12-hour light/dark. Adults were reared on agar-based diet with 0.8% cornmeal, 10% sugar, and 2.5% yeast

extract_protocol:
Ribo-tag extraction was performed during 10:00-12:00 PM time period. Flies were frozen and ground in nitrogen liquid. The fly powder was further homogenized in a Dounce tissue grinder containing 5 mL of homogenization buffer (50mM Tris, pH 7.4, 100mM KCl, 12mM MgCl2, 1mM DTT, 1% NP-40, 400 units/ml RNAsin, 100ug/ml of cycloheximide, 1mg/ml heparin and Protease inhibitors) to generate a 3% weight/volume homogenate. The supernatant was first pre-cleaned using SureBeads (By Bio Rad, catalog number: 161-4023) and then incubated with 15ul of anti-FLAG antibody (Sigma-Aldrich, St. Louis, MO, catalog number: F1804) overnight (about 19 hours) at 4 0C. The antibody/lysate mixture lysate was then incubated with SureBeads for 3 hours at 4 0C. Ribosome-bound RNA was purified using Qiagen RNeasy micro plus kit (Qiagen, Germantown MD).
RNA-seq libraries were constructed using 300 ng of total RNA and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich MA). Poly(A) mRNA (200bp) was obtained and double-stranded cDNA was synthesized according to company manual. Each library was ligated with a NEBNext Adaptor and barcoded with an adaptor-specific index. Libraries were pooled in equal concentrations. The multiplexed libraries were sequenced using Illumina HiSeq 3000 and single-end 50 bp reads format.

treatment_protocol: Flies were maintained on normal food until eclosion. Eclosed flies were collected and allowed to mate for 1 day before separating female and male. 20-25 females were collected in one food vial, allowing them to age under standard condition. For aging condition, flies were transferred to new food every 2 days. Prior to mRNA extraction,10mM Paraquat or water (control) was evenly distributed on standard food surface, let dry for 20 minutes, then flies were transferred on treatment food for 24 hours.

value: 28 days after eclosion

value: Paraquat fed

tag: Sex

value: Female


title: Aged_PQ_rep2


title: 775_N


title: WT_m6a_input_1

description: library strategy: meRIP-Seq


title: AAV9 miR-212/132 Doxorubicin_1

city: Hannnover

first: Shashi

middle: Kumar

last: Gupta

address: Carl-Neuberg Strasse 1

department: IMTTS

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 800ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 μm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’, except that ‘Multiplicative detrending’ algorithm was inactivated. Candidates with signal intensity less than 200 were filtered. Global normalization was performed. Differentially expressed Agilent IDs with cut-off of 1.25 fold and p value 0.05 were selected. Complete normalized data not provided.

label: Alexa Fluor 555

source_name: Heart treated with doxorubicin and AAV9 miR-212/132

label_protocol: 250ng of total RNA were used for synthesis of aminoallyl-UTP-modified (aaUTP) cRNA with the ‘Quick Amp Labeling kit, no dye’ (#5190-0447, Agilent Technologies) according to the manufacturer’s recommendations, except that reaction volumes were quartered and contained NTPmix was exchanged by NTP Set (ATP, CTP, GTP, UTP) and aminoallyl-UTP (Fermentas, Thermo Scientific; order numbers R1091, R0481, respectively). Final NTP concentrations used for in-vitro transcription were 2.5mM (ATP, CTP, GTP) and 1.25mM (UTP, aaUTP). The labeling of aaUTPcRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies) as described in the Amino Allyl MessageAmp™ II Kit Manual (#AM1753; Life Technologies) except that reaction volumes were quartered.

extract_protocol: Total RNA was extracted by using Trifast (Peqlabs) according to manufacturer's instructions

treatment_protocol: AAV9-Control or AAV9-miR-212/132 was injected to mice by intravenous injection. Next day doxorubicin was injected at dose of 5mg/kg via ip route. Doxorubicin was further given at same dose once every week for four more consecutive weeks. Mice were sacrificed one week after the last doxorubicin injection. Heart was explanted and RNA isolation was done.

