title: H4K12acChIP_H2Av_2.2_INP

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
50 bp single-end reads were mapped to the D. melanogaster (release 6) or independently to the D. virilis (release 1) genome using bowtie2 (Langmead and Salzberg, 2012) using standard parameters. Tag directories and input-normalized coverage files were generated using Homer (Heinz et al., 2010) with the parameters -fragLength 150 and -totalReads was set to the number of reads mapped to D.virilis genome.
Genome_build: dm6
Supplementary_files_format_and_content: D. virilis scaled and input normalized .bedgraph

organism: Drosophila melanogaster

source_name: Kc167 cells

extract_protocol:
70 to 130 million D. melanogaster Kc167 cells, resuspended in 20 ml of complete Schneider’s Drosophila Medium, were crosslinked by adding 1:10 of the volume of Fixing Solution (100 mM NaCl, 50 mM Hepes pH 8, 1mM EDTA, 0.5 mM EGTA, 10% methanol-free formaldehyde) and rotated at room temperature for 8 min. 1.17 ml of freshly-prepared 2.5 M glycine was added to stop the fixation (final conc. 125 mM). Cells were pelleted at 500 g for 10 min (4°C) and resuspended in 10 mL of ice-cold PBS. 3.5 million of fixed D. virilis cells (fixed as described for D. melanogaster cells) were added for every 70 million D. melanogaster cells. Cells were pelleted at 526 g for 10 min (4°C) and resuspended in 1 ml of PBS + 0.5% Triton-X-100 + 1X cOmplete EDTA-free Protease Inhibitor for every 70 million D. melanogaster cells and rotated at 4°C for 15 min to release nuclei. Nuclei were pelleted at 2000 g for 10 min and washed once with 10 ml of ice-cold PBS. Nuclei were suspended in 1 ml of RIPA buffer (10 mM Tris-HCl pH 8, 140 mM NaCl, 1mM EDTA, 0.1% Na-deoxycholate, 1% Triton-X-100, 0.1% SDS, 1 mM PMSF, 1X cOmplete EDTA-free Protease Inhibitor) + 2 mM CaCl2 for every 70 million D. melanogaster cells, divided into 1 ml aliquots and flash-frozen in liquid N2. 1 mL of fixed nuclei was quickly thawed and 1 µL of MNase (to 0.6 units) (Sigma-Aldrich, Cat. No N5386) added. Chromatin was digested for 35 min at 37°C. MNase digestion was stopped by transferring the samples on ice and adding 22 µL of 0.5 M EGTA. Samples were mildly sonicated using a Covaris S220 instrument with the following settings: 50 W peak power, 20% duty factor, 200 cycles/burst, 8 min total time. Insoluble chromatin was removed by centrifugation at 16,000 g for 30 min at 4°C. Soluble chromatin was pre-cleared by incubation with 10 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry (GE Healthcare, Cat. No 17-5280-11 and 17-0618-06) for every 100 µL of chromatin for 1 h at 4°C. 100 µL of pre-cleared chromatin were set aside (input) and kept overnight at 4°C, while each primary antibody was added to 300 µL of chromatin and incubated overnight at 4°C. 40 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry was added for each immunoprecipitation and rotated 3 h at 4°C. Beads were washed 5 times with 1 ml of RIPA (5 min rotation at 4°C, pelleted at 3000 g for 1 min between washes) and resuspended in 100 µL of TE (10 mM Tris pH 8, 1 mM EDTA). 0.5 µL of RNAseA (Sigma-Aldrich, Cat. No. R4875) was added to both input samples and resuspended beads, followed by incubation at 37°C for 30 min. After addition of 6 µL of 10% SDS, protease digestion (250 ng/ µL Proteinase K, Genaxxon, Cat.no. M3036.0100) and crosslink reversal were performed simultaneously at 68°C for 2 hr. DNA was purified using 1.8X Agencourt AMPure XP beads (Beckman Coulter, Cat No A63880) following the standard protocol and eluted in 30 µL of 5 mM Tris-HCl pH 8
Libraries for sequencing were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465). Libraries were sequenced on an Illumina HiSeq 1500 instrument at the Laboratory of Functional Genomic Analysis (LAFUGA, Gene Center Munich, LMU).

value: Kc167 cells

tag: RNAi treatment

tag: spike-in

value: Drosophila virilis cells (79f7Dv3)

tag: antibody

tag: sample type

value: input


title: H4K12acChIP_H2Av_2.1_INP

status: Public on May 19 2020

type: SRA

country: Germany

library_source: genomic

molecule: genomic DNA

tag: cell line


title: H4K12acChIP_H2Av_2.2_IP

value: IP


title: Set3_Control

city: New York

first: Elham

last: Azizi

state: NY

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
read alignment: TopHat
transcript assembly: Cufflinks
differential expression analysis: DESeq
Genome_build: mm9
Supplementary_files_format_and_content: raw counts per gene in .txt format

molecule: total RNA

organism: Mus musculus

source_name: Ovarian surface epithelium

growth_protocol: The ID8 IP2 cell line was cultured in DMEM with 10% FBS, 1% ITS Liquid Media Supplement, and 1% penicillin-streptomycin.

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104) and the RNase-Free DNase Set (QIAGEN, 79254)
libraries were created using Illumina TruSeq kit according to manufacturer's recommendations

treatment_protocol: ID8 IP2 cells were infected with virus derived from a pCCL vector encoding an HA-tagged Notch3 intracellular domain (codons 1664-2318) followed by an IRES-GFP (Notch3IC) or empty pCCL vector (Control).

tag: tissue

value: Ovarian surface epithelium

value: ID8 IP2


title: canine tissue from C034

city: Ithaca

first: Scott

last: Coonrod

state: New York

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

data_processing:
Library strategy: ChRO-seq
Single-read sequencing data were preprocessed and mapped to the canine genome assembly by proseq 2.0 pipeline (https://github.com/Danko-Lab/proseq2.0).
Single-read sequencing data were preprocessed to remove the adapter sequences and trim based on base quality, and deduplicating the reads based on unique molecular identifiers in RNA adapters.
Sequencing reads were mapped into a canine genome assembly (CanFam 3.1) using the Burrows-Wheeler Aligner software package.
Aligned BAM files were converted into bigWig format.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: BigWig files were generated from aligned BAM files by proseq 2.0 pipeline (https://github.com/Danko-Lab/proseq2.0).

organism: Canis lupus familiaris

source_name: canine splenic HSA

extract_protocol:
Nascent RNA were extracted as chromatin complex following ChRO-seq protocol (Mahat DB et al, Nat Protoc. 2016).
ChRO-seq libraries were prepared  following ChRO-seq protocol (Mahat DB et al, Nat Protoc. 2016).

tag: breed

value: German Shepherd Dog

tag: age

tag: Sex

value: male

value: spleen

tag: disease state

value: HSA

tag: rna fraction

value: nascent RNA


title: canine tissue from C442

value: Golden Retriever


title: 5_S5_L001

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads from rat VTA were mapped to rn6 using HISAT2v2.1.0.
Counts of reads mapping to genes were obtained using featureCounts against Ensembl v90 annotation.
Differential expression analysis was done using the DESeq2 package (v1.6.3) at a p-value cutoff of 0.05.
Genome_build: rn6
Supplementary_files_format_and_content: Counts in tab delimited text file generated using featureCounts

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
VTA tissue punches were homogenized in Trizol (Thermo Fisher), and RNA was isolated on RNeasy Microcolumns (Qiagen) following manufacturer’s instructions. RNA concentrations were assessed using a nanodrop spectrophotometer and RNA 260/280 and 260/230 ratios were confirmed at >1.8.
Following RNA purification, RNA-seq libraries were prepared according to Illumina protocols and sequenced on an Illumina HiSeq 4000 (or equivalent) sequencer.

treatment_protocol: Cocaine Self-Administration (SA) Prior to jugular catheterization, animals were food restricted (20 g per day; 3-4 days) and trained to respond to the “active” lever on a fixed ratio (FR) schedule 1 of reinforcement for food pellets (1 hr sessions per day). Following successful learning (~100 pellets per session), animals were implanted with jugular catheters and then given 5 days to recover before cocaine SA. Catheter patency was tested with 1 mg methohexital sodium (Brevital; Sigma-Aldrich, St. Louis, MO) the day prior to cocaine SA. Animals were then trained to respond on an “active” lever for cocaine hydrochloride diluted in 0.9% sterile saline, 1mg/kg/infusion IV (0.1 ml injection volume delivered over 4 s), with a 20 s timeout in between each infusion, which was indicated by a cue light located directly above the “active” lever; responding on the lever was recorded but without consequence.   Rodents were trained on this paradigm at a FR 1 (2 days), FR3 (1 day) and then FR5 (2 days; 1 hr sessions). Following completion of successful learning at FR5 (~15 rewards total), rodents were allowed extended access (6 hr sessions) cocaine for 10 days, with each cocaine infusion resulting in delivery of 0.5mg/kg/infusion of cocaine. Additionally, a separate group of rodents were put through the same paradigm but were only allowed to respond for saline (0.9%) (non-reinforcement controls). For RNA-seq analyses, cocaine vs. saline animals were infected intra-VTA with lentiviruses expressing either empty vector (RFP) or H3.3 WT controls vs. H3.3Q5A 24 hr after drug taking, and then euthanized following 30 days of withdrawal.

