title: S24-Liver_sequence

city: Chongqing

first: XINYU

last: LI

address: 1 YOUYI ROAD

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Rat genome (UCSC RN5) using BOWTIE software (V2.1.0).
To quantify the DNA methylation level of any specific region. A methylation score for any region in the genome was defined as number of reads per kb (according to A.K. Maunakea et al, 2010).
Genome_build: RN5
Supplementary_files_format_and_content: All the MeDIP-seq signal densities in WIG format for visualizing the DNA methylation profiles of each sample.

organism: Rattus norvegicus

source_name: liver cell from rat of streptozotocin treated father

growth_protocol: All animals (both males and females) were maintained on a regular chow diet and had free access to water throughout the study. At the end of the experiment, animals were sacrificed in a fed condition by CO2 inhalation. One rat per litter (no differentiation in gender was made) was used for each test.

extract_protocol:
For MeDIP, Genomic DNA was sonicated to ~200 - 900bp with a Bioruptor sonicator (Diagenode). 800 ng of sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol. After agarose size-selection to remove unligated adapters, the adaptor-ligated DNA was used for immunoprecipitation using a mouse monoclonal anti-5-methylcytosine antibody (Diagenode). For this, DNA was heat-denatured at 94°C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μL primary antibody overnight at 4°C with rocking agitation in 400 μL immunoprecipitation buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 100 μL of protein G magnetic beads (Life Technologies) were added and incubated for an additional 2 hours at 4°C with agitation. After immunoprecipitation, a total of five immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific mouse IgG immunoprecipitation was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/mL proteinase K for 2 hours at 65°C and then allowed to cool down to room temperature. MeDIP and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μL EB (Qiagen). 14 cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (300-1,000 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Agilent 2100 Bioanalyzer. An aliquot of each library was diluted in EB to 5 ng/μL and 1 μL was used in real-time PCR reactions to confirm the enrichment for methylated region.
The library was denatured with 0.1 M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8 pM concentration, amplified in situ using TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 2000 according to the manufacturer’s instructions.

treatment_protocol: Following dissection, tissues were snap-frozen in liquid nitrogen. Prior to extraction and to facilitate multiple extractions from the same tissue, samples were pulverized in liquid nitrogen and were never allowed to thaw.

value: Sprague Dawley

value: liver

value: 32 weeks


title: 6h_High_light_BiorepC

status: Public on Aug 03 2018

type: RNA

city: Colchester

first: Philip

middle: Mark

last: Mullineaux

address: Wivenhoe Park

department: School of Biological Sciences

country: United Kingdom

institute: University of Essex

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 200 slides were hybridized and scanned was randomized to minimize the impact on differences between samples of any potential variation in the processing conditions. According to this randomized experimental design combinations of labelled samples were hybridized to slides overnight at 42 oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Cy3 and Cy5 scans for each slide were combined and processed in ImaGene version 8.0 (BioDiscovery) to extract raw intensity and background corrected data values for each spot on the array
Quantified microarray data were Lowess normalized within print-tip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using a modified version of R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003).

label: Cy3, Cy5

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis thaliana plants (Col-0) were obtained from the European Arabidopsis Stock Centre, and were grown under a 8:16-h light:dark cycle at 23°C, 60% relative humidity, and light intensity of 150 µmol m-2 s-1. Arabidopsis seed was stratified for 3 d in 0.1% agarose at 4°C before sowing individual seeds onto a soil mix (Scotts Levingtons F2+S compost : fine grade vermiculite in a ratio of 6:1:) in pots (7cm x 7cm x 9 cm) . For the HL time series and LL parallel controls, two consecutive sowings, 24 hours apart, were grown to 42 days post sowing on the same growth room shelf and randomized across the shelf every day. Leaf 7 (Boyes et al., 2001) was tagged at 37 days post sowing.

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point from the 2 days (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: The HL exposure was a light intensity of 1500 (± 100) µmol m-2 s-1 from a white light emitting diode (LED) array (Isolight; Technologica Ltd, Colchester UK).  We used the 24 h staging of plant growth and 3 light Isolight arrays to treat 27 plants each day, allowing a maximum of 54 plants to be exposed over the two days of the experiment. The same number of plants were selected to be LL controls. The HL exposure began 1h after subjective dawn and was completed 1h before subjective dusk and was carried out in the chamber the plants were grown in. Each set of tagged leaves (4) at each time point and their LL controls (4) were sampled within 5 min at time 0 and each 0.5 h interval for the 6 h exposure. Two HL experiments were conducted with duplicate samplings of a full range of time points on each day. During the time series HL experiments, an individual plant from under each LED array and not destined to be sampled was monitored for  its response to HL by non-invasively determining the chlorophyll fluoerescence parameters Fq’/Fm’, Fq’/Fv’ and Fv’/Fm’  from leaf 7  in situ under each isolight using PAM-2000 portable fluorometers (Walz GmbH, Effeltrich, Germany).

tag: ecotype

tag: treatment

value: high light (HL)

tag: time (hour)

tag: tissue

value: leaf


title: 6h_Control_BiorepB

value: control low light (LL)


title: 5h_High_light_BiorepA


title: totalFly-control-30days-replicate3

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Microarray analysis was performed at Source Bioscience (Nottingham, UK). RNA quality was assessed by using an Agilent Bioanalyzer 2100 applying the RNA 6000 Nano Assay.  cDNA were hybridized  for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix).

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

label: Biotin

organism: Drosophila melanogaster

source_name: total fly_control diet_age 30d

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: The Drosophila melanogaster wild type strain W1118 (Bloomington Drosophila Stock Center #5905) was used for all experiments and grown over 30 days.

extract_protocol: Total RNA was extracted from whole flies by using TriFastTM (Peqlab, Nuernberg, Germany) according to manufacturer’s instructions. Prior to RNA extraction, 10 flies per group were homogenized in TriFastTM in a TissueLyser II (Qiagen, Hilden, Germany). RNA concentration and purity was detected via a NanoDrop (NanoDrop2000c; ThermoScientific, Waltham, MA, USA).

treatment_protocol: For RNA isolation flies were maintained either on a control or lithocholic acid (LCA)-supplemented medium for 30 days.

tag: strain

tag: genotype/variation

value: wild type

tag: gender

value: male

tag: age

value: 30 days

tag: diet

value: Control

value: whole fly


title: AEC donor 1, Mock, 4hr

city: Oklahoma City

first: J.

middle: Leland

last: Booth

state: OK

address: 800 N. Research Parkway

department: Internal Medicine Dept., Pulmonary and Critical Care Div.

country: USA

institute: Oklahoma University Health Sciences Center

hyb_protocol: Hybridization cocktails were created using standard array format with components from the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). Cocktails were incubated on GeneChip HuGene 2.0 ST Array, Format 100 (Affymetrix) for 18 h at 45 °C with rotation.  Arrays were then washed and stained using components of the GeneChip Hybridization, Wash, and Stain Kit and a Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) and Affymetrix GeneChip Command Console to generate intensity data.

data_processing: The data were normalized using RMA [PMID: 12925520]. Probes were annotated on a transcript level using hugene20sttranscriptcluster v. 8.4.0 Bioconductor package. Quality control included hierarchical clustering, principal components analysis. Only protein-coding genes were analyzed. Differentially expressed genes were detected using limma R package v. 3.28.21 [PMID: 25605792] controlling for the “Amp group” variability. Functional enrichment analysis (Gene Ontology Molecular Function, Biological Process, Cellular Component pathways) was performed using GOStats R package v. 2.42.0 [PMID: 17098774]. Volcano plots and heatmap visualization was performed in R/Bioconductor environment v. 3.3.1.

label: biotin

organism: Homo sapiens

source_name: primary human type I AEC_mock_4 hrs

label_protocol: 5 μg cDNA per sample were fragmented and biotinylated (Encore Biotin Module, NuGEN) following manufacturer’s instructions for hybridization with microarrays.

growth_protocol: Human lungs from deceased donors and rejected for transplant were obtained under a protocol approved by the University of Oklahoma Health Sciences Institutional Review Board. After perfusion with PBS and lavage with 150 mM NaCl solution, approximately 60g of lung tissue was digested in 200ml HBSS containing 8 U/ml porcine elastase and 150 KU/ml DNase for 60 min at 37°C.  After inactivation of the elastase with FBS, the softened tissue was minced into a slurry and passed sequentially through gauze and increasingly smaller pore size nylon mesh until a single cell dispersion was obtained.  Type II AEC were purified from this mixture by 3 sequential enrichment protocols: 1) Total cells were panned in flasks coated with human IgG.  2) Unattached cells were concentrated, then separated by Percoll gradient; and, 3) Cells in the interface band were negatively selected against anti-CD45 coated magnetic microbeads.  The isolated AEC II were added to 6-well BioCoat plates pre-coated with collagen I extracellular matrix and overlaid with human fibronectin in DMEM supplemented with 10% FBS, 1% solution of penicillin/streptomycin/amphotericin B, 5.0 μg/liter vancomycin, and 10.0 μg/liter ceftazidime at a concentration of 20,000 cells/cm2.  This initial cell density was optimized to drive differentiation toward a type I-like AEC phenotype.  The medium was changed every other day and by day 10 of culture, plated type II AEC had morphologically differentiated into confluent, type I-like AEC monolayers.

extract_protocol: When Thawed, the QIAzol cell lysates were bead mill homogenized in a TissueLyser II, then purified by the QIAcube automated workstation using miRNeasy Mini Purification Kits (all from Qiagen, Inc.) following the manufacturer's instructions. Product RNA was eluted in water, with final aliquots being stored in 10 mM Tris Cl, pH 8.0.  The resulting total RNA yields and purities were determined using a NanoDrop 2000c (Thermo Scientific).  RNA was reverse transcribed to cDNA and amplified using Ovation Pico WTA Systems V2 (NuGEN) following manufacturer’s instructions. Final amplified cDNA was purified using Agencourt RNAClean XP Beads, and the final yields and purities were determined by NanoDrop.