value: miR-212/132 overexpression

tag: disease state

value: doxorubicin-induced cardiotoxicity

tag: tissue

value: Heart

tag: gender

value: male


title: AAV9 miR-212/132 Doxorubicin_3


title: Aged_H2O_rep3

value: Control, water


title: AAV9 Control Doxorubicin_3

source_name: Heart treated with doxorubicin and AAV9 Control

value: control


title: 547_T


title: Aged_H2O_rep2


title: UGS 4C-seq-Tbx18_rep 1

city: Urbana

first: Soumya

last: Negi

state: Illinois

address: Institute of Genomic Biology, 1206 W Gregory Dr

department: Cell and Developmental Biology

institute: University of Illinois

description: Tbx18 promoter view-point

data_processing:
Library strategy: 4C-seq
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Illumina adapters were trimmed using Trimmomatic v0.32
ATAC-seq read alignment was done using bowtie2 v2.1.0
4C-seq read alignment and processing was done using HTStation
ATAC-seq peak calling was done using homer v4.7 using default options
Genome_build: mm9
Supplementary_files_format_and_content: The processed file for ATAC-seq is in wiggle format created by homer, and 4C-seq file is in bedGraph created by HTStation

source_name: mouse urogenital sinus (UGS)

extract_protocol:
Male urogenital sinuses were treated with collagenase to disaggregate into single-cells. For 4C-seq cells were crosslinked with 1% PFA for 10mins.Chromatin was digested with three additions of 400U DpnII, followed by ligation, and a second digest with 400U HindIII.
Primers with the barcode for illumina's sequencers were attached to the specific primers for each sample
For 4C-seq independent chromosomal libraries from biological replicates were amplified with Tbx18 viewpoint primers. For ATAC-seq, nextera transposon primers were used to amplify sequences.

value: Urogenital sinus (UGS)

value: Male


title: UGS 4C-seq-Tbx18_rep_2

description: Tbx18 promoter view-point


title: 044_N


title: Aged_H2O_rep1


title: Aged_PQ_rep3


title: UGS ATAC-seq

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Illumina adapters were trimmed using Trimmomatic v0.32
ATAC-seq read alignment was done using bowtie2 v2.1.0
4C-seq read alignment and processing was done using HTStation
ATAC-seq peak calling was done using homer v4.7 using default options
Genome_build: mm9
Supplementary_files_format_and_content: The processed file for ATAC-seq is in wiggle format created by homer, and 4C-seq file is in bedGraph created by HTStation


title: AAV9 Control Doxorubicin_2


title: Young_PQ_rep3

value: 14 days after eclosion


title: Young_H2O_rep3


title: Young_PQ_rep2


title: Young_H2O_rep2


title: Young_H2O_rep1


title: AAV9 miR-212/132 Doxorubicin_2


title: 210 days after bloom ncRNA seq repeat2

status: Public on Dec 28 2018

city: Shanghai

first: Huang

last: Huan

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress  Biology

institute: Chinese Academy of Sciences

data_processing:
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to Citrus sinensis(version2) using BWA 0.7.17-r1188
Genome_build: Citrus sinensis version 2 (http://citrus.hzau.edu.cn/orange/download/index.php)
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each read

organism: Citrus sinensis

source_name: fruits

growth_protocol: Newhall sweet orange (Citrus sinensis Osbeck) were all cultivated in a commercial orchard (Songyang, Zhejiang, China)

extract_protocol:
Total RNA (5µg) from each sample was used for separation of small RNA with 14~30nt in length on a 15% TBE-Urea Polyacrylamide Gel in XCell SureLock™ Mini-Cell (Thermo Fisher Scientific).
The small RNAs were recovered by ZR small-RNA PAGE Recovery Kit (Zymo Research, R1070). The enriched small RNAs were used for performing the library preparation with NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs, E7300L) according to the manufacturer’s instructions with different barcodes. Prepared libraries were assessed for quality by using NGS High-Sensitivity kit on the Fragment Analyzer (AATI) and for quantity by using Qubit 2.0 fluorometer (Thermo Fisher Scientific).