tag: self-administration

value: Saline

tag: virus

tag: region

value: Ventral tegmental area


title: canine tissue from C001


title: H4K12acChIP_H2Av_2.1_IP


title: canine tissue from C253


title: 4_48_L001

value: WT


title: 17_S17_L002


title: 3_S3_L001


title: H4K12acChIP_Tip60_1.2_IP

description: processed data file: H4K12acChIP_Tip60_1.2_IP.dvirNorm.INPnorm.bedgraph.gz

data_processing:
50 bp single-end reads were mapped to the D. melanogaster (release 6) or independently to the D. virilis (release 1) genome using bowtie2 (Langmead and Salzberg, 2012) using standard parameters. Tag directories and input-normalized coverage files were generated using Homer (Heinz et al., 2010) with the parameters -fragLength 150 and -totalReads was set to the number of reads mapped to D. virilis genome.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: D. virilis scaled and input normalized .bedgraph.

extract_protocol:
70 to 130 million D. melanogaster Kc167 cells, resuspended in 20 ml of complete Schneider’s Drosophila Medium, were crosslinked by adding 1:10 of the volume of Fixing Solution (100 mM NaCl, 50 mM Hepes pH 8, 1mM EDTA, 0.5 mM EGTA, 10% methanol-free formaldehyde) and rotated at room temperature for 8 min. 1.17 ml of freshly-prepared 2.5 M glycine was added to stop the fixation (final conc. 125 mM). Cells were pelleted at 500 g for 10 min (4°C) and resuspended in 10 mL of ice-cold PBS. 3.5 million of fixed D. virilis cells (fixed as described for D. melanogaster cells) were added for every 70 million D. melanogaster cells. Cells were pelleted at 526 g for 10 min (4°C) and resuspended in 1 ml of PBS + 0.5% Triton-X-100 + 1X cOmplete EDTA-free Protease Inhibitor for every 70 million D. melanogaster cells and rotated at 4°C for 15 min to release nuclei. Nuclei were pelleted at 2000 g for 10 min and washed once with 10 ml of ice-cold PBS. Nuclei were suspended in 1 ml of RIPA buffer (10 mM Tris-HCl pH 8, 140 mM NaCl, 1mM EDTA, 0.1% Na-deoxycholate, 1% Triton-X-100, 0.1% SDS, 1 mM PMSF, 1X cOmplete EDTA-free Protease Inhibitor) + 2 mM CaCl2 for every 70 million D. melanogaster cells, divided into 1 ml aliquots and flash-frozen in liquid N2. 1 mL of fixed nuclei was quickly thawed and 1 µL of MNase (to 0.6 units) (Sigma-Aldrich, Cat. No N5386) added. Chromatin was digested for 35 min at 37°C. MNase digestion was stopped by transferring the samples on ice and adding 22 µL of 0.5 M EGTA. Samples were mildly sonicated using a Covaris S220 instrument with the following settings: 50 W peak power, 20% duty factor, 200 cycles/burst, 8 min total time. Insoluble chromatin was removed by centrifugation at 16,000 g for 30 min at 4°C. Soluble chromatin was pre-cleared by incubation with 10 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry (GE Healthcare, Cat. No 17-5280-11 and 17-0618-06) for every 100 µL of chromatin for 1 h at 4°C. 100 µL of pre-cleared chromatin were set aside (input) and kept overnight at 4°C, while each primary antibody was added to 300 µL of chromatin and incubated overnight at 4°C. 40 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry was added for each immunoprecipitation and rotated 3 h at 4°C. Beads were washed 5 times with 1 ml of RIPA (5 min rotation at 4°C, pelleted at 3000 g for 1 min between washes) and resuspended in 100 µL of TE (10 mM Tris pH 8, 1 mM EDTA). 0.5 µL of RNaseA (Sigma-Aldrich, Cat. No. R4875) was added to both input samples and resuspended beads, followed by incubation at 37°C for 30 min. After addition of 6 µL of 10% SDS, protease digestion (250 ng/ µL Proteinase K, Genaxxon, Cat.no. M3036.0100) and crosslink reversal were performed simultaneously at 68°C for 2 hr. DNA was purified using 1.8X Agencourt AMPure XP beads (Beckman Coulter, Cat No A63880) following the standard protocol and eluted in 30 µL of 5 mM Tris-HCl pH 8.
Libraries for sequencing were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465). Libraries were sequenced on an Illumina HiSeq 1500 instrument at the Laboratory of Functional Genomic Analysis (LAFUGA, Gene Center Munich, LMU).

tag: chip antibody


title: Set1_Notch3IC


title: canine tissue from C369

value: mixed breed


title: canine tissue from C001NM

source_name: canine splenic normal tissue

value: healthy normal


title: canine tissue from C034NM


title: H4K12acChIP_Tip60_2_IP

description: processed data file: H4K12acChIP_Tip60_2_IP.dvirNorm.INPnorm.bedgraph.gz


title: H4K12acChIP_Tip60_1.2_INP

value: Input


title: H4K12acChIP_Tip60_1.1_IP

description: processed data file: H4K12acChIP_Tip60_1.1_IP.dvirNorm.INPnorm.bedgraph.gz

value: Drosophila virilis cells (79f7Dv3)


title: 11_S11_L001

value: Cocaine


title: 2_47_L001

value: RFP


title: H4K12acChIP_Tip60_2_INP


title: 1_46_L001


title: canine tissue from C356

value: Rhodesian ridge

value: female


title: H4K12acChIP_Tip60_1.1_INP


title: canine tissue from C340


title: canine tissue from C349

value: Ches Bay ret


title: 200551600067_R07C01

type: genomic

city: London

first: Oliver

last: Robinson

state: London

address: St Mary's Campus, Norfolk Place

department: School of Public Health

country: United Kingdom

institute: IMPERIAL COLLEGE LONDON

description: normal blood sample

hyb_protocol: Then, bisulfite-converted DNA was used for hybridization on the Infinium HumanMethylation EPIC BeadChip, following the Illumina Infinium HD Methylation protocol. Briefly, a whole genome amplification step was followed by enzymatic end-point fragmentation and hybridization to HumanMethylation EPIC BeadChips at 48°C for 17 h, followed by single nucleotide extension. The incorporated nucleotides were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP).

scan_protocol: the BeadChip was scanned using the Illumina HiScan SQ scanner. The intensities of the images were extracted using in-house software written for the R statistical computing environment. The methylation score for each CpG was represented as a β-value according to the fluorescent intensity ratio representing any value between 0 (unmethylated) and 1 (completely methylated).

data_processing:
DNA methylation (DNAm) data were pre-processed and normalized using in-house software written for the R statistical computing environment, including background and color bias correction, quantile normalization, and Beta MIxture Quantile dilation (BMIQ) procedure to remove type I/type II probes bias, as described elsewhere (Fiorito et al., 2017). DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values). Cross-reactive and polymorphic probes - with minor allele frequency greater than 0.01 in Europeans (Y. A. Chen et al., 2013) - were excluded. Methylation measures were set to missing if the detection p-value was greater than 0.01. Samples with the bisulfite conversion control fluorescence intensity lower than 10,000 for both type I and type II probes and those with total call rate lower than 95% were excluded. Finally, samples were excluded if the predicted sex (based on chromosome X methylation) did not match that self-reported.
DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values).

organism: Homo sapiens

source_name: blood samples

extract_protocol: bisulphite conversion of 500 ng of each DNA sample was performed using the EZ DNA Methylation-Lightning Kit according to the manufacturer’s protocol (Zymo Research, Orange, CA).

value: M

tag: person id

value: normal


title: H4K12acChIP_GST.2_IP

description: processed data file: H4K12acChIP_GST.2_IP.dvirNorm.INPnorm.bedgraph.gz

value: GST

value: IP


title: H4K12acChIP_GST.2_INP


title: canine tissue from C085

value: Bloodhound

value: spleen

value: HSA

value: nascent RNA


title: H4K12acChIP_GST.1_INP

description:
Samples H2AvChIP_GST_INP and H4K12acChIP_GST.1_INP are the same input sample.
processed data file: H4K12acChIP_GST.1_IP.dvirNorm.INPnorm.bedgraph.gz


title: canine tissue from B829

value: Flat Coated Ret

value: male


title: H4K12acChIP_GST.1_IP

description: processed data file: H4K12acChIP_GST.1_IP.dvirNorm.INPnorm.bedgraph.gz


title: canine tissue from C073

value: Lab Ret


title: H4K12acChIP_GFP_IP

description: processed data file: H4K12acChIP_GFP_IP.dvirNorm.INPnorm.bedgraph.gz

value: GFP

value: Drosophila virilis cells (79f7Dv3)


title: H4K12acChIP_DomB2_IP

description: processed data file: H4K12acChIP_B2_IP.dvirNorm.INPnorm.bedgraph.gz

value: DomB


title: H4K12acChIP_DomB2_INP

description:
Samples H2AvChIP_DomB2_INP and H4K12acChIP_DomB2_INP are the same input sample.
processed data file: H4K12acChIP_B2_IP.dvirNorm.INPnorm.bedgraph.gz

value: Input


title: H4K12acChIP_GFP_INP

description:
Samples H2AvChIP_GFP_INP and H4K12acChIP_GFP_INP are the same input sample.
processed data file: H4K12acChIP_GFP_IP.dvirNorm.INPnorm.bedgraph.gz


title: canine tissue from B554

value: mixed


title: canine tissue from B743

value: German Shepherd Dog

value: female


title: X14.EW: Adropin treated, biological rep 2

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Affymterix GeneChip Human Genome U219 ArrayStrip (16 h, 45°C).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: HAC15 cell line