treatment_protocol: After differentiation in 6-well plates, the type I AEC from the three donors were infected with 1 × 106 cfu/ml (MOI ≈ 2) B. anthracis, Sterne strain 7702 (pX01+, pX02-) endospores in fresh DMEM-10 and incubated for 4 and 24 h at 37°C in 5% CO2.  A volume of spore diluent (sterile di-water) equal to that of the spores was used as a negative control.  At the end of incubation, the cell monolayers were washed twice with 2 ml PBS, lysed by addition of 700 μl/well QIAzol Lysis Reagent (Qiagen Inc.), and immediately stored at -80°C.

tag: subject id

value: donor 1

tag: age (yrs)

tag: race

value: caucasian

tag: Cause of death

value: stroke

tag: cell type

value: primary human type I alveolar epithelial cells (AECs)

tag: treated with

value: spore diluent (mock) for 4hrs


title: 5h_Control_BiorepA


title: AEC donor 2, Mock, 4hr

value: donor 2

value: trauma, anoxia, secondary cardiovascular failure


title: 5h_Control_BiorepD


title: 5.5h_High_light_BiorepC


title: 5h_Control_BiorepB


title: 5.5h_Control_BiorepB


title: 5.5h_Control_BiorepD


title: 5.5h_High_light_BiorepA


title: 5h_High_light_BiorepB


title: 6h_High_light_BiorepD


title: 6h_Control_BiorepD


title: 6h_Control_BiorepC


title: 5.5h_Control_BiorepC


title: C22-Liver_sequence

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

source_name: liver cell from rat of citrate-buffer treated father

value: Sprague Dawley

value: liver


title: 5h_Control_BiorepC


title: 5.5h_High_light_BiorepD

value: high light (HL)


title: 5.5h_High_light_BiorepB

value: leaf


title: 5h_High_light_BiorepD


title: GmSDLG_H3_br2

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (v1.1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.19).  Reads from the biological replicates were combined before performing the peak-calling step.
H3K4me3 peaks were identified using MACS2.0 (version 2.0.10), using default parameters except for effective genome size= 7.8e8, and qvalue cutoff=1e-02.  H3K27me3 broad peaks were identified using the SICER algorithm (v1.1), using the following parameters: window size=200, fragment size=220, effective genome fraction=0.8, gap size=600, FDR=0.05.
Genome_build: Glycine max v1.1
Supplementary_files_format_and_content: Peak coordinates are in bed format.  H3K4me3 peaks (macs2) output: chrom, start, end, name, score (-log10_qvalue).  H3K27me3 peaks (SICER) output: chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold.

organism: Glycine max

source_name: Seedlings

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts  were incubated overnight with either 3ug of anti-Histone H3 (Abcam, ab1791), 1ug of anti-H3K4me3 (Abcam, ab8580), or 10ug of anti-H3K27me3 (Abcam, ab6002).  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.  Late maturation embryo nuclei were isolated on a Percoll/sucrose gradient and the nuclei pellet was frozen prior to sonication.
ChIP libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Cotyledon-stage embryos were dissected out of 2.5 to 3.5 mm long seeds, early maturation embryos from 6 to 7 mm seeds, mid-maturation embryos from seeds weighing between 200 and 250 mg, late maturation embryos from completely yellow seeds weighing between 230 and 500 mg and seedlings collected 8 days after seed sowing.  All tissues except the late maturation embryos were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.  Late maturation embryos were frozen and ground in liquid nitrogen before being crosslinked on ice for 15 minutes.

tag: cultivar

value: Williams 82

tag: Stage

value: Seedlings

tag: antibody


title: 6h_Control_BiorepA

tag: ecotype

tag: treatment

value: control low light (LL)


title: GmSDLG_H3_br1


title: GmSDLG_H3K27me3_br2

description: SDLG-K27_cat-W200-G600-islands-summary-FDR0.5.bed.gz


title: GmSDLG_H3K27me3_br1


title: GmSDLG_H3K4me3_br2


title: GmSDLG_H3K4me3_br1


title: 4h_High_light_BiorepD

tag: time (hour)

tag: tissue


title: GmLM_H3K27me3_br1

description: AA1-K27_cat-W200-G600-islands-summary-FDR0.5.bed.gz

source_name: embryos

extract_protocol:
Late maturation embryo nuclei were isolated on a Percoll/sucrose gradient and the nuclei pellet was frozen prior to sonication.
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts  were incubated overnight with either 3ug of anti-Histone H3 (Abcam, ab1791), 1ug of anti-H3K4me3 (Abcam, ab8580), or 10ug of anti-H3K27me3 (Abcam, ab6002).  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.  Late maturation embryo nuclei were isolated on a Percoll/sucrose gradient and the nuclei pellet was frozen prior to sonication.
ChIP libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol:
Late maturation embryos were frozen and ground in liquid nitrogen before being crosslinked on ice for 15 minutes.
Cotyledon-stage embryos were dissected out of 2.5 to 3.5 mm long seeds, early maturation embryos from 6 to 7 mm seeds, mid-maturation embryos from seeds weighing between 200 and 250 mg, late maturation embryos from completely yellow seeds weighing between 230 and 500 mg and seedlings collected 8 days after seed sowing.  All tissues except the late maturation embryos were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.  Late maturation embryos were frozen and ground in liquid nitrogen before being crosslinked on ice for 15 minutes.

value: Late maturation stage


title: GmLM_H3K27me3_br2


title: GmLM_H3K4me3_br2


title: GmLM_H3_br2


title: GmLM_H3K4me3_br1


title: GmLM_H3_br1


title: GmEM_H3_br2

value: Early maturation stage


title: GmEM_H3K27me3_br2

description: EM_K27_cat-W200-G600-islands-summary-FDR0.05.bed.gz


title: GmEM_H3_br1


title: GmEM_H3K27me3_br1


title: 4h_Control_BiorepB


title: 4h_High_light_BiorepC


title: 4h_Control_BiorepD


title: 4h_High_light_BiorepB


title: GmEM_H3K4me3_br2


title: GmCOT_H3_br2

value: Cotyledon stage


title: GmEM_H3K4me3_br1


title: 4.5h_High_light_BiorepD


title: GmCOT_H3_br1


title: 5.5h_Control_BiorepA


title: 4.5h_Control_BiorepC


title: 4h_Control_BiorepA


title: 4h_High_light_BiorepA


title: 3h_High_light_BiorepD


title: 4.5h_Control_BiorepB


title: GmCOT_H3K27me3_br1

description: COT-K27_cat-W200-G600-islands-summary-FDR.05.bed.gz


title: 4h_Control_BiorepC


title: 4.5h_High_light_BiorepC


title: GmCOT_H3K27me3_br2


title: 3h_High_light_BiorepC


title: 4.5h_Control_BiorepD


title: 4.5h_Control_BiorepA


title: 4.5h_High_light_BiorepA


title: GmCOT_H3K4me3_br2


title: 4.5h_High_light_BiorepB


title: GmCOT_H3K4me3_br1


title: GmMM_H3_br2

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts  were incubated overnight with either 3ug of anti-Histone H3 (Abcam, ab1791), 1ug of anti-H3K4me3 (Abcam, ab8580), or 10ug of anti-H3K27me3 (Abcam, ab6002).  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Mid-maturation embryos were dissected from seeds weighing between 200 and 250 mg .  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

value: Mid-maturation stage


title: 3h_High_light_BiorepB


title: 3h_Control_BiorepD


title: GmMM_H3_br1


title: HCT116_siPRKDC_rep3

city: Bethesda

first: Suntae

last: Kim

state: MD

address: Bldg 37, room 6128

department: Genetics Branch

institute: CCR, NCI, NIH

description: HCT116 cells treated with siPRKDC, replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression array signal intensities were Log2 transformed and quantile normalized using GenomeStudio (Illumina) and R v.3.0.2 with lumi package (Du et al., 2008). Differential expression between groups was assessed using an empirical Bayes method for the moderated T-statistics; all probes were corrected for multiple testing using Benjamini and Hochberg’s false discovery rate (FDR).

source_name: HCT116 cells, 48h siPRKDC

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep-96 RNA Amplification Kit (Cat #4393543)

growth_protocol: TC32 cell lines were grown in RPMI-1640 (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (Invitrogen) and HCT116 cell lines were grown in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (Invitrogen).

extract_protocol: RNA was extracted with Maxwell® 16 LEV simplyRNA Cells Kit. RNA quantity was measured usind the Nanodrop.

treatment_protocol: To generate whole transcriptome profiles of each cells, total RNA was purified from untransfected or siRNA-transfected each cells (4x105 cells at plating in six-well plates) 48 hours post siRNA-transfection.

tag: cell line

value: human colorectal carcinoma

value: siPRKDC

tag: treatment duration

tag: dose

value: 20 nM


title: 3h_Control_BiorepB


title: HCT116_siPRKDC_rep2

description: HCT116 cells treated with siPRKDC, replicate 2


title: HCT116_siPRKDC_rep1

description: HCT116 cells treated with siPRKDC, replicate 1


title: HCT116_siNeg_rep3

description: HCT116 cells treated with siNeg, replicate 3

source_name: HCT116 cells, 48h siNeg

value: siNeg


title: HCT116_siNeg_rep1

description: HCT116 cells treated with siNeg, replicate 1


title: 3h_Control_BiorepA


title: 3h_Control_BiorepC


title: GmMM_H3K27me3_br1


title: GmMM_H3K27me3_br2


title: GmMM_H3K4me3_br2


title: TC32_siNeg_rep3

description: TC32 cells treated with siNeg, replicate 3

source_name: TC32 cells, 48h siNeg

value: Ewing sarcoma


title: TC32_siPRKDC_rep2

description: TC32 cells treated with siPRKDC, replicate 2

source_name: TC32 cells, 48h siPRKDC


title: 3.5h_High_light_BiorepD


title: 3.5h_High_light_BiorepB


title: 3.5h_High_light_BiorepC


title: GmMM_H3K4me3_br1


title: TC32_siPRKDC_rep3

description: TC32 cells treated with siPRKDC, replicate 3


title: TC32_siNeg_rep1

description: TC32 cells treated with siNeg, replicate 1


title: HCT116_40 µM_nu7441_48h_rep2

description: HCT116 cells treated with 40 µM nu7441 48h, replicate 2

source_name: HCT116 cells, 40 µM nu7441 48h treated

growth_protocol: All cell lines were grown in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (Invitrogen).