tag: cultivar

tag: development stage

value: 210 DAB

value: pericarp


title: 210 days after bloom bsseq repeat2

description: treated with bisulfite

data_processing:
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to Citrus sinensis (version2) from the Citrus Genome Database using BSMAP 2.87
methratio.py python script of BSMAP was used to extract metylation ratios from BSMAP results with parameters -z and -r
two replicates were merged to generate wiggle files
Genome_build: Citrus sinensis (version 2)
Supplementary_files_format_and_content: Methylation ratio in bigwig files

extract_protocol: Genomic DNA was extracted from fruits and sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China)  for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

value: Newhall sweet orange (Citrus sinensis Osbeck)


title: 210 days after bloom bsseq repeat1

description: treated with bisulfite


title: 210 days after bloom ncRNA seq repeat1


title: 180 days after bloom bsseq repeat1

description: treated with bisulfite

value: 180 DAB


title: PBMCs-PCR1 (healthy control group)-Rep1

city: weifang

first: yurong

last: fu

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University

institute: weifang medical universtiy

description: CircRNA expression in PBMCs prepared from active TB patients

hyb_protocol: Arraystar Human Circular RNA Microarray V2 (8x15K, Arraystar Inc., MD, USA) covers 13,617 human circRNAs and was used to identify circRNAs with differential expression between active TB samples and controls. Briefly,1 μg of each labeled cRNA was fragmented by adding 10×Blocking Agent (5 μl) and 25×Fragmentation Buffer (1 μl), then the mixture was heated at 60°C for 30 min, finally 2 × Hybridization buffer (25 μl) was added to dilute the labeled cRNA. The resulting hybridization solution (50 μl) was dispensed into the gasket slide and then assembled to the circRNA expression microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner 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 using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were kept for subsequent differential analysis.

source_name: Peripheral blood mononuclear cells,PCR1 (one of three healthy control subjects)

label_protocol: Sample labeling was performed utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar Inc., MD, USA). Briefly, total RNA from each sample was treated with RNase R (EpicentreInc., Madison, WI, USA) to remove linear RNAs and enrich circRNAs. Then, the enriched circRNAs were amplified and transcribed into fluorescently-labeled cRNAs utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar Inc., MD, USA). The labeled cRNAs were purified with a RNeasy Mini Kit (Qiagen, Hilden, Germany). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were then quantified with a NanoDrop ND-1000 spectrophotometer.

extract_protocol: For RNA preparation,total RNA was isolated from plasma with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Total RNA concentration and quality of each sample were determined with NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA). RNA integrity and DNA contamination were measured by electrophoresis on a denaturing agarose gel. Only RNA samples with high quality were used for subsequent microarray analysis.

treatment_protocol: Plasma samples from active TB patients and healthy controls were collected by centrifugation, immediately aliquoted and stored in liquid nitrogen until further use. All the TB patients had no history of radiotherapy or chemotherapy before blood collection.

value: Peripheral blood mononuclear cells


title: 120 days after bloom bsseq repeat2

description: treated with bisulfite

value: 120 DAB


title: 120 days after bloom bsseq repeat1

description: treated with bisulfite


title: 150 days after bloom bsseq repeat1

description: treated with bisulfite

value: 150 DAB


title: 150 days after bloom bsseq repeat2

description: treated with bisulfite


title: PBMCs-PTC3 (active TB group)-Rep1

source_name: Peripheral blood mononuclear cells, PTC3 (one of three patients with active TB)

value: Female


title: Young_PQ_rep1

tag: developmental stage

value: Paraquat fed


title: 90 days after bloom bsseq repeat2

description: treated with bisulfite

value: 90 DAB


title: AAV9 Control Doxorubicin_1

tag: strain

value: doxorubicin-induced cardiotoxicity

value: Heart


title: PBMCs-PTC2 (active TB group)-Rep1

source_name: Peripheral blood mononuclear cells, PTC2 (one of three patients with active TB)

tag: age


title: 90 days after bloom bsseq repeat1

description: treated with bisulfite


title: 210 days after bloom rna-seq repeat3

data_processing:
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to Citrus sinensis(version 2) from the Citrus Genome Database using STAR(020201)
Differetial gene expresssion was analysed by DESeq
wiggle files were normalized to reads per million of mapped reads
Genome_build: citrus sinensis (version 2)

extract_protocol:
Total RNAs were extracted using the TRIzol (Invitrogen) method, and RNase-free Dnase (Qiagen) was used to remove contaminating DNA before RNA-seq.
Total RNAs were sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library preparation and sequencing using standard Illumina protocols.