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: The commercially available HAC15 cell line (ATCC® CRL-3301TM, VA, USA) was cultured in a defined medium consisting of DMEM/F-12 without phenol red (Thermo Fisher Scientific, Waltham, MA, USA), 10% Cosmic Calf Serum (Hyclone, GE Healthcare, MA USA), 1% ITS + Premix (Corning, NY, USA), and 1% P/S (Merck Millipore, Darmstadt, Germany). The cells at low passages (p0-p1) underwent starvation in the DMEM/F-12 medium supplemented with 10% charcoal-stripped fetal bovine serum (FBS) (Thermo Fisher Scientific, MA, USA) and 1% P/S for 24h.

extract_protocol: Total RNA isolation was performed using the modified Chomczynski method with the use of TRI Reagent (Sigma, St Louis, MO, USA) and the RNeasy Mini Elute Cleanup Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions

treatment_protocol: Subsequently, the cells were treated with the following compounds: ACTH (Synacthen) 10-7 M (Basel, Switzerland), forskolin 25μM (Merck Millipore, Germany), and adropin 10-8 M (Bachem, Switzerland) for another 24h. The cells cultured in the medium with 10% charcoal-stripped FBS served as controls. Immediately after 24h of incubation, the cells and culture media were collected and stored at -80C

value: human adrenal carcinoma cell line


title: X15.EW: Adropin treated, biological rep 3

description: Gene expression data


title: canine tissue from B307

value: Pit Bull


title: canine tissue from B280

value: Lab Cross


title: H4K12acChIP_DomB1.2_INP

description: processed data file: H4K12acChIP_B1.2_IP.dvirNorm.INPnorm.bedgraph.gz


title: H4K12acChIP_DomB1.2_IP

value: IP


title: X13.EW: Adropin treated, biological rep 1

description: Gene expression data


title: X12.EW: Forskolin treated, biological rep 4

description: Gene expression data


title: canine tissue from B297NM

value: Boxer

value: spleen

value: healthy normal


title: X11.EW: Forskolin treated, biological rep 3

description: Gene expression data


title: X16.EW: Adropin treated, biological rep 4

description: Gene expression data


title: canine tissue from B307NM

value: nascent RNA


title: canine tissue from B180

value: Golden Retriever

value: HSA


title: H4K12acChIP_DomB1.1_IP

description: processed data file: H4K12acChIP_B1.1_IP.dvirNorm.INPnorm.bedgraph.gz


title: X10.EW: Forskolin treated, biological rep 2

description: Gene expression data


title: X09.EW: Forskolin treated, biological rep 1

description: Gene expression data


title: X07.EW: ACTH treated, biological rep 3

description: Gene expression data


title: X05.EW: ACTH treated, biological rep 1

description: Gene expression data


title: X06.EW: ACTH treated, biological rep 2

description: Gene expression data


title: X04.EW: Control, biological rep 4

description: Gene expression data


title: X03.EW: Control, biological rep 3

description: Gene expression data


title: H4K12acChIP_DomB1.1_INP

description:
Samples H2AvChIP_DomB1_INP and H4K12acChIP_DomB1.1_INP are the same input sample.
processed data file: H4K12acChIP_B1.1_IP.dvirNorm.INPnorm.bedgraph.gz


title: H4K12acChIP_DomA2_IP

description: processed data file: H4K12acChIP_A2_IP.dvirNorm.INPnorm.bedgraph.gz

value: DomA


title: H4K12acChIP_DomA1.2_IP

description: processed data file: H4K12acChIP_A1.2_IP.dvirNorm.INPnorm.bedgraph.gz

value: Drosophila virilis cells (79f7Dv3)


title: Set2_Notch3IC

value: Ovarian surface epithelium

value: ID8 IP2


title: canine tissue from B775

value: Std Poodle

value: male


title: H4K12acChIP_DomA2_INP

description:
Samples H2AvChIP_DomA2_INP and H4K12acChIP_DomA2_INP are the same input sample.
processed data file: H4K12acChIP_A2_IP.dvirNorm.INPnorm.bedgraph.gz

value: Input


title: X02.EW: Control, biological rep 2

description: Gene expression data

value: human adrenal carcinoma cell line


title: shFLNB 2nd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cells

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). ZFP36 overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: shRNA against human FLNB transfection of HeLa cells was performed using lipofectAMINE 2000

value: HeLa cells

tag: cell type

value: FLNB knockdown


title: 918: Female Kidney, Yersinia ruckeri/70mg/L propylthiouracil

city: Denton

first: Leah

middle: Marie

last: Thornton Hampton

state: Texas

address: 1155 Union Cir

department: Biology

institute: University of North Texas

data_processing:
Adaptor sequences and low-quality reads were removed from raw sequences using Trimmomatic v0.38 (Bolger et al. 2014). Specifically, trimming was applied using a sliding window approach with a minimum quality score of 20 followed by a minimum length filter of 36bp as recommended by Williams et al. (2016) and Bolger et al. (2014).
Sequence quality was assessed before and after trimming using FastQC.
Two samples from each treatment group containing the greatest number quality filtered of reads were combined, and a de novo assembly was generated with Trinity v2.4.0 using default settings (Haas et al. 2013).
The de novo assembly was then annotated against the UniProtKB Swiss-Prot (www.uniprot.org) database using BLASTX with a cutoff E-value of less than 1.0 x 10-5.
Individual samples were aligned to the de novo assembly using RNAseq by Expectation Maximization (RSEM v.1.3; Li & Dewey, 2011) to obtain gene-level counts.
Genome_build: UniProtKB Swiss-Prot, Downloaded 4/30/2019
Supplementary_files_format_and_content: Excel sheet with normalized counts for each sample, log2 fold change, p-value, gene identifier/Assembly file

organism: Pimephales promelas

source_name: kidney

extract_protocol:
Kindey was removed approximately 8 hours following pathogen injection, placed on dry ice and stored at -80°C until RNA extraction. RNA was extracted using the Promega Maxwell 16 LEV simplyRNA Purification Kit per manufacturer protocol.
To prepare cDNA libraries, the NEBNext Ultra II RNA Library Prep kit in conjunction with the NEBNext poly(A) mRNA magnetic isolation module and NEBNext Multiplex Oligos for Illumina (New England BioLabs, Ipswich, MA) were utilized according to manufacturer protocols with an input of 500ng total RNA. Library quality (e.g. fragment size, presence of adaptors) was assessed using the Experion DNA 1K Analysis kit in conjunction with the Experion Automated Electrophoresis System (BioRad, Hercules, CA). Finally, libraries were quantified using the NEBNext Library Quant Kit (BioRad, Hercules, CA) and shipped to University of Texas Health Science Center San Antonio where paired end sequencing (100bp) was performed on the Illumina HiSeq 3000 platform.
Adaptor sequences and low-quality reads were removed from raw sequences using Trimmomatic v0.38 (Bolger et al. 2014). Specifically, trimming was applied using a sliding window approach with a minimum quality score of 20 followed by a minimum length filter of 36bp as recommended by Williams et al. (2016) and Bolger et al. (2014). Sequence quality was assessed before and after trimming using FastQC. Two samples from each treatment group containing the greatest number quality filtered of reads were combined, and a de novo assembly was generated with Trinity v2.4.0 using default settings (Haas et al. 2013).  The de novo assembly was then annotated against the UniProtKB Swiss-Prot (www.uniprot.org) database using BLASTX with a cutoff E-value of less than 1.0 x 10-5. Individual samples were aligned to the de novo assembly using RNAseq by Expectation Maximization (RSEM v.1.3; Li & Dewey, 2011) to obtain gene-level counts.