treatment_protocol: To generate whole transcriptome profiles of HCT116 colorectal carcinoma cell line, total RNA was purified from DMSO vehicle or nu7441 treated cells (4x105 cells at plating in six-well plates) 48 hours post treatment.

value: 40 µM


title: 3.5h_Control_BiorepD


title: 3.5h_High_light_BiorepA


title: TC32_siNeg_rep2

description: TC32 cells treated with siNeg, replicate 2


title: HCT116_40 µM_nu7441_48h_rep1

description: HCT116 cells treated with 40 µM nu7441 48h, replicate 1


title: HCT116_40 µM_nu7441_48h_rep3

description: HCT116 cells treated with 40 µM nu7441 48h, replicate 3


title: 3.5h_Control_BiorepC

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps


title: HCT116_Vehicle_rep3

description: HCT116 cells treated with DMSO vehicle control, replicate 3

source_name: HCT116 cells, 0.1% DMSO vehicle 48h treated

value: Vehicle control


title: At_miR2118cOX_2

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA
miR2118c overexpression rep 2  in Arabidopsis

library_source: transcriptomic

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Medicago Genome v3.5
Supplementary_files_format_and_content: tag count file

source_name: miR2118c overexpression

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Plant RNA reagent (Ambion, Life Technologies, USA) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001). PARE libraries were constructed according to the protocols by German et al., 2009 and Zhai et al., 2014.

value: leaves

tag: genotype/variation

value: miR2118c overexpression


title: TC32_siPRKDC_rep1

description: TC32 cells treated with siPRKDC, replicate 1


title: At_miR2118cOX_1

description:
small RNA
miR2118c overexpression  rep1 in Arabidopsis


title: HCT116_Vehicle_rep1

description: HCT116 cells treated with DMSO vehicle control, replicate 1


title: HCT116_Vehicle_rep2

description: HCT116 cells treated with DMSO vehicle control, replicate 2


title: 3.5h_Control_BiorepB

value: leaf


title: 3.5h_Control_BiorepA


title: 6h_High_light_BiorepB

value: high light (HL)


title: At_miR2118bOX_2

description:
small RNA
miR2118b overexpression rep 2  in Arabidopsis

source_name: miR2118b overexpression

value: miR2118b overexpression


title: At_miR2118bOX_1

description:
small RNA
miR2118b overexpression  rep1 in Arabidopsis


title: SKNMC_40 µM_nu7441_48h_rep3

description: SKNMC cells treated with 40 µM nu7441 48h, replicate 3

source_name: SKNMC cells, 40 µM nu7441 48h treated

growth_protocol: All cell lines were grown in RPMI-1640 (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (Invitrogen).

treatment_protocol: To generate whole transcriptome profiles of Ewing sarcoma cell lines, total RNA was purified from DMSO vehicle or nu7441 treated cells (4x105 cells at plating in six-well plates) 48 hours post treatment.

value: SKNMC


title: SKNMC_40 µM_nu7441_48h_rep2

description: SKNMC cells treated with 40 µM nu7441 48h, replicate 2


title: At_miR2118aOX_2

description:
small RNA
miR2118a overexpression rep 2  in Arabidopsis

source_name: miR2118a overexpression

value: miR2118a overexpression


title: At_miR2118aOX_1

description:
small RNA
miR2118a overexpression  rep1 in Arabidopsis


title: At_miR2109OX_2

description:
small RNA
miR2109 overexpression rep 2  in Arabidopsis

source_name: miR2109 overexpression

value: miR2109 overexpression


title: At_miR2109OX_1

description:
small RNA
miR2109 overexpression  rep1 in Arabidopsis


title: 2h_High_light_BiorepC


title: TC32_40 µM_nu7441_48h_rep3

description: TC32 cells treated with 40 µM nu7441 48h, replicate 3

source_name: TC32 cells, 40 µM nu7441 48h treated


title: SKNMC_Vehicle_rep1 (2)

description: SKNMC cells treated with DMSO vehicle control, replicate 1

source_name: SKNMC cells, 0.1% DMSO vehicle 48h treated


title: TC32_40 µM_nu7441_48h_rep2

description: TC32 cells treated with 40 µM nu7441 48h, replicate 2


title: SKNMC_Vehicle_rep2 (2)

description: SKNMC cells treated with DMSO vehicle control, replicate 2


title: At_miR1507OX_1

description:
small RNA
miR1507 overexpression rep1  in Arabidopsis

source_name: miR1507 overexpression

value: miR1507 overexpression


title: SKNMC_40 µM_nu7441_48h_rep1

description: SKNMC cells treated with 40 µM nu7441 48h, replicate 1


title: SKNMC_Vehicle_rep3 (2)

description: SKNMC cells treated with DMSO vehicle control, replicate 3


title: At_OX_control_1

description:
small RNA
Empty vector control for miRNA overexpression lines in Arabidopsis

source_name: Empty vector control

value: Empty vector control


title: 2h_High_light_BiorepA

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps


title: 2h_Control_BiorepC

value: control low light (LL)


title: TC32_Vehicle_rep3 (2)

description: TC32 cells treated with DMSO vehicle control, replicate 3

source_name: TC32 cells, 0.1% DMSO vehicle 48h treated


title: 2h_Control_BiorepB


title: TC32_Vehicle_rep1 (2)

description: TC32 cells treated with DMSO vehicle control, replicate 1


title: 2h_Control_BiorepD


title: TC32_Vehicle_rep2 (2)

description: TC32 cells treated with DMSO vehicle control, replicate 2


title: 2h_High_light_BiorepB


title: 2h_Control_BiorepA


title: 2.5h_High_light_BiorepD


title: 2.5h_High_light_BiorepC


title: TC32_40 µM_nu7441_48h_rep1

description: TC32 cells treated with 40 µM nu7441 48h, replicate 1


title: At_OX_control_2


title: Mt_OX_control_R2

description:
polyA RNA
Medicago RNA-seq library for miRNA overexpression control   rep2

organism: Medicago truncatula

source_name: Medicago hairy roots

value: Jemalong A17

value: hairy roots

value: miRNA overexpression control


title: 2.5h_High_light_BiorepB


title: p9

city: New York

first: Thomas

middle: W

last: Battaglia

state: NY

address: 423 E 23rd Street

department: Medicine

institute: NYU School of Medicine

hyb_protocol: Hydridized according to the manufacturer's protocol. the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. Data Collection is carried out in the nCounterÎ Digital Analyzer. At the highest standard data resolution, 555_1155 fields of view (FOV) are collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts. Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV) format. (http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf)

data_processing: Probe set summarization was performed using the R/Bioconductor package NanoStringNorm and normalized using the package DESeq2.

label: Nanostring fluorescence oligonucleotide probe (3'-biotin)

organism: Mus musculus

source_name: Terminal Ileum

label_protocol: Labeled according to the manufacturer's protocol.  The probe pair consists of a Reporter Probe, which carries the signal on its 5' end, and a Capture Probe which carries a biotin on the 3' end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to target and yet still be individually resolved and identified during data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols

tag: mouseid

tag: antibiotics

value: Control

tag: gender

value: M

tag: week

tag: day

value: Ileum

tag: batch


title: p72


title: p8

value: Tylosin


title: p69

value: F


title: p68


title: Mt2118cOX

description:
PARE
Medicago miR2118c overexpression PARE

value: miR2118c overexpression PARE


title: Mt_OX_control_R1

description:
polyA RNA
Medicago RNA-seq library for miRNA overexpression control   rep1


title: 2h_High_light_BiorepD

value: high light (HL)

value: leaf


title: p67


title: p66


title: 3h_High_light_BiorepA


title: p58


title: 2.5h_Control_BiorepC


title: Mt2118bOX

description:
PARE
Medicago miR2118b overexpression PARE

value: miR2118b overexpression PARE


title: 2.5h_High_light_BiorepA


title: 2.5h_Control_BiorepA


title: p48


title: p52


title: F1-NC

city: Beijing

first: Sihua

last: Gao

address: No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing100029

institute: Beijing University of Chinese Medicine

description: Gene expression of male offspring in normal mice

hyb_protocol: Each slide was hybridised with 1.65 μg Cy3-labelled cRNA using the Gene Expression Hybridization kit (cat. no. 5188-5242; Agilent Technologies) in a hybridisation oven (cat. no. G2545A; Agilent Technologies) according to the manufacturer’s instructions. After 17 h of hybridisation, the slides were washed in staining dishes (cat. no. 121; Thermo Fisher Scientific, Waltham, MA, USA) using the Gene Expression Wash Buffer kit (cat. no. 5188-5327; Agilent Technologies) as instructed by the manufacturer.

scan_protocol: Slides were scanned with the Microarray Scanner (cat. no. G2565CA; Agilent Technologies) using the following default settings: dye channel = green, scan resolution = 3 μm, PMT = 100%, and 20 bit. Data were extracted with Feature Extraction v.10.7 (Agilent Technologies).

data_processing: Raw data were normalised with the quantile algorithm of GeneSpring v.12.6.1 (Agilent Technologies).

source_name: Sperm, F0-NC, replicate 1

label_protocol: Total RNA was amplified and labelled with the Low-Input Quick Amp WT Labeling kit (cat. no. 5190-2943; Agilent Technologies) following the manufacturer’s instructions. Labelled cRNA was purified with the RNeasy Mini kit (cat. no. 74106).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini kit (cat. no. 1038703; Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA integration was analysed with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: Sperm was collected from F0-HFD (n = 6) and F0-NC (n = 6) mice and their male offspring (F1-HFD [n = 6] and F1-NC [n = 6], respectively). Mice were sacrificed by cervical dislocation, and sperm from the epididymis was transferred to a preheated human tubal fluid culture and centrifuged at 1,000 rpm for 5 min. Sperm capacitation was measured for 30 min, and the sperm supernatant was centrifuged again and collected.