title: PBMCs-PCR2 (healthy control group)-Rep1

source_name: Peripheral blood mononuclear cells,PCR2 (one of three healthy control subjects)


title: 180 days after bloom rna-seq repeat3


title: 180 days after bloom rna-seq repeat1


title: PBMCs-PCR3 (healthy control group)-Rep1

source_name: Peripheral blood mononuclear cells,PCR3 (one of three healthy control subjects)


title: 150 days after bloom rna-seq repeat3


title: 150 days after bloom rna-seq repeat2


title: PBMCs-PTC1 (active TB group)-Rep1

source_name: Peripheral blood mononuclear cells, PTC1 (one of three patients with active TB)


title: 180 days after bloom bsseq repeat2

description: treated with bisulfite


title: 150 days after bloom rna-seq repeat1


title: 120 days after bloom rna-seq repeat3


title: 120 days after bloom rna-seq repeat2


title: 120 days after bloom rna-seq repeat1


title: 90 days after bloom rna-seq repeat3


title: 210 days after bloom rna-seq repeat1


title: 210 days after bloom rna-seq repeat2


title: 90 days after bloom rna-seq repeat2


title: 90 days after bloom rna-seq repeat1


title: 180 days after bloom rna-seq repeat2


title: EV

city: Birmingham

first: Philip

last: Kitchen

address: IBR Building

institute: University of Birmingham

data_processing:
Trimming of low quality bases (Phred score < 30) and adapter contamination using TrimGalore!
Alignment to hg19 using Bowtie2
Removal of multi-mapped reads (i.e. reads where primary and secondary alignments have equal mapping scores) and duplicates
Removal of reads mapping to 'blacklisted' regions associated with artifactual high signal, from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz
Calling of peaks using MACS2. Peaks called using EV sample as control for background.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file - List of peaks from MACS2 with nearest TSS, genomic feature and gene ID annotations.
Supplementary_files_format_and_content: BigWig file - coverage tracks

source_name: CCLP1 cholangiocarcinoma cell line

growth_protocol: Grown in DMEM High Glucose (Sigma-Aldrich cat no.5796) + 10% FBS + Non-essential amino acids + penicillin/streptomycin

extract_protocol:
Cross-linked with 4% formaldehyde for 10 mins at room temp. Sonicated to 300-500bp. ChIP using cell signalling technology antibody #9B11 (anti-myc tag). DNA purified using Ampure.
NEBNext Ultra II kit


title: FTM (flank, young)

city: Yufu-shi

first: Takashi

last: Sakai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi,

department: Faculty of Medicine

institute: Oita University

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

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

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

source_name: non-lesional skin of neck, young FTM

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

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

value: STOCK a/a Tmem79ma Flgft/J

value: whole sikin

value: female


title: FTM (neck, young)

source_name: non-lesional skin of flank, young FTM


title: dMfn 1 KO 1

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

description: mitochondrial DNA (mtDNA)

data_processing:
The fatsq files were checked for good quality using the fastqc tool
on the first  run, reads were mapped to the mouse genome w.o. mitochndria using bowtie (v. 2.1.0)
Taking the unmapped reads for a second mapping step they were first trimmed with fastx_trimmer (v. 0.0.13.2) to ensure higher quality
A second mapping run was done with bwa (v 0.6.2-r126, with parameter n=0.04) only to the mitochondria genomic sequence
Inserts bigger than 600nt were extracted from the mapped bam files and were used to create the plots.
Genome_build: NCBIM37.66