value: kidney

tag: treatment

value: 7 mo

value: female


title: 922: Female Kidney, Yersinia ruckeri/70mg/L propylthiouracil


title: H4K12acChIP_DomA1.1_IP

description: processed data file: H4K12acChIP_A1.1_IP.dvirNorm.INPnorm.bedgraph.gz

tag: RNAi treatment

tag: spike-in

value: IP


title: 816: Female Kidney, Yersinia ruckeri/25mg/L propylthiouracil


title: X01.EW: Control, biological rep 1

description: Gene expression data


title: 912: Female Kidney, Yersinia ruckeri/70mg/L propylthiouracil


title: H4K12acChIP_DomA1.2_INP

tag: sample type


title: shCtrl 1st

tag: cell line

value: control plasmid


title: shCtrl 2nd


title: shFLNB 1st


title: H4K12acChIP_DomA1.1_INP

description:
Samples H2AvChIP_DomA1_INP and H4K12acChIP_DomA1.1_INP are the same input sample.
processed data file: H4K12acChIP_A1.1_IP.dvirNorm.INPnorm.bedgraph.gz


title: Pig9TM

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software( version 3.0.2, 10X Genomics)
Sample alignment with the count function from Cell Ranger software (version 3.0.2,10X Genomics)
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

organism: Sus scrofa

source_name: Pig corneoscleral wedges

extract_protocol:
Corneoscleral segments were dissected in Ames' medium, digested in papain, and manually triturated into single cell suspensions in ovomucoid solution. The cells were resuspended in 0.04% non-acetylated BSA in Ames to solutions of ~1000 cells/uL and loaded into Chromium Single Cell Chips for a targeted recovery of 6,000 cells.
Single cell libraries were made with Chromium 3’ v3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.

treatment_protocol: Eyes were enucleated immediately after the pigs were sacrificed. The eyes were transported on ice in Ames' medium (Sigma-Aldrich; equilibrated with 95% O2/5% CO2) for one hour.

tag: tissue

value: corneoscleral wedges

tag: animal number


title: H2AvChIP_H2Av2.2_IP

description: processed data file: H2AvChIP_H2Av2.2_IP.dvirNorm.INPnorm.bedgraph.gz


title: X08.EW: ACTH treated, biological rep 4

description: Gene expression data


title: 718: Female Kidney, Yersinia ruckeri

value: Yersinia ruckeri

tag: age


title: 804: Female Kidney, Yersinia ruckeri/25mg/L propylthiouracil

tag: Sex


title: 712: Female Kidney, Yersinia ruckeri


title: 914: Female Kidney, Yersinia ruckeri/70mg/L propylthiouracil


title: H2AvChIP_H2Av2.1_IP

description: processed data file: H2AvChIP_H2Av2.1_IP.dvirNorm.INPnorm.bedgraph.gz


title: 814: Female Kidney, Yersinia ruckeri/25mg/L propylthiouracil


title: H2AvChIP_H2Av2.2_INP


title: Pig6TM


title: 820: Female Kidney, Yersinia ruckeri/25mg/L propylthiouracil


title: Setaria panicle stage 3

city: Huntsville

first: Alex

last: Harkess

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: PARE

data_processing:
PARE-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 20 nucleotides.
Supplementary_files_format_and_content: Tag counts

organism: Setaria viridis

source_name: panicle

extract_protocol:
Trizol RNA
The library construction is based on a PARE protocol modified by Sandra Mathioni and used the Illumina TruSeq sRNA Indexes for the 3 prime adapter. The PARE library was constructed by Sandra Mathioni at the Donald Danforth Plant Science Center and sequenced on an Illumina HiSeq 2500 at the University of Delaware.
PARE-seq

value: Setaria panicle stage 3


title: Setaria spikelet stage 4

description: PARE

source_name: spikelet

value: Setaria spikelet stage 4


title: Setaria leaf

description: PARE

source_name: leaf

value: Setaria leaf


title: H2AvChIP_GST_IP

description: processed data file: H2AvChIP_GST_IP.dvirNorm.INPnorm.bedgraph.gz

value: GST

value: Drosophila virilis cells (79f7Dv3)


title: H2AvChIP_H2Av2.1_INP


title: 710: Female Kidney, Yersinia ruckeri


title: 704: Female Kidney, Yersinia ruckeri


title: H2AvChIP_DomB2_IP

description: processed data file: H2AvChIP_B2_IP.dvirNorm.INPnorm.bedgraph.gz

value: DomB


title: H2AvChIP_GFP_INP

description:
Samples H2AvChIP_GFP_INP and H4K12acChIP_GFP_INP are the same input sample.
processed data file: H2AvChIP_GFP_IP.dvirNorm.INPnorm.bedgraph.gz

value: GFP

value: Input


title: H2AvChIP_GFP_IP

description: processed data file: H2AvChIP_GFP_IP.dvirNorm.INPnorm.bedgraph.gz


title: C30 (Sample 22)

city: Seoul

first: Cecile

last: Segonzac

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Plant Science

country: South Korea

institute: Seoul National University

data_processing:
Sequencing reads were quality trimmed and filtered using Trimmomatic v0.36
Reads were aligned to Brassica rapa reference genome v1.5 (http://brassicadb.org/brad/datasets/pub/BrassicaceaeGenome/Brassica_rapa/V1.0/Bra_Chromosome_V1.5/) using HISAT2
Transcripts were assembled, read counts and FPKM values were calculated using StringTie v2.0
DEG (Differentially Expressed Genes) analysis was performed with DESeq2
Genome_build: http://brassicadb.org/brad/datasets/pub/BrassicaceaeGenome/Brassica_rapa/V1.0/Bra_Chromosome_V1.5/Brapa_sequence_v1.5.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample as defined by Stringtie, excel table file summarizing the foldchange of DEG in different treatments realtive to corresponding water treatments

organism: Brassica rapa

source_name: B. rapa leaf

growth_protocol: B. rapa plants were grown on soil in a short day condition (10h-light, 14h-dark) for 17 days

extract_protocol:
Total RNA was extracted from the leaf tissue using Accuzol total RNA extraction reagent (Bioneer) according to the manufacturer's instructions
1µg of total RNA was used for RNA-seq library preparation for each sample. RNA-seq libraries were prepared with TruSeq Stranded mRNA LT Sample Prep kit according to the manufacturer’s instructions.

treatment_protocol: Water or water solution of flg22 (100nM) or chitin (100µg/mL) for 30 or 180 min

tag: genotype

value: Wild type

value: 1st true leaf

value: chitin (100µg/mL)

tag: treatment time

value: 30 min

tag: biological replicate


title: H2AvChIP_GST_INP

description:
Samples H2AvChIP_GST_INP and H4K12acChIP_GST.1_INP are the same input sample.
processed data file: H2AvChIP_GST_IP.dvirNorm.INPnorm.bedgraph.gz


title: W180 (Sample 23)

value: water

value: 180 min


title: Setaria spikelet stage 3

description: PARE

value: Setaria spikelet stage 3


title: H2AvChIP_DomB2_INP

description:
Samples H2AvChIP_DomB2_INP and H4K12acChIP_DomB2_INP are the same input sample.
processed data file: H2AvChIP_B2_IP.dvirNorm.INPnorm.bedgraph.gz


title: 1010: Female Kidney, Hank's Balanced Salt Solution

value: kidney

value: Hank's Balanced Salt Solution

value: 7 mo

value: female


title: 1008: Female Kidney, Hank's Balanced Salt Solution


title: W30 (Sample 21)


title: 1004: Female Kidney, Hank's Balanced Salt Solution


title: H2AvChIP_DomB1_IP

description: processed data file: H2AvChIP_B1_IP.dvirNorm.INPnorm.bedgraph.gz

value: IP


title: F180 (Sample 20)


title: W180 (Sample 19)


title: H2AvChIP_DomB1_INP

description:
Samples H2AvChIP_DomB1_INP and H4K12acChIP_DomB1.1_INP are the same input sample.
processed data file: H2AvChIP_B1_IP.dvirNorm.INPnorm.bedgraph.gz


title: F30 (Sample 18)


title: C180 (Sample 24)


title: fha2_Rep1 [fha_1]

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2.
The reads mapped on the exon were counted using RSEM. The differentially expressed genes were identified with |log2FC| >=1 and q value<0.05 using DEseq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads for each Sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates under long-day conditions (16 h light, 8 h dark, 22℃)

extract_protocol:
Total RNA was extracted from 0.05 g samples of 11-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq

tag: ecotype background

value: Col

tag: genotype/variation

value: 11-day-old seedlings


title: H2AvChIP_DomA2_IP

description: processed data file: H2AvChIP_A2_IP.dvirNorm.INPnorm.bedgraph.gz

value: DomA

value: Drosophila virilis cells (79f7Dv3)

tag: chip antibody


title: rlt1/2_Rep2 [rlt_2]


title: rlt1/2_Rep1 [rlt_1]


title: W30 (Sample 17)


title: chr11/17_Rep2 [chr_2]


title: Sample 3 from MNC

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: NS_M_miR_v1.5.rlf was used as Reporter Library File

hyb_protocol: Samples were  hybridized for 18 h at 65C according to the instructions at nCounter® miRNA Expression Assay User Manual (NanoString tecnology)

scan_protocol: After hybridization samples were placed in the prep station of nCounter FLEX analysis system, there hybridized samples were purified and immobilized in a sample cartridge (cartridge ID 207911430919) according to standard protocol. Then the sample cartridge was scanned on the nCounter FLEX digital analyzer (Scanner ID 1410C0216)

data_processing: The raw data were processed in nSolver Analysis Software 4.0. We used CodeSetContent(Housekeeping) standart normalization

source_name: blood monocytes

label_protocol: 100 ng of  total RNA was used for the miRNA Sample Preparation Protocol according to the instructions at nCounter® miRNA Expression Assay User Manual. Then prepared samples were labed with  Reporter CodeSet and Capture ProbeSet from Mouse miRNA V 1.5 panel according to the instructions at nCounter® miRNA Expression Assay User Manual(NanoString tecnology)

extract_protocol: Sorted cells from 5 animals were pooled. The total RNA was isolated from cells by using RNeasy Plus Mini Kit (Qiagen) with additional purification and concentration with RNA Clean& Concentrator (Zymo Research).