tag: cell type

value: sperm

value: male


title: F1-HFD

description: Gene expression of male offspring in obese mice

source_name: Sperm, F1-HFD, replicate 1


title: 2.5h_Control_BiorepD


title: F0-HFD

description: Gene expression after high-fat diet fed in mice sperm

source_name: Sperm, F0-HFD, replicate 1


title: 1h_High_light_BiorepD


title: F0-NC

description: Gene expression of normal mouse sperm


title: 2.5h_Control_BiorepB


title: Mt2109OX

description:
PARE
Medicago miR2109 overexpression PARE

value: miR2109 overexpression PARE


title: HCT116_siNeg_rep2

description: HCT116 cells treated with siNeg, replicate 2

source_name: HCT116 cells, 48h siNeg

value: human colorectal carcinoma

value: siNeg

value: 20 nM


title: p42


title: p45


title: p37


title: p43


title: MtOX_control

description:
PARE
Medicago overexpression PARE control

value: Jemalong A17

value: hairy roots

value: overexpression PARE control


title: p20


title: p21


title: MIMall_2

description:
small RNA
Medicago target mimics for miR1507, miR2109, and miR2118a/b/c  rep 2


title: p44


title: MIMall_1

description:
small RNA
Medicago target mimics for miR1507, miR2109, and miR2118a/b/c  rep 1


title: p19

value: M


title: 1h_High_light_BiorepB

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps


title: 1h_High_light_BiorepA


title: p18

value: Ileum


title: Mt1507OX

description:
PARE
Medicago miR1507 overexpression PARE

value: miR1507 overexpression PARE


title: 1h_Control_BiorepC

value: control low light (LL)


title: p14

value: Control

value: F


title: p12


title: p1

value: Tylosin


title: p10


title: p31


title: 1h_High_light_BiorepC

value: high light (HL)

value: leaf


title: 1h_Control_BiorepD


title: 1h_Control_BiorepB


title: 1h_Control_BiorepA


title: jp95


title: 1.5h_High_light_BiorepD


title: MIM2109_2

description:
small RNA
Medicago target mimics for miR2109 rep 2

value: target mimics for miR2109


title: jp94


title: MIM2109_1

description:
small RNA
Medicago target mimics for miR2109 rep 1


title: 1.5h_High_light_BiorepB


title: 1.5h_High_light_BiorepC


title: MIM1507_2

description:
small RNA
Medicago target mimicsfor  miR1507 rep 2

value: target mimics for miR1507


title: MIM2118_2

description:
small RNA
Medicago target mimics for miR2118 rep 2

value: target mimics for miR2118


title: MIM2118_1

description:
small RNA
Medicago target mimics for miR2118 rep 1


title: MIM1507_1

description:
small RNA
Medicago target mimics for miR1507 rep 1


title: jp660


title: jp657


title: jp654


title: jp652


title: jp653


title: MIM_control_1

description:
small RNA
Medicago target mimics empty vector control rep 1

value: target mimics empty vector control


title: jp651


title: Glo1+/- Aorta rep3

city: Los Angeles

first: Xia

last: Yang

address: 610 Charles E Young Dr East

institute: UCLA

description:
Replicate 3
9703982078_H

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.32.0). It was vst transformed and rsn normalized.

source_name: Glo1+/- Aorta

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The Glo1+/- mice were originally generated in Dr. Michael Brownlee’s lab and received as a gift from Dr. Abraham Palmer’s lab and re-derived at the University of California, Los Angeles (UCLA). Genomic DNA was extracted from mouse ears (N=4-5 per gender) and analyzed by PCR using Kapa Mouse Genotyping Kit (Kapa Biosystems, Wilmington, MA, USA). Mice were provided with ad libitum standard chow diet (Newco Distributors Inc., Rancho Cucamonga, CA, USA) and water.

extract_protocol: Liver, gonadal adipose, and aorta tissues from 36-week old female mice were flash frozen in liquid nitrogen. About 10-15 mg tissue for liver, kidney and aorta and 30 mg for adipose tissue was homogenized and processed using an RNeasy mini kit (QIAGEN GmbH, Hilden, Germany) for RNA isolation. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA) and Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: Heterozygous knockout (Glo1+/-) mice on C57BL/6J (B6) background were created by embryo implantation into a wild-type (WT) B6 female mouse

tag: strain

value: female

tag: genotype

value: aorta


title: 1.5h_High_light_BiorepA

tag: ecotype


title: 1.5h_Control_BiorepB

tag: treatment


title: jp623


title: 1.5h_Control_BiorepC

tag: time (hour)


title: WT Aorta rep3

description:
Replicate 3
9703982078_E

source_name: WT Aorta

value: WT

tag: tissue


title: Glo1+/- Aorta rep2

description:
Replicate 2
9703982078_G


title: 0.5h_High_light_BiorepD


title: Mt_miR2118cOX_2

description:
small RNA
miR2118c overexpression rep 1  in Medicago

value: Jemalong A17

value: hairy roots

value: miR2118c overexpression


title: 1.5h_Control_BiorepD


title: MIM_control_2

description:
small RNA
Medicago target mimics empty vector control rep 2


title: 1.5h_Control_BiorepA


title: WT Aorta rep2

description:
Replicate 2
9703982078_D


title: Glo1+/- Aorta rep1

description:
Replicate 1
9703982078_F


title: Mt_miR2118cOX_1

description:
small RNA
miR2118c overexpression  rep1 in Medicago


title: Mt_miR2118bOX_2

description:
small RNA
miR2118b overexpression rep 2  in Medicago

value: miR2118b overexpression


title: Mt_miR2118bOX_1

description:
small RNA
miR2118b overexpression  rep1 in Medicago


title: jp622

value: Ileum


title: jp618

value: M


title: Mt_miR2118aOX_2

description:
small RNA
miR2118a overexpression rep 2  in Medicago

value: miR2118a overexpression


title: Mt_miR2118aOX_1

description:
small RNA
miR2118a overexpression  rep1 in Medicago


title: Mt_miR2109OX_2

description:
small RNA
miR2109 overexpression rep 2  in Medicago

value: miR2109 overexpression


title: 0.5h_High_light_BiorepC

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps

value: high light (HL)


title: jp602

value: Tylosin

value: F


title: jp601


title: Glo1+/- Kidney rep1

description:
Replicate 1
9703982074_H

source_name: Glo1+/- Kidney

value: kidney


title: Glo1+/- Kidney rep3

description:
Replicate 3
9703982078_B


title: jp617


title: 0.5h_Control_BiorepD

value: control low light (LL)

value: leaf


title: Mt_miR2109OX_1

description:
small RNA
miR2109 overexpression  rep1 in Medicago


title: WT Kidney rep3

description:
Replicate 3
9703982074_G

source_name: WT Kidney

value: female


title: jp47


title: jp46


title: Glo1+/- Kidney rep2

description:
Replicate 2
9703982078_A


title: Mt_miR1507OX_2

description:
small RNA
miR1507 overexpression rep 2  in Medicago

value: miR1507 overexpression


title: 0.5h_High_light_BiorepB


title: 0.5h_Control_BiorepC


title: WT Kidney rep2

description:
Replicate 2
9703982074_F

value: WT


title: WT Kidney rep1

description:
Replicate 1
9703982074_E


title: 0.5h_High_light_BiorepA


title: 0.5h_Control_BiorepB


title: 0.5h_Control_BiorepA


title: jp458

value: Control


title: WT Aorta rep1

description:
Replicate 1
9703982078_C

value: aorta


title: Glo1+/- Liver rep2

description:
Replicate 2
9703982074_C

source_name: Glo1+/- Liver

value: liver


title: Glo1+/- Liver rep3

description:
Replicate 3
9703982074_D


title: Mt_miR1507OX_1

description:
small RNA
miR1507 overexpression rep1  in Medicago

value: Jemalong A17

value: hairy roots


title: jp456

value: M

value: Ileum


title: Mt_OX_control_1

description:
small RNA
Empty vector control for miRNA overexpression lines in Medicago

value: Empty vector control


title: Mt_OX_control_2


title: 0h_Zero_BiorepD

value: Zero


title: 16d_DeNodRoot

description:
small RNA
Medicago 16dpi denodule root, wildtype

source_name: Medicago 16dpi denodule roots

value: 16dpi denodule roots

value: wildtype


title: 0h_Zero_BiorepC


title: jp424

value: Tylosin


title: Mt2118aOX

description:
PARE
Medicago miR2118a overexpression PARE

value: miR2118a overexpression PARE


title: jp41


title: jp418

value: F


title: 16d_Nodule

description:
small RNA
Medicago 16dpi nodules, wildtype

source_name: Medicago 16dpi nodules

value: 16dpi nodules


title: 14d_DeNodRoot

description:
small RNA
Medicago 14dpi denodule root, wildtype

source_name: Medicago 14dpi denodule roots

value: 14dpi denodule roots


title: 14d_Nodule

description:
small RNA
Medicago 14dpi nodules, wildtype

source_name: Medicago 14dpi nodules

value: 14dpi nodules


title: WT Liver rep1

description:
Replicate 1
9703982073_G

source_name: WT Liver

value: female

value: WT


title: 0h_Zero_BiorepA

value: leaf


title: WT Liver rep3

description:
Replicate 3
9703982074_A

value: liver


title: Glo1+/- Adipose rep3

description:
Replicate 3
9703982073_F

source_name: Glo1+/- Adipose

value: gonadal adipose


title: MTF

description:
small RNA
Medicago flower, wildtype

source_name: Medicago flowers

value: Jemalong A17

value: flowers


title: WT Liver rep2

description:
Replicate 2
9703982073_H


title: Glo1+/- Liver rep1

description:
Replicate 1
9703982074_B


title: jp40

source_name: Terminal Ileum

value: M

value: Ileum


title: jp251

value: Control


title: jp288


title: Glo1+/- Adipose rep2

description:
Replicate 2
9703982073_E


title: MTS

description:
small RNA
Medicago seedling, wildtype

source_name: Medicago seedlings

value: seedlings

value: wildtype


title: MTR

description:
small RNA
Medicago root, wildtype

source_name: Medicago roots

value: roots


title: jp233

value: Tylosin

value: F


title: MTL

description:
small RNA
Medicago  leaf, wildtype

source_name: Medicago leaves

value: leaves


title: Rapeseed treated with 4BM1-3

first: Lili

last: Geng

address: Hiandian district, Yuanmingyuan West road No.2

institute: Institute of Plant Protection, Chinese Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: ftp://brassicadb.org/Bra_Chromosome_V1.5/。
Supplementary_files_format_and_content: Excel file include FPKM values for each sample

organism: Brassica napus

source_name: Brassica napus L.