source_name: Heart

extract_protocol: libraries were prepared for sequencing using standard Illumina protocols

value: 5 weeks


title: Littermate control 3

description: mitochondrial DNA (mtDNA)

value: Mfn1 loxP/ loxP, Mfn2 loxP/ loxP, Cre-


title: Deletor mouse 1

description: Total DNA

source_name: Skeletal muscle

value: Skeletal muscle

value: 20 weeks

value: Twinkle in-frame duplication of amino acids 353-365 (dup353-365)


title: dMfn 1 KO 3

description: mitochondrial DNA (mtDNA)


title: dMfn 1 KO 2

description: mitochondrial DNA (mtDNA)


title: Littermate control 1

description: mitochondrial DNA (mtDNA)


title: SAM24350896 Bone Marrow WT T16 LPS WT_T16

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from Bone Marrow Derived Macrophages

extract_protocol:
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen)
and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).
The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.

tag: cell type

value: Bone Marrow Derived Macrophages

tag: primary tissue

value: Bone Marrow

value: WT

tag: time

tag: treatment

value: LPS

tag: group


title: SAM24350881 Bone Marrow KO T0 Untreated KO_T0

tag: genotype

value: Stk40 KO

value: Untreated


title: SAM24350888 Bone Marrow WT T6 LPS WT_T6


title: SAM24350883 Bone Marrow KO T0 Untreated KO_T0


title: SAM24350902 Bone Marrow WT T32 LPS WT_T32


title: mycPRH

tag: cell line


title: SAM24350891 Bone Marrow KO T16 LPS KO_T16


title: SAM24350884 Bone Marrow WT T0 Untreated WT_T0


title: SAM24350886 Bone Marrow WT T6 LPS WT_T6


title: SAM24350889 Bone Marrow KO T6 LPS KO_T6


title: SAM24350890 Bone Marrow WT T6 LPS WT_T6


title: SAM24350897 Bone Marrow KO T32 LPS KO_T32


title: Littermate control 2

description: mitochondrial DNA (mtDNA)


title: SAM24350882 Bone Marrow WT T0 Untreated WT_T0


title: SAM24350899 Bone Marrow KO T32 LPS KO_T32


title: SAM24350880 Bone Marrow WT T0 Untreated WT_T0


title: SAM24350901 Bone Marrow KO T32 LPS KO_T32


title: SAM24350894 Bone Marrow WT T16 LPS WT_T16


title: SAM24350900 Bone Marrow WT T32 LPS WT_T32


title: SAM24350885 Bone Marrow KO T6 LPS KO_T6


title: SAM24350887 Bone Marrow KO T6 LPS KO_T6


title: SAM24350879 Bone Marrow KO T0 Untreated KO_T0


title: SAM24350893 Bone Marrow KO T16 LPS KO_T16


title: TPK11

city: Chicago

first: Tao

last: Pan

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: Input sample

data_processing:
RNA-seq and m6A-seq reads were aligned to mouse genome mm10 by HISAT2 version 2.1.0
m6A enriched region were detected by exomePeak R package. RNA-Seq data(no IP, input RNA) in the same condition was used as input information
m6A differentially enriched region between GF and SPF sample were detected by MeTDiff R package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample…

source_name: Specific pathogen free

growth_protocol: SPF mice are housed under specific pathogen free conditions and the mice have been tested free of designated pathogens. GF mice are housed in tightly controlled and monitored isolators to prevent contamination. They are microbiologically sterile and no living organisms can be cultured from germ-free mice specimens.