tag: strain

value: Balb/C

value: Blood


title: fha2_Rep2 [fha_2]


title: W180 (Sample 15)

value: Wild type

value: 1st true leaf


title: Sample 2 from MNC


title: 1002: Female Kidney, Hank's Balanced Salt Solution


title: H2AvChIP_DomA2_INP

description:
Samples H2AvChIP_DomA2_INP and H4K12acChIP_DomA2_INP are the same input sample.
processed data file: H2AvChIP_A2_IP.dvirNorm.INPnorm.bedgraph.gz

value: Input


title: H2AvChIP_DomA1_INP

description:
Samples H2AvChIP_DomA1_INP and H4K12acChIP_DomA1.1_INP are the same input sample.
processed data file: H2AvChIP_A1_IP.dvirNorm.INPnorm.bedgraph.gz


title: Col_Rep2 [col_2]

source_name: wild type_seedlings

value: wild type


title: H2AvChIP_DomA1_IP

description: processed data file: H2AvChIP_A1_IP.dvirNorm.INPnorm.bedgraph.gz


title: chr11/17_Rep1 [chr_1]


title: Sample 4 from KC

source_name: Kupffer cells

value: Liver


title: C30 (Sample 14)

value: chitin (100µg/mL)

value: 30 min


title: Sample 1 from MNC


title: Sample 3 from KC


title: Col_Rep1 [col_1]


title: W30 (Sample 13)

value: water


title: Sample 4 from MNC


title: F180 (Sample 12)

value: 180 min


title: C180 (Sample 16)


title: DomA_r3

data_processing:
50 bp single reads were mapped to the D. melanogaster (release 6) or independently to the D. virilis (release 1) genome using STAR (version 2.5.3a) with the GTF annotation dmel-all-r6.17.gtf or dvir-all-r1.07.gtf, respectively. Multi-mapping reads were filtered out by the parameter --outFilterMultimapNmax 1. Genic reads were counted with the parameter --quantMode GeneCounts.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: *tab: Tab-separated text files include read counts per gene.

source_name: Kc167 cells

extract_protocol:
Two million of Kc167 cells were pelleted at 500 g for 5 min. Cells were resuspended in 1mL of PBS and 1 million of D. virilis 79f7Dv3 cells were added. Cells were pelleted at 500 g for 5 min and total RNA was extracted using RNeasy Mini Kit (QIAgen, Cat No. 74104), including DNase digestion step (QIAgen, Cat No. 79254).
mRNA was purified using Poly(A) RNA selection kit (Lexogen, Cat. No M039100). Both total RNA and mRNA quality was verified on a 2100 Bioanalyzer (Agilent Technologies, Cat. No G2939BA). Libraries for sequencing were prepared using NEBnext Ultra II directional RNA library prep kit for Illumina (New England Biolabs, Cat. No E7760L).


title: Tip60_r3


title: Sample 1 from KC


title: W180 (Sample 11)


title: H2Av_r3


title: WTSDAY_rep2

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

data_processing:
Basecalls performed using Illumina CASAVA1.7 software.
Fragments blasted using HISAT2 software.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/280/675/GCF_000280675.1_ASM28067v1/GCF_000280675.1_ASM28067v1_genomic.fna.gz
Supplementary_files_format_and_content: The data was filed with FPKM of each detected genes and formed excel file.

organism: Beauveria bassiana

source_name: WT_hyphal body

growth_protocol: The wild-type and Sur7 mutant strains were constructed and stored at Microbiology Institution of Zhejiang University. All growing strains were initiated from 100 μl aliquots of 107 conidia/mL suspension, and incubated on either nutrient-limiting condition (CDA media) or nutrient-sufficient condition (SDAY media) at 25℃ 12:12 L:D for 5 days.

extract_protocol:
otal RNA was extracted from three replicating cultures of Δsur7 and WT under the action of an RNAisoTM Plus Reagent (TaKaRa, Dalian, China), respectively.
Library was constructed with the NEBNext Ultra RNA library Prep kit from Illumina. Library preparation and high-throughput sequencing were performed by Novogene (Beijing, China) with Illumina HiSeq 4000 platform.

treatment_protocol: No specific treatment for each strain

value: ARSEF 2860

tag: growing condition

value: nutrient-sufficient condition

tag: growing days

value: grown for 5 days

value: hyphal body


title: WTSDAY_rep3


title: WTSDAY_rep1


title: F30 (Sample 10)

tag: treatment


title: WTCDA_rep3

value: nutrient-limiting condition


title: Sample 2 from KC


title: Control_r3

tag: RNAi treatment

value: GST

tag: spike-in

value: Drosophila virilis cells (79f7Dv3)


title: DomB_r2

tag: cell line

value: DomB


title: W30 (Sample 9)

value: Wild type

tag: tissue


title: Tip60_r2


title: WTCDA_rep1


title: DomA_r2

value: DomA


title: C180 (Sample 8)

value: 1st true leaf


title: 48 hpf retina rep

city: Shanghai

first: Baijie

last: Xu

address: 320 Yue Yang Road

institute: Institute of Neuroscience, CAS

description: AB fishes/wild type

data_processing:
Single-cell FASTQ sequencing reads (Novogene) aligned to the zebrafish genome (Zv10) were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite (v2.1.0) provided in 10x genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
To further analyze the data, we used an analysis pipeline provided by the Seurat R package (http://satijalab.org/seurat/).
We subtract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression.
For post-embryonic samples, we subtract the ciliary marginal zone (CMZ) cell clusters based on marker genes' expression.
Genome_build: Zv10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

organism: Danio rerio

source_name: Retina

extract_protocol:
We dissected 24-, 36-, 48-, 72-hpf retinas of wild-type zebrafishes and isolated via papin solution. 14-dpf retinas were dissected from PCNA-GFP transgenic fishes. And after isolation by papin solution, the GFP positive cells which could label the ciliary marginal zone (CMZ) cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer (BD Falcon) were loaded onto the Chromium Single Cell Chip(10x Genomics) according to the manufacturer’s protocol.
Single-cell RNA-seq libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3' Library &Gel Bead kit v2 Chip kit (10x Genomics) following the manufacturer’s protocol.

value: AB

value: wildtype

value: whole retina

tag: developmental stage

value: 48 hpf


title: DomB_r3


title: C30 (Sample 6)

value: chitin (100µg/mL)

value: 30 min


title: SUR7SDAY_rep3

source_name: Sur7 mutant_hyphal body

value: ARSEF 2860 deleting Sur7


title: WTCDA_rep2

value: ARSEF 2860


title: Control VAT Replicate 3

city: Chengdu

first: Hongtao

last: Liu

state: Sichuan

address: No.82, qinglong street, qingyang district, chengdu

department: General surgery

institute: Chengdu third people's hospital

description: Gene expression in visceral adipose tissue

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

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

data_processing: Images from scanning were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded

source_name: control VAT

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

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood freshly drawn from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2

value: Visceral adipose tissue

tag: gender

value: female

tag: disease state

value: control


title: Obese VAT Replicate 1

source_name: obese VAT

value: male

value: obese


title: Control VAT Replicate 2


title: Control VAT Replicate 1


title: W180 (Sample 3)

tag: genotype

value: water

value: 180 min


title: Obese VAT Replicate 3


title: SUR7SDAY_rep2

value: nutrient-sufficient condition

value: grown for 5 days

value: hyphal body


title: 72 hpf retina rep

data_processing:
Single-cell FASTQ sequencing reads (Novogene) aligned to the zebrafish genome (Zv10) were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite (v2.1.0) provided in 10x genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
To further analyze the data, we used an analysis pipeline provided by the Seurat R package (http://satijalab.org/seurat/).
We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression.
For post-embryonic samples, we substract the ciliary marginal zone (CMZ) cell clusters based on marker genes' expression.
Genome_build: Zv10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

extract_protocol:
We dissected 24-, 36-, 48-, 72-hpf retinas of wild-type zebrafishes and isolated via papin solution. 14-dpf retinas were dissected from PCNA-GFP transgenic fishes. And after isolation by papin solution, the GFP positive cells which could label  the ciliary marginal zone (CMZ) cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer (BD Falcon) were loaded onto the Chromium Single Cell Chip(10x Genomics) according to the manufacturer’s protocol.
Single-cell RNA-seq libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3' Library &Gel Bead kit v2 Chip kit (10x Genomics) following the manufacturer’s protocol.