growth_protocol: B. napus L. seeds were sown in MS agar plates, and 10-day-old seedings were transferred into plots containing nutrition soil and vermiculite (2:1) under suitable conditions, which was 14 h light (7,000 Lux) and a 10 h dark cycle

extract_protocol:
The total RNA of rapeseed leaves was extracted by TRIZOL reagent and subsequently was treated by DNaseⅠ(Takara)
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Brassica napus L were treated with Bt strain 4F5, 4BM1, and stilled water as control.  B. thuringiensis inoculum, the final density was 7.5×109 cfu, was sprayed on the root of 6-week-old rapeseed plants. The same volume of distilled water (DW) treatment as control. Five days after induction, rapeseed leaves were collected. For each treatment, 3 rapeseed seedlings were used.

value: Leaves

tag: Stage

value: 6-week-old rapesees


title: 0h_Zero_BiorepB

value: Zero


title: jp232


title: jp168


title: jp284


title: jp175


title: Rapeseed treated with 4BM1-2


title: jp176


title: Rapeseed treated with 4BM1-1


title: WT Adipose rep3

description:
Replicate 3
9703982073_C

source_name: WT Adipose

value: female

value: WT


title: Rapeseed treated with 4F5-3


title: WT Adipose rep1

description:
Replicate 1
9703982073_A

value: gonadal adipose


title: SK15_JK CD63-

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: Exosome Not bound by CD63

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix microRNA GeneChips version 4.0 (Affymetrix, Inc).   Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to labeling.  300ng of total RNA was used for labeling with the Affymetrix FlashTag kit (cat#901910).

growth_protocol: The Jurkat T cell line (E6.1) was purchased from ATCC. The cells were maintained using RPMI 1640 containing 10% FBS, glutamine, penicillin, and streptomycin (Gibco). The Jurkat and JinB8 T cells used for experiments were maintained less than 6 weeks in culture.

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: The cultured Jurkat were washed with IXPBs followed by a second wash with HITES medium (DMEM/F12 supplemented with, bovine serum albumin, hydrocortisone, insulin, transferrin, and trace elements). EVs were isolated from Jurkat T cells were cultured overnight using HITES medium. The conditioned media from Jurkat T cells were collected, and cell debris were removed using centrifugation at 300 g for 5 minutes and 2500 g for 10 minutes respectively. Centrifuged media were concentrated using Ultra-4 centrifugal filters to about 1 ml volume and further centrifuged at 10,000 rpm for 10 minutes. EVs were isolated using an Exo-Quick kit (SBI) by incubating overnight at 4°C. CD63 and CD47 positive EVs were captured using Biotin conjugated antibodies.

value: Jurkat cell line exosomes

value: Myeloid


title: Rapeseed treated with 4F5-2


title: jp134


title: jp135

value: M


title: WT Adipose rep2

description:
Replicate 2
9703982073_B


title: SK10_JK CD47-

source_name: Exosome Not bound by CD47


title: Rapeseed treated with 4F5-1


title: jp127

value: Ileum


title: SK14_JK CD63-


title: SK05_JK CD63+

source_name: Exosome bound by CD63


title: jp125


title: SK06_JK CD63+


title: SK12_JK CD47-


title: SK04_JK CD63+


title: Glo1+/- Adipose rep1

description:
Replicate 1
9703982073_D


title: Rapeseed treated with distilled water-1

value: distilled water-1


title: jp167

value: Control


title: SK03_JK CD47+

source_name: Exosome bound by CD47


title: SK02_JK CD47+


title: Rapeseed treated with distilled water-2

value: distilled water-2


title: Infected_treated_S60 alone_rep2

status: Public on Aug 02 2018

city: Baltimore

first: Noton

middle: K

last: Dutta

address: 1550 Orleans Street, Room 110

institute: Johns Hopkins University

description:
Gene expression after10wks inf Lung, treated with Simvastatin 60 for 4 wks_rep2
SAMPLE 9B

hyb_protocol: Agilent mouse GE 4x 44K v2 microarrays (G4846A) were used, which contain 41,000 unique probes targeting 39,430 Entrez gene RNAs. 0.825 ug of each Cy3-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

scan_protocol: Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software

data_processing: Agilent FE processed signal intensities were imported into GeneSpring GX 10 (Agilent Technologies). Quantile normalization was done by setting intensity thresheld to 1 and log2 transformation. Differentially expressed genes were identified by unpaired T-Test and volcano plot with cut-off p=0.05 and two-fold change.

label_protocol: Sample amplification and labeling procedures were carried out by using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). ) with minor modifications. Briefly, 0.4 ug total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporates a T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: Female BALB/c mice were aerosol-infected with M. tuberculosis H37Rv using the Inhalation Exposure System (Glas-Col, Terre Haute, IN, USA) calibrated to deliver ∼10^2 cfu per lung. The mice were randomized into different treatment groups and five mice from each group were sacrificed at predefined timepoints.

extract_protocol: Total RNA was isolated from lung samples using TriZol reagent (Invitrogen) followed by RNeasy mini kit with DNase on-column digestion (Qiagen). RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol

treatment_protocol: Drugs were either dissolved or suspended in distilled water and administered daily (five times weekly) by oesophageal gavage. The following doses were used: 10 mg/kg isoniazid; 10 mg/kg rifampicin; 150 mg/kg pyrazinamide, 100mg/kg etthumbutol; and 30 to 180 mg/kg pravastatin. Six weeks after M. tuberculosis infection, separate groups of mice were left untreated (negative controls) or were treated once daily with the standard regimen isoniazid/rifampicin/pyrazinamide/ethumbutol (positive control) or isoniazid/rifampicin/pyrazinamide/ethumbutol + pravastatin (experimental regimen) for 1 month. Rifampicin doses were separated from the accompanying drugs by 1 h to minimize drug–drug interactions.

value: BALB/c

value: Lung

tag: infected with

value: M. tuberculosis H37Rv

value: Female

tag: age

value: 20 weeks


title: Infected_treated_S60 alone_Srep1

description:
Gene expression after10wks inf Lung, treated with Simvastatin 60 for 4 wks_rep1
SAMPLE 9A


title: Infected_treated_RHZE+P90_rep2

description:
Gene expression after10wks inf Lung, treated with RHZE + P90 for 4 wks_rep2
SAMPLE 7B


title: Infected_treated_P1800 alone_rep2

description:
Gene expression after10wks inf Lung, treated with P180 for 4 wks_rep2
SAMPLE 5B


title: Infected_treated_P90 alone_rep2

description:
Gene expression after10wks inf Lung, treated with P90 for 4 wks_rep2
SAMPLE 4B


title: Infected_treated_RHZE +P90_rep1

description:
Gene expression after10wks inf Lung, treated with RHZE + P90 for 4 wks_rep1
SAMPLE 7A


title: Infected_untreated_rep1

description:
Gene expression after 10wks infected Lung, Untreated
SAMPLE 2A

source_name: 10wks inf Lung, Untreated_rep1


title: Infected_treated_P180 alone_rep1

description:
Gene expression after10wks inf Lung, treated with P180 for 4 wks_rep1
SAMPLE 5A


title: Infected_treated_RHZE_P180_rep2

description:
Gene expression after10wks inf Lung, treated with RHZE + P180 for 4 wks_rep2
SAMPLE 8B


title: Infected_treated_RHZE+ P180_rep1

description:
Gene expression after10wks inf Lung, treated with RHZE +p180 for 4 wks_rep1
SAMPLE 8A


title: Infected_treated_P30 alone_rep2

description:
Gene expression after10wks inf Lung, treated with P30 for 4 wks_rep2
SAMPLE 3B


title: Infected_untreated_rep2

description:
Gene expression after10wks inf Lung, Untreated_rep2
SAMPLE 2B

source_name: 10wks inf Lung, Untreated_rep2


title: Infected_treated_RHZE_rep1

description:
Gene expression after10wks inf Lung, treated with RHZE for 4 wks_rep1
SAMPLE 6A


title: Infected_treated_RHZE_rep2

description:
Gene expression after10wks inf Lung, treated with RHZE for 4 wks_rep2
SAMPLE 6B


title: SK01_JK CD47+


title: islet preparation 4 under cytokine treatment

city: Bruxelles

first: Decio

middle: Laks

last: Eizirik

address: Route de Lennik 808

department: Faculté de Médecine

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Sequencing reads were mapped to the Homo sapiens genome (version GRCh37/hg19) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options the GENCODE 18 annotation of genes transcripts. The Tophat mapper reports all mappings and split-mappings.
GTF files: Mapped reads were used to quantify human transcripts from the GENCODE 18 annotation dataset, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

molecule: polyA RNA

source_name: islets of Langerhans

growth_protocol: Human islet preparations were obtained from heart-beating organ donors with no medical history of diabetes or metabolic disorders. The islets were isolated using collagenase digestion and density gradient purification. They were cultured in M199 culture medium containing 5.5 mM glucose and shipped within 1-5 days following isolation. Upon arrival, the human islet cells were cultured in Ham's F-10 medium containing 6.1 mM glucose, 10% fetal bovine serum (FBS), 2 mM GlutaMAX, 50 μM 3-isobutyl-1-methylxanthine, 1% BSA, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated from Maria using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands) which favours purification of RNA molecules longer than 200 nucleotides. mRNA was purified from 1 μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments.
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2000 system

treatment_protocol: The islets were exposed or not to cytokines in the same medium as used for preparation but without FBS for 2 days. The following cytokine concentrations were used: recombinant human IL-1β (specific activity 1.8x107 U/mg) at 50 U/ml; recombinant human IFN-γ (specific activity 2x107 U/mg) at 1000 U/ml.