extract_protocol:
MeRIP-seq/m6A-seq. MeRIP experiments were carried out according to previously published protocols (Nature 485, 201-206 (2012).). Briefly, polyA selection and ribodepletion-treated mRNA samples (1 ug of each) from tissues (brain, intestine, kidney, liver) were used for RNA fragmentation followed by immunoprecipitation with EpiMark N6-Methyladenosine Enrichment Kit (NEB, E1610S). 2 ul of N6-Methyladenosine antibody was reacted with 40 ul Protein G Magnetic Beads prewashed by 250 ul Reaction buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) for 2 h at 4°C. The beads were washed twice with 250 ul Reaction buffer, fragmented RNAs were added to beads and incubated for 3 h at 4°C. Afterwards, the beads were washed twice with 250 ul Low Salt Reaction Buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) and twice with 250 ul High Salt Reaction Buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). RNAs were eluted from the protein G magnetic beads in 30 ul of Buffer RLT (Qiagen, 79216) followed by precipitation in 100% ethanol. RNAs were dissolved in 12 ul RNase-free water. 120 ng of input RNA and immunoprecipitated RNAs were used for library preparation using Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacture's instructions. The concentration and quality of libraries were checked by the Agilent 2100 bioanalyzer. RNA sequencing was carried out at the University of Chicago Genomics Facility on an Illumina HiSeq2500 platform to generate 100-bp paired reads.
Tissues were homogenized in TRIzol with glass beads using homogenizer. Total RNA was isolated from frozen tissues using TRIzol reagent following the manufacturer's protocol.

treatment_protocol: Mice tissues (brain, intestine, kidney, liver) were dissected from SPF mice (4-week-old male C57BL/6 mice) and GF mice (4-week-old male C57BL/6 mice). All tissues were freshly frozen on dry ice and stored at –80°C.

tag: brain

value: Kidney

value: male


title: TPK12

description: Input sample

tag: Sex


title: TPK8

description: Input sample

source_name: Germ free


title: TPK7

description: Input sample


title: SAM24350898 Bone Marrow WT T32 LPS WT_T32


title: SAM24350895 Bone Marrow KO T16 LPS KO_T16


title: TPK6

description: IP sample


title: TPK9

description: Input sample


title: TPK2

description: IP sample


title: TPK4

description: IP sample


title: TPK1

description: IP sample


title: TPK5

description: IP sample


title: TPL11

description: Input sample

value: Liver


title: TPL8

description: Input sample


title: TPL10

description: Input sample


title: TPL9

description: Input sample


title: TPL12

description: Input sample


title: TPI12

description: Input sample

value: Intestine


title: TPL2

description: IP sample


title: TPL7

description: Input sample


title: TPL6

description: IP sample


title: TPL5

description: IP sample


title: TPL4

description: IP sample


title: TPL3

description: IP sample


title: TPI9

description: Input sample


title: TPL1

description: IP sample


title: TPI11

description: Input sample


title: TPI10

description: Input sample


title: TPI8

description: Input sample


title: TPI6

description: IP sample


title: TPI5

description: IP sample


title: TPI4

description: IP sample


title: TPI3

description: IP sample


title: TPB12

description: Input sample

value: Brain


title: TPI2

description: IP sample


title: TPI1

description: IP sample


title: TPB9

description: Input sample


title: TPB8

description: Input sample


title: TPB6

description: IP sample


title: TPB7

description: Input sample


title: 2D Collagen 4

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

data_processing:
Reads were aligned to mm10 using STARversion 020201 and default parameters
Gene counting was performed using htseq-count version 0.6.1p1 and default parameters
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts (by DESeq2) for each Sample

source_name: murine oviductal epithelial (MOE) cell line

growth_protocol: At confluence cells were collected with trypsin and plated on 2D or 3D collagen

extract_protocol:
RNA was isolated with TRIzol and purified with a Qiagen Rnease kit per the manufacter's intructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MOE Cells were plated on 2D or 3D collagen gels for 6 hours in standard MOE media without EGF.

value: 2D Collagen

tag: mouse strain

value: FVB

value: murine oviductal epithelial cells


title: 3D Collagen 3

value: 3D Collagen


title: 3D Collagen 1


title: 3D Collagen 4


title: TPB1

description: IP sample

tag: tissue


title: TPB3

description: IP sample


title: 2D Collagen 3


title: TPB2

description: IP sample


title: 2D Collagen 1


title: TPB5

description: IP sample


title: 3D Collagen 2


title: TPB4

description: IP sample


title: 2D Collagen 2


title: TPI7

description: Input sample