value: AB

value: wildtype

value: 72 hpf


title: Tip60_r1

value: Drosophila virilis cells (79f7Dv3)


title: Obese VAT Replicate 2


title: 14 dpf retina rep

value: CMZ

value: 14 dpf


title: Control_r2

value: GFP


title: H2Av_r2


title: 2702: Patient 19

city: Paris

first: Julie

last: Delyon

address: 1 avenue Claude Vellefaux

department: Dermatology

country: France

institute: Hopital Saint-Louis

description: mRNA expression

data_processing: Normalization methods with the housekeeping gene PPIA (copy number / PPIA *1000 (mean of 2 duplicate experiments))

label: SYBR Green

source_name: Tumor sample

label_protocol: high-capacity cDNA reverse transcription kit (Life technologies, USA)

extract_protocol: TRIzol and RNeasy FFPE kit

value: Dermatofibrosarcoma protuberans (DFSP)

value: Tumor sample


title: DomA_r1

first: Tamas

last: Schauer

institute: Helmholtz Zentrum München

value: DomA


title: SUR7CDA_rep3

value: ARSEF 2860 deleting Sur7

value: nutrient-limiting condition


title: 72 hpf retina

value: whole retina


title: W180 (Sample 7)

value: Wild type

value: 1st true leaf

value: water

tag: treatment time

value: 180 min


title: W30 (Sample 1)

value: 30 min

tag: biological replicate


title: 14 dpf retina

value: AB

value: wildtype


title: 2701: Patient 18

description: mRNA expression


title: F30 (Sample 2)


title: 24 hpf retina

value: 24 hpf


title: SUR7SDAY_rep1

value: nutrient-sufficient condition

value: grown for 5 days

value: hyphal body


title: DomB_r1

value: DomB

value: Drosophila virilis cells (79f7Dv3)


title: 2703: Patient 20

description: mRNA expression

value: Dermatofibrosarcoma protuberans (DFSP)

value: Tumor sample


title: 2301: Patient 15

description: mRNA expression


title: F180 (Sample 4)


title: ubp12ubp13_GFP_REF6_1

city: Uppsala

first: Claudia

last: Köhler

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

data_processing:
Low quality ends (phred of <20) and adapter sequences were removed with Trimmomatic (version 0.38)
Reads with low average quality were discarded too (phred <25 for the H2Aub1/H2A.Z ChIP-seq experiment, and <28 for the H3K27me3 and REF6 experiments).
For all experiments, reads were mapped to the Arabidopsis reference TAIR10 genome using bowtie2 (version 2.2.9), unpaired mode for the H2Aub1/H2A.Z experiment, and paired mode for the H3K27me3 and REF6 experiments. For the latter two, 50 bp was taken as the minimum distance between mates and 500 bp the maximum distance.
After mapping duplicated reads were removed with Picardtools.
ChIP-seq experiment fragment length was estimated with R function estimate.mean.fraglen for H2Aub/H2A.Z experiment. After that original fragments were reconstructed using either the estimated fragment lengths (for the first experiment) or both mates of a pair (for second and third experiments).
Genome was divided in 50bp bins, and the number of reconstructed fragments in these bins were obtained.
The number of fragments (+1) was divided by the total base coverage (in billion bases). The latter value was obtained by adding up the lengths of all reconstructed fragments.
For each bin the mean was taken of the values in the two replicates.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files

source_name: rosette leaves

growth_protocol: Plants were grown on 1/2 MS MES agar for 15 days, then transferred to soil where they grew for 2 more weeks. Grown under LD conditions.

extract_protocol:
Rosette leaves were harvested one hour before darkness. ChIP was performed as described before [Villar and Köhler 2010, Plant Cromatin Immunoprecipitation], with the following modifications: no vacuum infiltration with DMA was performed. Vacuum infiltration with formaldehyde was performed for 2x10min. For quenching the formaldehyde, the solution was poured off, after which 0.125 M glycine was added and another 5-min vacuum infiltration was performed. Vacuum infiltration was performed at room temperature. Around 200 mg cross-linked plant material was used for nuclei extraction. Sonication of the chromatin was done for eight 30-s ON, 30-s OFF cycles. Overnight antibody binding was performed directly after sonication, followed by addition of washed protein A dynabeads (Thermofisher) to each ChIP aliquot. For bead washing, the LiCl wash step was skipped. De-crosslinking and subsequent DNA recovery steps performed using the Ipure kit v2 (Diagenode, Liège, Belgium). The Ovation Ultralow Sytem V2 (NuGEN, Redwood city, CA, USA) was used for library preparation
The MicroPlex Library Preparation kit v2 (Illumina) was used for library preparation.

value: rosette leaves

tag: ecotype

value: anti-GFP (A11122, ThermoFisher Scientific; Waltham, MA, USA)


title: 1501: Patient 13

description: mRNA expression


title: d4_HIV_8h_S23_R1_001

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

data_processing:
RNA libraries were run on Illumina NovaSeq6000, basecalling was performed using Real-Time Analysis (RTA) v3.3.3
bcl files were converted to fastq files with bcl2fastq v2.20.0.422
Quality of fastq files was checked with CLC Genomics Workbench 12.0.3 and fastqc
mapping of fastq files to homo sapiens (hg 38) sequence and calculation of Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed using CLC Genomics Workbench 12.0.3 (Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.8; Similarity fraction = 0.8)
Genome_build: hg38
Supplementary_files_format_and_content: csv of mapped data

source_name: whole blood

growth_protocol: Human PBMCs were isolated from buffy coats by Ficoll-Hypaque centrifugation. PBLs were generated by IL-2 (10 ng/ml)/PHA (1 μg/ml) stimulation of PBMCs for 3-4 days, resulting in >90% CD3+ T-cell cultures. Purification of human CD4+ T-cells was performed by negative selection using EasySep Direct Human CD4+ T-Cell Isolation kit. Isolated cells were either lysed directly after purification or activated by IL-2 (1 μg/ml)/PHA (1 μg/ml) in RPMI 1640 containing 10% heat-inactivated fetal calf serum, 1% penicillin-streptomyin and 2 mM L-glutamine. Infection assays were performed in the presence of IL-2 (1 μg/ml).

extract_protocol:
Total RNA extraction from primary cells and DNase treatment were performed with Maxwell LEV simplyRNA purification Kit. Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer.
RNA sequencing library was generated from 100 ng total RNA using NEBNext® Single Cell/Low Input RNA Library following the manufacturer´s protocol.

treatment_protocol: 30 min prior to HIV-1Ba-L transduction, T-cells were left untreated or treated with 100 EFV (100 nM). Inhibitor treatment was maintained during the subsequent virus inoculation.

tag: cells

value: CD4+ T cells

tag: inoculation

value: untreated

tag: time point of rna extraction post inoculation

value: 8 h

tag: donor


title: SUR7CDA_rep2

tag: strain

value: ARSEF 2860 deleting Sur7

tag: growing condition

value: nutrient-limiting condition

tag: growing days


title: 48 hpf retina

value: AB

value: whole retina

value: 48 hpf


title: d4_HIV_8h_EFV_S24_R1_001

tag: treatment

value: EFV


title: H2Av_r1

city: Munich

address: Feodor-Lynen-Straße 21

tag: cell line

tag: RNAi treatment

tag: spike-in


title: ExVivo_BMDM_M(IL-4)_rep3

city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

institute: wannan medical college

description: Gene expression in IL-4 stimulated BMDM

hyb_protocol: Each SBC mouse(8*60K) array slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: The slides were scanned using an Agilent Microarray Scanner G2565C (Agilent Technologies) with default settings with the following settings: Dye channel: Green, Scan resolution = 3 μm, PMT: 100%, and 20-bit.

data_processing: The Agilent Feature Extraction software (version 10.7) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring software 11.0 (Agilent Technologies).

source_name: Bone marrow-derived macrophages, M(IL-4), replicate3

label_protocol: Total RNA from each sample was amplified and labeled by using a Low Input Quick Amp WT Labeling Kit (Agilent Technologies), following the manufacturer’s instructions. Labeled cRNA were purified using an RNeasy mini kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured using a NanoDrop ND-2000.

growth_protocol: Bone marrow-derived macrophages (BMDMs) were isolated from BALB/c mice by flushing the femurs with Dulbecco’s modified Eagle’s medium (DMEM) medium. Macrophages plated on 6-well plates (1 × 106 cells/well) were maintained in DMEM supplemented with 20% fetal bovine serum and 20% L929 supernatant at 37°C and 5% CO2 for 7 days.

extract_protocol: Total RNA was extracted using TRIzol (Life Technologies), following the manufacturer’s instructions. RNA quantity and quality were measured by using a NanoDrop ND-2000, and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies) and denaturing agarose gel electrophoresis. Total RNA was further purified using an RNeasy mini kit (Qiagen) and RNase-Free DNase Set (Qiagen).

treatment_protocol: After 7 d of culture, the medium was removed, and the cells were cultured in RPMI 1640 supplemented with 10% FBS for an additional 24 h. Macrophages were further stimulated for 48 h either with 100 ng/mL LPS and 20 ng/mL IFN-γ (for M(LPS+IFN-γ) polarization) or 20 ng/mL IL-4 (for M(IL-4) polarization) in DMEM containing 10% FBS.