value: islets of Langerhans


title: islet preparation 5 under control condition


title: islet preparation 5 under cytokine treatment


title: Pooled Serum 8 from Health Chinese Subjects

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
The image files generated by the sequencer were then processed to produce digital data. The subsequent procedures included summarizing data production, evaluating sequencing quality and depth, calculating length distribution of small RNAs, and filtrating contaminated reads.
After masking the adaptor sequences, the clean reads were aligned against the miRBase database 16.0 based on the Smith-Waterman algorithm. Only candidate with identical sequence and length compared to reference miRNA was counted as miRNA matching.
For normalization, the sequencing frequency of each plant miRNA was normalized to the total amount of mammalian miRNAs.
Genome_build: miRBase 16.0
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each samples

source_name: Pooled Serum from Health Chinese Subjects

extract_protocol:
8 pooled samples (each pooled from 10 healthy Chinese subjects, mean age 50.9 ± 7.9) was conducted in the Healthy Physical Examination Center of the Jinling Hospital. The health condition checkup included detailed history, physical, radiological examinations, blood tests, and abdominal sonography. Subjects who showed no abnormalities during the medical checkup were enrolled. Written informed consent was obtained from all donors prior to the study, and the study was approved by the ethics committee of Nanjing University, China. Venous blood samples (∼5 ml) were collected from each donor and placed in a serum separator tube. Samples were processed within 1 h. Separation of the serum was accomplished by centrifugation at 800× g for 10 min at room temperature, followed by a 15 min high-speed centrifugation at 10 000× g at room temperature to completely remove the cell debris. The supernatant serum was recovered and stored at −80 °C until analysis.  Total RNA was extracted from 100 ml of serum using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: healthy Chinese subjects

tag: mean age

value: Serum


title: Pooled Serum 5 from Health Chinese Subjects


title: Infected_treated_P90 alone_rep1

description:
Gene expression after10wks inf Lung, treated with P90 for 4 wks_rep1
SAMPLE 4A


title: Pooled Serum 7 from Health Chinese Subjects


title: Pooled Serum 4 from Health Chinese Subjects


title: Pooled Serum 1 from Health Chinese Subjects


title: Pooled Serum 2 from Health Chinese Subjects


title: Pooled Serum 6 from Health Chinese Subjects


title: Pooled Serum 3 from Health Chinese Subjects


title: Infected_treated_P30 alone_rep1

description:
Gene expression after10wks inf Lung, treated with P30 for 4 wks_rep1
SAMPLE 3A


title: jp100

tag: mouseid

tag: antibiotics


title: islet preparation 4 under control condition


title: islet preparation 3 under cytokine treatment


title: islet preparation 2 under cytokine treatment


title: islet preparation 2 under control condition


title: islet preparation 3 under control condition


title: islet preparation 1 under control condition


title: islet preparation 1 under cytokine treatment


title: Sample 21: 14 days after S.aureus infection

city: Aalborg East

first: Yijuan

last: Xu

address: Fredrik Bajers vej 7H

department: Department of Chemistry and Bioscience

country: Denmark

institute: Aalborg University

description:
14 days after S.aureus infection
To remove host RNA, MICROBEnrich (Ambion) was used after RNA extraction. RiboZero rRNA Removal Kit  was used to remove ribosomal RNA.

data_processing:
Basecalls performed using CASAVA version 1.8.2, Hiseq control software: HCS 1.5.15.1/RTA 1.13/SAV 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Then using RNA-seq analysis function in CLC genomic workbench v. 9.5.2, the reads were mapped to SAU060112 genome allowing a minimum length fraction of 80% and minimum similarity fraction of 80%. The resulting output is a table summarizing the read mapping which includes Reads Per Kilobase of exon per Megabase of library size (RPKM), total mapped reads, uniquely mapped reads etc. for each gene.
The RNA-seq analysis output for each sample were used as input for Differential Expression for RNA-seq analysis i CLC Genominc workbench.
Genome_build: CCXN00000000
Supplementary_files_format_and_content: tab-delimited text files include gene length, unique gene reads, total gene reads, RPKM values, chromosome region start and end for each Sample

organism: Staphylococcus aureus

source_name: S. aureus infected cage fluid

extract_protocol:
RNA was extracted with RiboPure Bacteria Kit (Ambion). Genomic DNA was removed with Dnase I treatment. MicroExpress (Ambion) was used to remove ribosomal RNA.
Illumina Trusq RNA sample preparation Kit v2 according to manufacturers instruction

treatment_protocol: The samples were centrifuged at 13 000 g for 2 minutes. The pellets were snap-frozen in liquid nitrogen and stored at -80 C until RNA extraction

tag: genome

value: 14 days after injection of S. aureus into the cage,  and moxifloxacin treatment between day 3 to 7


title: Sample 22: 14 days after S.aureus infection

source_name: S. aureus infected cage


title: Sample 20: 9 days after S.aureus infection

description:
9 days after S.aureus infection
To remove host RNA, MICROBEnrich (Ambion) was used after RNA extraction. RiboZero rRNA Removal Kit  was used to remove ribosomal RNA.

value: 9 days after injection of S. aureus into the cage


title: Sample 18: 9 days after S.aureus infection


title: Sample 19: 9 days after S.aureus infection


title: LNCaP ERG Input

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: LNCaP ERG Input ChIP-seq

data_processing:
ChIP-seq reads were mapped to the human reference genome (hg19) using Bowtie2(Langmead and Salzberg, 2012) version 2.1.0 with parameters –k 1.
Peaks were called against input reads using MACS2(Zhang et al., 2008) version 2.1.0 at q=1e-3.
Peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to unmappable chromosomes (only chr1-22,X,Y included). Duplicate reads were removed using samtools rmdup for all downstream analyses.
ChIP-seq track densities were generated per million mapped reads with MACS2 2.1.0 using parameters –B –SPMR.
Genome_build: hg19

source_name: LNCaP (CaP)

growth_protocol: All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10-20% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, 2-5M cells were crosslinked with 1% formaldehyde for 10 min at 37 °C. This reaction was subsequently quenched with 0.125M glycine.
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). Cells were harvested following 48h exposure to lentivirus and either 4 days (LNCaP) or 8 days (VCaP) of selection. The overexpression constructs used in LNCaP cell experiments were selected with blasticidin. The knockdown constructs used in VCaP cell experiments were selected with puromycin.

value: ERG Input


title: LNCaP ERG-R367K Input

description: LNCaP ERG-R367K Input ChIP-seq

value: ERG-R367K Input


title: LNCaP ERG H3K27me3

description: LNCaP ERG H3K27me3 ChIP-seq

value: ERG H3K27me3


title: Sample 15: 9 days after S.aureus infection


title: Sample 14: 9 days after S.aureus infection


title: LNCaP ERG H3K27ac

description: LNCaP ERG H3K27ac ChIP-seq

value: ERG H3K27ac


title: LNCaP Empty AR

description: LNCaP Empty AR ChIP-seq

value: Empty AR


title: LNCaP Empty H3K27me3

description: LNCaP Empty H3K27me3 ChIP-seq

value: Empty H3K27me3


title: Sample 16: 9 days after S.aureus infection


title: Sample 13: 9 days after S.aureus infection


title: LNCaP Empty Input

description: LNCaP Empty Input ChIP-seq

value: Empty Input


title: LNCaP ERG AR

description: LNCaP ERG AR ChIP-seq

value: ERG AR


title: LNCaP Empty H3K27ac

description: LNCaP Empty H3K27ac ChIP-seq

value: Empty H3K27ac


title: LNCaP ERG-R367K BAF155

description: LNCaP ERG-R367K BAF155 ChIP-seq

value: ERG-R367K BAF155


title: Sample 17: 9 days after S.aureus infection


title: Sample 12: 9 days after S.aureus infection


title: Sample 23: 14 days after S.aureus infection


title: LNCaP ERG BAF155

description: LNCaP ERG BAF155 ChIP-seq

value: ERG BAF155


title: Sample 11: 7 days after S.aureus infection

description:
7 days after S.aureus infection
To remove host RNA, MICROBEnrich (Ambion) was used after RNA extraction. RiboZero rRNA Removal Kit  was used to remove ribosomal RNA.

value: 7 days after injection of S. aureus into the cage


title: Sample 10: 7 days after S.aureus infection


title: LNCaP ERG-R367K ERG

description: LNCaP ERG-R367K ERG ChIP-seq

value: ERG-R367K ERG


title: LNCaP ERG ERG

description: LNCaP ERG ERG ChIP-seq

value: ERG ERG


title: Sample 9: 7 days after S.aureus infection


title: Sample 6: 7 days after S.aureus infection


title: Sample 8: 7 days after S.aureus infection


title: LNCaP Empty ERG

description: LNCaP Empty ERG ChIP-seq

value: Empty ERG


title: VCaP shARID1A Input

description: VCaP shARID1A Input ChIP-seq

source_name: VCaP (CaP)

value: shARID1A Input


title: VCaP shCt Input

description: VCaP shCt Input ChIP-seq

value: shCt Input


title: Sample 4: 7 days after S.aureus infection


title: Sample 5: 7 days after S.aureus infection


title: VCaP shARID1A BAF155

description: VCaP shARID1A BAF155 ChIP-seq

value: shARID1A BAF155


title: VCaP shCt AR

description: VCaP shCt AR ChIP-seq

value: shCt AR


title: VCaP shERG AR

description: VCaP shERG AR ChIP-seq

value: shERG AR


title: Sample 7: 7 days after S.aureus infection


title: Sample 2: 3 days after S.aureus infection

description:
3 days after S.aureus infection
To remove host RNA, MICROBEnrich (Ambion) was used after RNA extraction. RiboZero rRNA Removal Kit  was used to remove ribosomal RNA.

value: 3 days after injection of S. aureus into the cage


title: VCaP shCt BAF155

description: VCaP shCt BAF155 ChIP-seq

value: shCt BAF155


title: Tg26+KLF15OE rep2 [435TG26K15OE_S71]

city: Stony Brook

first: Sandeep

last: Mallipattu

address: HSC-T16 Room 80E

department: Division of Nephrology and Hypertension

institute: Stony Brook University School of Medicine

data_processing:
Illumina software used for basecalling.
FastQC to perform Quality Controls and generate QC report for the input RNA-seq data
STAR for the read alignment
featureCounts for assigning reads to genes
edgeR Bioconductor package were used to compute CPM and RPKM
Genome_build: mm10
Supplementary_files_format_and_content: one tab-delimited text files include RPKM values for all Samples

extract_protocol:
Glomeruli were isolated, keep in RNAlater and store at -80c freezer, and RNA was harvested using Qiagen Rneasy mini kit. Illumina TruSeq® Stranded mRNA Library Prep for NeoPrep™ Kit was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: FVB/NJ

value: post natal week 10

tag: genotype/variation

value: glomeruli


title: VCaP shERG Input

description: VCaP shERG Input ChIP-seq

value: shERG Input


title: Sample 1: 3 days after S.aureus infection


title: Tg26+KLF15OE rep3 [443TG26K15OE_S72]


title: Tg26+KLF15OE rep1 [412TG26K15OE_S70]


title: VCaP shERG ERG

description: VCaP shERG ERG ChIP-seq

value: shERG ERG


title: VCaP shERG BAF155

description: VCaP shERG BAF155 ChIP-seq

value: shERG BAF155


title: Sample 3: 3 days after S.aureus infection


title: VCaP shARID1A ERG

description: VCaP shARID1A ERG ChIP-seq

value: shARID1A ERG


title: LNCaP Empty BAF155

description: LNCaP Empty BAF155 ChIP-seq

value: Empty BAF155


title: Tg26 rep3 [649TG26_S69]


title: VCaP shCt ERG

description: VCaP shCt ERG ChIP-seq

value: shCt ERG


title: Tg26 rep2 [441TG26_S68]


title: Tg26 rep1 [413TG26_S67]


title: KLF15OE rep3 [50K150E_S74]


title: KLF15OE rep1 [49K15OE_S73]


title: WT rep2 [964WT_S77]

value: Wt


title: SW13 BRG1 Empty 2 [RNA-seq]

description: SW13 BRG1 Empty 2 RNA-seq

data_processing:
RNA-seq reads were mapped to the human reference genome (hg19) using STAR(Dobin et al., 2013) version 2.3.1 with default parameters.
RPKM values for biological duplicate RNA-seq samples were generated using GFold(Feng et al., 2012) version 1.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: read_cnt containing GeneSymbol, GeneName, Read Count, Gene Exon Length, RPKM columns

source_name: SW13 BRG1 Empty

extract_protocol:
All RNA was produced using the RNeasy Mini Kit (Qiagen).
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). Cells were harvested following 48h exposure to lentivirus and either 2 days  (SW13), 4 days (LNCaP) or 8 days (VCaP) of selection. The overexpression constructs used in LNCaP cell experiments were selected with blasticidin. The knockdown constructs used in VCaP cell experiments were selected with puromycin. SW13 cells were selected with both blasticidin and puromycin as the empty and V5-ERG vectors were blasticidin resistant, while the V5-luciferase, V5-BRG1 and V5-BRG1 K785R constructs were puromycin resistant. RNA-seq samples were prepared in duplicate with independent infection, selection and cell culture.

tag: cell line

tag: cell type

value: adrenacorticoid carcinoma cell line (ACC)

value: BRG1 Empty


title: WT rep1 [13WT_S76]


title: WT rep3 [974WT_S78]


title: SW13 BRG1-K785R ERG 2 [RNA-seq]

description: SW13 BRG1-K785R ERG 2 RNA-seq

source_name: SW13 BRG1-K785R ERG

value: BRG1-K785R ERG


title: SW13 BRG1-K785R ERG 1 [RNA-seq]

description: SW13 BRG1-K785R ERG 1 RNA-seq


title: KLF15OE rep2 [500K15OE_S75]


title: SW13 BRG1 ERG 1 [RNA-seq]

description: SW13 BRG1 ERG 1 RNA-seq

source_name: SW13 BRG1 ERG

value: BRG1 ERG


title: SW13 BRG1 Empty 1 [RNA-seq]

description: SW13 BRG1 Empty 1 RNA-seq


title: SW13 BRG1-K785R Empty 2 [RNA-seq]

description: SW13 BRG1-K785R Empty 2 RNA-seq

source_name: SW13 BRG1-K785R Empty

value: BRG1-K785R Empty


title: RNA from MCF7 cells, 30 minutes, 43C heat shock (30HS), no ribosomal RNA depletion

city: Miami

first: Stephen

last: Lee

state: Florida

department: Biochemistry & Molecular Biology

institute: University of Miami

data_processing:
Illumina Nextseq 500 uses Reat-Time Analysis (RTA) version 2 for base calling and quality scoring. Bcl2fastq converts output bcl files to fastq files.
RNA-seq data were aligned to ribosomal RNA data obtained from DASHR (5'ETS, 18S, ITS1, 5.8S, ITS2, 28S, 3'ETS) and SILVA (rRNA data from Bacteria, Archaea, Eukarya) with STAR 2.5.0 default parameters
Remaining unmapped reads were aligned to human genome assembly GRCh38 (gencode v27) using parameters suitable for long RNA-seq pipeline
Genome-wide Alu elements (retrieved from UCSC genome browser) were filtered out of BAM/BED files, as indicated with *_filtered.bam files
Genome_build: GRCh38 (gencode v27)
Supplementary_files_format_and_content: BED, alignment files

molecule: nuclear RNA

source_name: MCF7 mammary gland cell culture

growth_protocol: MCF7 cells were grown at 37C, 5% CO2 in a humidified incubator in DMEM medium supplemented with 5% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
RNA from the digitonin-insoluble fraction of cell lysates were harvested using TriZol.
Illumina TruSeq Stranded Total RNA sample prep kit was used, without ribosomal RNA depletion, to construct the sequencing libraries. Samples are barcoded for multiplexing.

treatment_protocol: No treatment versus 30 minutes, heat shock in 43C, 5% CO2 in a humidified incubator in DMEM medium supplemented with 5% fetal bovine serum and 1% penicillin/streptomycin

tag: isolate

value: mammary gland, breast; derived from metastatic site:pleural effusion

tag: disease

value: adenocarcinoma

value: 30 minutes, 43C heat shock


title: SW13 BRG1-K785R Empty 1 [RNA-seq]

description: SW13 BRG1-K785R Empty 1 RNA-seq


title: SW13 GFP ERG 1 [RNA-seq]

description: SW13 GFP ERG 1 RNA-seq

source_name: SW13 GFP ERG

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). Cells were harvested following 48h exposure to lentivirus and either 2 days  (SW13), 4 days (LNCaP) or 8 days (VCaP) of selection. The overexpression constructs used in LNCaP cell experiments were selected with blasticidin. The knockdown constructs used in VCaP cell experiments were selected with puromycin. SW13 cells were selected with both blasticidin and puromycin as the empty and V5-ERG vectors were blasticidin resistant, while the V5-GFP, V5-BRG1 and V5-BRG1 K785R constructs were puromycin resistant. RNA-seq samples were prepared in duplicate with independent infection, selection and cell culture.

value: GFP ERG


title: SW13 GFP Empty 2 [RNA-seq]

description: SW13 GFP Empty 2 RNA-seq

source_name: SW13 GFP Empty

value: GFP Empty


title: SW13 GFP ERG 2 [RNA-seq]

description: SW13 GFP ERG 2 RNA-seq


title: SW13 GFP Empty 1 [RNA-seq]

description: SW13 GFP Empty 1 RNA-seq


title: LNCaP ETV1 2 [RNA-seq]

description: LNCaP ETV1 2 RNA-seq

source_name: LNCaP ETV1

value: LNCaP (CaP)

value: Prostate cancer cell line


title: RNA from MCF7 cells, no treatment (NT), no ribosomal RNA depletion

tag: treatment


title: SW13 BRG1 ERG 2 [RNA-seq]

description: SW13 BRG1 ERG 2 RNA-seq


title: LNCaP ETV1 1 [RNA-seq]

description: LNCaP ETV1 1 RNA-seq


title: LNCaP ERG 2 [RNA-seq]

description: LNCaP ERG 2 RNA-seq

source_name: LNCaP ERG

value: ERG


title: LNCaP Empty 2 [RNA-seq]

description: LNCaP Empty 2 RNA-seq

source_name: LNCaP Empty

value: Empty


title: 107 osteoarthritis

first: Muhammad Farooq

last: Rai

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: Gene expression in TKA cartilage

hyb_protocol: For hybridization, amplified RNA samples were suspended in Agilent 2X Gene Expression buffer, Agilent 10X blocking agent, and Kreablock. The hybridization solution was applied to human SurePrint G3 Human 8X60K microarrays (Catalog # G4851C, Agilent Technologies) and incubated with streptavidin-cyanine 5 at 65oC for 20h. Washing procedures were performed according to Agilent Gene Expression protocol.

scan_protocol: Slides were  scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence as per manufacturer’s specification.