value: BALB/c

tag: tissue

value: Bone marrow-derived macrophages


title: SUR7CDA_rep1

value: grown for 5 days

value: hyphal body


title: 36 hpf retina

value: wildtype

tag: developmental stage

value: 36 hpf


title: Control_r1

value: GST

value: Drosophila virilis cells (79f7Dv3)


title: 2401: Patient 17

description: mRNA expression

tag: disease state

value: Dermatofibrosarcoma protuberans (DFSP)

value: Tumor sample


title: ubp12ubp13_input_REF6_1

value: rosette leaves

tag: genotype

tag: chip antibody

value: none (input)


title: MacaTMRimLS1 (Fascicularis8CSWL)

description: V3 library prep protocol

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0 for v2 samples and version 3.1.0 for v3 samples, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0 for v2 samples and version 3.1.0 for v3 samples, 10X Genomics)
Genome_build: MacFas5
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

organism: Macaca fascicularis

source_name: Macaque corneoscleral segment, 22 y/o

extract_protocol:
Tissues were dissected in Ames' medium, digested in papain, and manually triturated into single cell suspensions in ovomucoid solution. The cells were resuspended in 0.04% non-acetylated BSA in Ames to solutions of ~1000 cells/uL and loaded into Chromium Single Cell Chips for a targeted recovery of 6,000 cells.
Single cell libraries were made with Chromium 3’ v2 or v3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 or v3 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: Eyes were enucleated immediately after the macaques were sacrificed. The eyes were transported on ice in Ames' medium (Sigma-Aldrich; equilibrated with 95% O2/5% CO2) for one hour.

value: Macaque corneoscleral segment

tag: age


title: 904: Patient 10

description: mRNA expression


title: wt_GFP_REF6_1

tag: ecotype

value: wt

value: anti-GFP (A11122, ThermoFisher Scientific; Waltham, MA, USA)


title: d3_HIV_8h_S19_R1_001

tag: cells

value: CD4+ T cells

tag: inoculation

value: untreated

value: 8 h


title: ubp12ubp13_input_REF6_2


title: MacaCWLS1 (Fascicularis2CSWL)

description: V2 library prep protocol

source_name: Macaque corneoscleral segment, 5 y/o

value: 5 y/o


title: 2302: Patient 16

description: mRNA expression


title: MacaTMRS1 (Fasciculars1TMonlyR)

description: V2 library prep protocol

source_name: Macaque trabecular meshwork, 5 y/o

value: Macaque trabecular meshwork


title: 1502: Patient 14

description: mRNA expression


title: ubp12ubp13_GFP_REF6_2


title: d3_HIV_3h_S17_R1_001

tag: time point of rna extraction post inoculation

value: 3 h

tag: donor


title: ExVivo_BMDM_M(LPS+IFN-γ)_rep2

description: Gene expression in LPS+IFN-r stimulated BMDM

source_name: Bone marrow-derived macrophages, M(LPS+IFN-γ), replicate 2

tag: strain

value: BALB/c

value: Bone marrow-derived macrophages


title: ExVivo_BMDM_M(LPS+IFN-γ)_rep1

source_name: Bone marrow-derived macrophages, M(LPS+IFN-γ), replicate 1


title: d3_HIV_3h_EFV_S18_R1_001

value: EFV


title: 1001: Patient 12

description: mRNA expression


title: wt_input_REF6_2


title: 905: Patient 11

description: mRNA expression


title: d4_HIV_3h_EFV_S22_R1_001


title: ubp12ubp13_H3_H3K27me3_2

description: UBP_R1R2_H3_fromK27_genomecov_covscale.bw

data_processing:
For RNA-seq adapters were removed with cutadapt v1.18 (Martin, 2011), and only reads longer than 25 nt were kept for mapping.
For the H2Aub1 ChIP-seq experiment (single end sequencing including H2Aub1, H3) adapter trimming and low quality read filtering was done with reaper (Davis et al., 2013). Reads with Phred <30 or shorter than 10nt were discarded.
For the H3K27me3 ChIP-seq experiment (paired-end sequencing including H3K27me3, H3) low quality ends were trimmed, and low quality reads were filtered with Trimmomatic v 0.38 (Bolger, 2012), removing ends with phred <20, removing reads with average phred <28, and removing reads with length <20.
For ChIP-seq experiments, alignment of reads to the TAIR10 genome was performed with Bowtie2 (Langmead and Salzberg, 2012), with the default minimum score threshold. For RNA-seq the program tophat v2.11 (Kim 2013) was used, and only reads with mapping quality over 30 were kept.
For the RNA-seq experiment, raw read counts per gene were obtained using Htseq v0.11.1 (Anders, 2014), and are provided.
For H3K27me3 ChIP-seq all duplicate reads were removed with Picard Tools
For H2Aub1 ChIP-seq experiment mean fragment/insert length was estimated using the R function estimate.mean.fraglen.
For both the H2Aub1 and H3K27me3 ChIP-seq experiment peaks were called using MACS2 in broad mode. The direct output (.broadPeak files) of MACS2 is provided.
For both the H2Aub1 and H3K27me3 ChIP-seq experiment genome-wide coverage in 50bp bins was calculated using Deeptools multiBamSummary and scaled by calculating the median coverage across all bins, dividing the coverage value in all bins by that median value, and then multiplying it by 50. Then the H3 coverage was subtracted from the H2Aub1 or H3K27me3 coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNAseq data is provided in raw read counts for each gene. ChIP-seq data is provided as bigwigfiles that list median-scaled read count in 50bp bins of H2Aub1 or H3K27me3 minus median-scaled read count for H3. For the ChIP-seq data also the broadPeak output from MACS2 has been provided. A bed file with regions with significantly gained H2Aub1 in both replicates has been provided as well.

extract_protocol:
Rosette leaves were harvested one hour before darkness. ChIP was performed as described before [Villar and Köhler 2010, Plant Cromatin Immunoprecipitation], with the following modifications: no vacuum infiltration with DMA was performed. Vacuum infiltration with formaldehyde was performed for 2x5min. For quenching the formaldehyde, the solution was poured off, after which 0.125 M glycine was added and another 5-min vacuum infiltration was performed. Vacuum infiltration was performed at room temperature. Around 300 and 500 mg cross-linked plant material was used for nuclei extraction for the H2Aub1 and H3K27me3 experiment, respectively. Sonication of the chromatin was done for eight 30-s ON, 30-s OFF cycles. Overnight antibody binding was performed directly after sonication, followed by addition of washed protein A dynabeads (Thermofisher) to each ChIP aliquot. For bead washing, the LiCl wash step was skipped. De-crosslinking and subsequent DNA recovery steps performed using the Ipure kit v2 (Diagenode, Liège, Belgium).
The Ovation Ultralow Sytem V2 (NuGEN, Redwood city, CA, USA) was used for library preparation

value: anti-H3 07-690, Merck Millipore, Burlington, MA, USA lot no #3011824


title: wt_GFP_REF6_2


title: CIA-15wk-2

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description:
Replicate 2
SAMPLE 8

hyb_protocol: The RNA was amplified and hybridized to the Illumina MouseRef-8 v2.0 Expression BeadChip according to standard Illumina protocols.

scan_protocol: Illumina BeadScan 500 System

data_processing: The bead-level data were converted into probe intensities by using beadarray package in R software, and then the intensities were normalized using the quantile normalization by Matlab software

source_name: Synovial tissue, collagen-induced arthritis, 15 weeks, replicate 2

growth_protocol: Male DBA/1 mice (Jackson Laboratory, Bar Harbor, ME) at 6-8 weeks of age were used for experiments. The mice were maintained under specific pathogen-free conditions and were used according to guidelines of the Institutional Animal Care and Use Committee.

extract_protocol: For microarray analysis, the animals were sacrificed at 3 time points (6, 9, and 15 weeks) and ankle joints, with the exception of the hind foot that received the booster immunization, were then harvested from each mouse. Subsequently, the skin of paws and ankles was removed and the synovial tissues around the ankle joints were obtained using sterilized microsurgery scissors and forceps. Total RNA was extracted from pooled mouse synovial tissues using RNAzol B (Invitrogen Life Technologies, Gaithersburg, MD)) and a RNease Kit (Qiagen, Valencia, CA). The total RNA integrity (RIN) was assessed by Bioanalyzer 2100 (Agilent, Santa Clara, CA), and on average, the RIN for all the samples was 9.5.

treatment_protocol: For all the samples except the wild type (controls), DBA/1 mice (Jackson Laboratory) were immunized with bovine type II collagen (CII; Chondrex, Redmond, WA), as described previously (1,2,3). Briefly, CII was dissolved in 0.05 N-acetic acid at 4°C and emulsified with complete Freund's adjuvant (CFA) (ratio 1:1). The mice were injected intradermally at the base of the tail with 0.1 ml of the emulsion (containing 100 μg of CII) as a primary immunization. Two weeks after primary immunization, booster injections with 50 g of CII in incomplete Freund’s adjuvant (Chondrex) were given through the footpad.