data_processing: Gridding and analysis of images were performed using Feature Extraction software v. 11.5.1.1 (Agilent Technologies).

source_name: Knee cartilage

label_protocol: 20 ng of RNA transcripts were amplified with the use of Sigma-WTA2 kit (Sigma-Aldrich) and then complementary DNA (cDNA) was labelled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Briefly, 3 g of cDNA was mixed with Kreatech 10X labeling buffer and Kreatech cyanine 5/DY-ULS. The reaction mixture was incubated at 85oC for 15 min in the dark and then quenched on ice for 3 min. Labelled cDNA was purified with Qiagen purification columns according to the supplier’s protocol (Qiagen).

extract_protocol: RNA was isolated using a combination of TRIzol:Chloroform (5:1 ratio) method and Minispin columns (Qiagen).  The pulverized tissues were first dissolved in 1 ml of TRIzol reagent (Invitrogen) followed by addition of 0.2 ml of Chloroform. Sample were then vortexed and transferred to phase lock gel tubes. Tubes were centrifuged for 15 min at 4°C. The clear aqueous layer was transferred by decanting of pipetting and 1 volume of 70% RNase-free ethanol was added to precipitate RNA. Finally, RNA was collected using RNeasy spin columns (Qiagen). The quality of the RNA was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: A small segment of the healthy-appearing cartilage was harvested from femoral notch of 12 patients during arthroscopic partial meniscectomy and a location-matched segment was obtained from 12 patients during total knee arthroplasty. Tissues were homogenized prior to RNA isolation.

value: Knee cartilage

tag: age (years)

tag: Sex

value: Female

tag: bmi (kg/m2)


title: VCaP shARID1A 2 [RNA-seq]

description: VCaP shARID1A 2 RNA-seq

source_name: VCaP shARID1A

value: VCaP (CaP)

tag: infected with


title: LNCaP Empty 1 [RNA-seq]

description: LNCaP Empty 1 RNA-seq


title: 108 osteoarthritis

description: Gene expression in TKA cartilage

tag: tissue


title: VCaP shERG 1 [RNA-seq]

description: VCaP shERG 1 RNA-seq

source_name: VCaP shERG

value: shERG


title: VCaP shARID1A 1 [RNA-seq]

description: VCaP shARID1A 1 RNA-seq


title: VCaP shERG 2 [RNA-seq]

description: VCaP shERG 2 RNA-seq


title: LNCaP ERG 1 [RNA-seq]

description: LNCaP ERG 1 RNA-seq


title: 114 osteoarthritis

description: Gene expression in TKA cartilage


title: 113 osteoarthritis

description: Gene expression in TKA cartilage


title: 111 osteoarthritis

description: Gene expression in TKA cartilage

value: Male


title: 109 osteoarthritis

description: Gene expression in TKA cartilage


title: 112 osteoarthritis

description: Gene expression in TKA cartilage


title: 105 osteoarthritis

description: Gene expression in TKA cartilage


title: VCaP shCt 1 [RNA-seq]

description: VCaP shCt 1 RNA-seq

source_name: VCaP shCt

value: shCt


title: 104 osteoarthritis

description: Gene expression in TKA cartilage


title: 106 osteoarthritis

description: Gene expression in TKA cartilage


title: VCaP shCt 2 [RNA-seq]

description: VCaP shCt 2 RNA-seq


title: 012 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: 102 osteoarthritis

description: Gene expression in TKA cartilage


title: 103 osteoarthritis

description: Gene expression in TKA cartilage


title: 011 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: 008 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: 013 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: bulk ATAC 54-1 Day 7 PbxKO guide 4

city: Seattle

first: Cole

last: Trapnell

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
Accessible genomic DNA
54_1_bulk_multi_cov_counts.txt.gz

data_processing:
BCL files were converted to fastq format with bcl2fastq v2.16.
Barcode sequences were corrected to expected barcodes with custom python script.
Reads were trimmed (for adapter read-through) with Trimmomatic v0.32.
Reads were mapped to hg19 with bowtie v2.2.3.
Reads not mapping to the assembled nuclear chromsomes, as well as reads with invalid cell barcodes, were filtered using samtools v1.1 and grep.
Duplicate reads from each cell were filtered out with a custom python script.
Filtered out barcodes with few reads using custom R script.
Called peaks using MACS2 v2.1.1
Overlapped reads with summits of accessibility using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: "counts.txt.gz": Gzipped multiple column tab-separated vector in sparse matrix format - Column 1 = location information for each hypersensitivity summit; Column 2 = barcode representing single cell; Column 3 = count of reads from that barcode overlapping that hypersensitivity summit
Supplementary_files_format_and_content: ".indextable.txt": 2 column tab-separated vector - Column 1 = list of valid barcode combinations included in experiment; Column2 = time of collection
Supplementary_files_format_and_content: "54_1_bulk_multi_cov_counts.txt.gz":  Multiple column tab-separated vector - Columns 1-3 = bed format genomic coordinates, Remaining Columns = count of reads overlapping the genomic coordinates from the named bulk ATAC seq library

extract_protocol:
Nuclei were isolated (please see publication for more details).
Please see publication for details on library construction.

value: Immortalized skeletal muscle myoblasts

tag: crispr perturbation target

value: Pbx1 knockout

tag: crispr guide

value: Pbx1 knockout 4

tag: time

value: Day 7


title: bulk ATAC 54-1 Day 7 PbxKO guide 3

value: Pbx1 knockout 3


title: 010 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: 007 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: bulk ATAC 54-1 Day 7 PbxKO guide 2

value: Pbx1 knockout 2


title: bulk ATAC 54-1 Day 7 MeisKO guide 6

value: Meis1 knockout

value: Meis1 knockout 6


title: bulk ATAC 54-1 Day 7 PbxKO guide 1

value: Pbx1 knockout 1


title: bulk ATAC 54-1 Day 7 MeisKO guide 5

value: Meis1 knockout 5


title: bulk ATAC 54-1 Day 7 MeisKO guide 1

value: Meis1 knockout 1


title: 004 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage

value: Knee cartilage


title: bulk ATAC 54-1 Day 7 NTC guide 5

value: Non template control

value: Non template control 5


title: 003 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage

value: Female


title: bulk ATAC 54-1 Day 7 MeisKO guide 3

value: Meis1 knockout 3


title: 005 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: bulk ATAC 54-1 Day 7 PbxKO guide 6

value: Pbx1 knockout 6


title: bulk ATAC 54-1 Day 7 NTC guide 4

value: Immortalized skeletal muscle myoblasts

value: Non template control 4


title: bulk ATAC 54-1 Day 7 NTC guide 3

value: Non template control 3


title: bulk ATAC 54-1 Day 7 NTC guide 2

value: Non template control 2

value: Day 7


title: bulk ATAC 54-1 Day 0 PbxKO guide 6

value: Pbx1 knockout

value: Day 0


title: bulk ATAC 54-1 Day 0 PbxKO guide 4

value: Pbx1 knockout 4


title: 001 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage


title: bulk ATAC 54-1 Day 0 PbxKO guide 3

value: Pbx1 knockout 3


title: bulk ATAC 54-1 Day 0 PbxKO guide 1

value: Pbx1 knockout 1


title: bulk ATAC 54-1 Day 0 PbxKO guide 2

value: Pbx1 knockout 2


title: bulk ATAC 54-1 Day 0 MeisKO guide 5

value: Meis1 knockout

value: Meis1 knockout 5


title: NHLF SOX11 siRNA  unstimulated 24 hours

city: Saga

first: Satoshi

last: Nunomura

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

country: Japan

institute: Saga Medical School

hyb_protocol: 0.6 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes and hybridized to Agilent Expression Arrays at 65°C for 17 hours using GE Hybridyzation kit  (Agilent). The hybridized arrays were washed with GE Wash Buffers Pack (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NHLF SOX11 siRNA, 24hr, 0 ng/mL of IL-13

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp labeling Kit, One-Color  (Agilent) according  to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NHLF  were maintained in DMEM supplied with 10% fetal bovine serum, 100 units/mL penicillin and 100 ug/mL streptomycin.

extract_protocol: RNA was prepared using RNAiso plus following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: NHLF cells were treated with SOX11 siRNA or control siRNA and then incubated with or without IL-13 for 24 hr in DMEM supplied with 10% fetal bovine serum.

value: Normal human primary lung fibroblasts (NHLF)


title: mRNA_NHLF_IL-13_24hr

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

description: Gene expression at 24 hr after stimulation with IL-13 10 ng/ml

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green, and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instruction, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: NHLF (Lonza, and Walkersville, MD) were cultured in DMEM + 10F FBS.

extract_protocol: miRNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: NHLF were treated with 10 ng/ml of IL-13 on 1, 4, and 24 hr.

value: Normal Human Lung fibrobasts (NHLF)

tag: time (hours)


title: NHLF Control siRNA  stimulated 24 hours

source_name: NHLF Control siRNA, 24hr, 50 ng/mL of IL-13


title: bulk ATAC 54-1 Day 0 MeisKO guide 3

value: Meis1 knockout 3


title: mRNA_NHLF_IL-13_4hr

description: Gene expression at 4 hr after stimulation with IL-13 10 ng/ml


title: mRNA_NHLF_IL-13_1hr

description: Gene expression at 1 hr after stimulation with IL-13 10 ng/ml


title: mRNA_NHLF_IL-13_0hr

description: Gene expression at 0 hr after stimulation with IL-13 10 ng/ml


title: bulk ATAC 54-1 Day 0 NTC guide 5

value: Non template control

value: Non template control 5


title: bulk ATAC 54-1 Day 0 NTC guide 4

value: Immortalized skeletal muscle myoblasts

value: Non template control 4


title: 009 arthroscopic partial meniscectomy

description: Gene expression in APM cartilage

value: Knee cartilage

value: Female


title: bulk ATAC 54-1 Day 0 MeisKO guide 1

value: Meis1 knockout 1


title: bulk ATAC 54-1 Day 7 NTC guide 1

value: Non template control 1

value: Day 7