tag: gender

value: Male

value: Synovial tissues from ankle joints

tag: Stage

value: 15 weeks after immunization


title: ExVivo_BMDM_M(IL-4)_rep2

description: Gene expression in IL-4 stimulated BMDM

source_name: Bone marrow-derived macrophages, M(IL-4), replicate2


title: d4_HIV_3h_S21_R1_001

tag: treatment


title: ubp12ubp13_H3_H3K27me3_1

value: rosette leaves


title: 201: Patient 4

description: mRNA expression

value: Dermatofibrosarcoma protuberans (DFSP)

value: Tumor sample


title: wt_H3K27me3_H3K27me3_2

value: WT

value: anti-H3K27me3 07-449, Merck Millipore, lot no #2686928


title: d3_HIV_8h_EFV_S20_R1_001

value: CD4+ T cells


title: ubp12ubp13_H3K27me3_H3K27me3_2


title: wt_H3K27me3_H3K27me3_1


title: ExVivo_BMDM_M(IL-4)_rep1

description: Gene expression in IL-4 stimulated BMDM

source_name: Bone marrow-derived macrophages, M(IL-4), replicate1


title: ExVivo_BMDM_M(LPS+IFN-γ)_rep3

source_name: Bone marrow-derived macrophages, M(LPS+IFN-γ), replicate3


title: 903: Patient 9

description: mRNA expression


title: ubp12ubp13_H3K27me3_H3K27me3_1


title: 104: Patient 3

description: mRNA expression


title: 901: Patient 7

description: mRNA expression


title: wt_input_REF6_1

value: wt

value: none (input)


title: 103: Patient 2

description: mRNA expression


title: 203: Patient 6

description: mRNA expression


title: 902: Patient 8

description: mRNA expression


title: d2_HIV_144h_S15_R1_001

value: untreated


title: 202: Patient 5

description: mRNA expression


title: d2_ui_312h_EFV_S14_R1_001

value: control


title: d2_ui_312h_S13_R1_001


title: CIA-9wk-2

description:
Replicate 2
SAMPLE 6

source_name: Synovial tissue, collagen-induced arthritis, 9 weeks, replicate 2

value: 9 weeks after immunization


title: d2_HIV_144h_EFV_S16_R1_001


title: CIA-15wk-1

description:
Replicate 1
SAMPLE 7

source_name: Synovial tissue, collagen-induced arthritis, 15 weeks, replicate 1


title: d1_ui_312h_S7_R1_001


title: d1_ui_312h_EFV_S8_R1_001


title: d2_ui_48h_EFV_S12_R1_001


title: PP6

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

description: Plants under flooding stress for 48 hours

data_processing:
For quality analysis of the reads was used FastQC Ver. 0.11.7 software and later the Trimmomatic Ver. 0:35 program to remove adapters and poor quality bases in each library. The reads were mapped against the Prunus persica reference genome Ver. 2.0 (The Genome Database for Rosaceae - GDR, https://www.rosaceae.org) using Star Ver. 2.6 software. HTSeq Ver. 0.11.1 software was used to count.txt mapped reads.
Identification of differentially expressed genes (DEGs) was performed in the R Ver. 3.5.2 statistical environment with the edgeR Ver. 3.8 package, obtained from the Bioconductor repository. The raw reads were transformed to count.txts per million (CPM), keeping the genes with CPM values >1, and then normalised by the trimmed mean of M values method (TMM), considering DEGs with false discovery rates (FDRs) of <0.05 by the edgeR test.
Genome_build: Prunus persica Ver. 2.0 https://phytozome.jgi.doe.gov/pz/portal.html
Supplementary_files_format_and_content: tab-delimited text files include count.txt values by gene for each sample

organism: Prunus domestica x Prunus domestica subsp. insititia

source_name: Flooding R3

growth_protocol: Plum trees [Prunus insititia x Prunus domestica] cultivar Julior, propagated through cuttings were cultivated in 5-liter pots filled with orchard soil from Centro Agropecuário da Palma (typical dystrophic red-yellow argisol) and kept in a greenhouse with controlled temperature (± 30ºC), with high temperatures ranging 40-42°C (daytime) and minimum temperatures between 18-21ºC (night-time), humidity of about 80 ± 5%, and irrigation until field capacity daily.

extract_protocol:
Collected leaf tissues were immediately frozen in liquid nitrogen. Total RNA was extracted using  Plant RNA Reagent Purelink® (Life Technologies) and treated with DNase I (Invitrogen Inc., Carlsbad, CA, USA). Illumina TruSeq RNA Sample Preparation® V2 (IlluminaTM) kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: I) control: plants received irrigation daily until field capacity; and II) plants exposed to flood stress, maintaining a water level of approximately 3 cm above the ground.

tag: cultivar

value: Julior

value: Leaf tissue

value: 10 months old

tag: phenotype

value: Tolerant to flooding stress


title: CIA-9wk-1

description:
Replicate 1
SAMPLE 5

source_name: Synovial tissue, collagen-induced arthritis, 9 weeks, replicate 1

value: Male

tag: tissue

value: Synovial tissues from ankle joints


title: d2_ui_48h_S11_R1_001


title: PP3

description: Plants under normal condition

source_name: Control R3


title: U2OS/ADM clone3

city: Shenyang

first: Yanfeng

last: Cheng

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description:
Test
long non-coding RNAs
SAMPLE 6

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/cn/analyze/
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control ratios.

source_name: Adriamycin-resistant cell line

label_protocol: RT2 lncRNA qPCR Assay were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. 1 mg RNA was reverse transcribed to cDNA in 20μl system by First Strand cDNA Synthesis Kit for RT-PCR (Merck & Co., Inc., Kenilworth, NJ, USA). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: U2OS cells were exposed to intermittent and continues stepwise increase of ADM concentrations from 0.2mg/l ADM. 24h later, ADM was removed, and cells were cultured with fresh medium until the proliferation rate returned to the identical rate of parental cells. At this point the ADM concentrations increased and repeated the above process. During this 6-month long period, three clones of each cell line named U2OS/ADM-1, 2, 3 were induced, respectively.

extract_protocol: Total RNA was isolated by Rneasy mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol.

tag: cell line

value: adriamycin-resistant U2OS

value: osteosarcoma

tag: Sex

value: female


title: CIA-6wk-2

description:
Replicate 2
SAMPLE 4

source_name: Synovial tissue, collagen-induced arthritis, 6 weeks, replicate 2

value: 6 weeks after immunization


title: wt_H3_H3K27me3_2

description: Col_R1R2_H3_fromK27_genomecov_covscale.bw

source_name: rosette leaves

value: rosette leaves

tag: genotype

value: WT

value: anti-H3 07-690, Merck Millipore, Burlington, MA, USA lot no #3011824


title: d1_HIV_144h_S9_R1_001

source_name: whole blood

value: CD4+ T cells


title: wt_H3_H3K27me3_1

tag: chip antibody


title: d1_ui_48h_EFV_S6_R1_001

value: EFV


title: CIA-6wk-1

description:
Replicate 1
SAMPLE 3

source_name: Synovial tissue, collagen-induced arthritis, 6 weeks, replicate 1


title: U2OS/ADM clone1

description:
Test
long non-coding RNAs
SAMPLE 4


title: PP1

description: Plants under normal condition

source_name: Control R1

tag: age


title: 3_3D26_18_5GY+DCO 1_d7

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

hyb_protocol: Hybridization cocktails containing 5.5 µg of fragmented, end-labelled cDNA were prepared and applied to Clariom S arrays. Hybridization was performed in 45°C hybridization oven at 60 rpm for 16 hours. Using the GeneChip® Fluidics Station 450 the hybridized Clariom S Arrays were washed and stained (Fluidics Protocol FS450_0001).

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G controlled by GeneChip®Operating Software (GCOS) version 1.4 to produce CEL intensity files.

data_processing:
Data analysis from the exon arrays were processed using GeneSpring GX 14.9 software (Agilent Technologies).
Affymetrix.TranscriptomeChip.Clariom_S_Human_na36_hg38_2016-06-21

source_name: dermal fibroblasts and keratinocytes

label_protocol: 300µg total RNA from each model were processed using the WT Expression Kit (Ambion)  to generate amplified sense-strand cDNA. Fragmentation and labeling was done using the Affymetrix® GeneChip® WT Terminal Labeling Kit Assay (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: Normal primary human keratinocytes and fibroblasts were isolated from biopsies of adult non-keratinized oral mucosa (inside of the cheeks) obtained from volunteers after oral surgery. Normal primary human keratinocytes and fibroblasts were isolated from skin biopsies of adult volunteers. The epidermal sheet was separated from the dermis by incubating the samples for 2 h at 37°C in a dispase-containing solution (5,000 caseinolytic units; BD Biosciences, Franklin Lakes, NY, USA). To generate a single cell suspension, the epidermal part was minced and digested with 10 ml trypsin 0.25% (Lonza, Basel, Switzerland) for 20 min in a 5 % CO2 incubator at 37°C. Digestion was stopped with equal volume of Trypsin Neutralization Solution (TNS) (Lonza). Single cell suspension of NHOK was grown in serum free Keratinocyte Growth Medium (KGM;Lonza) at 37°C in a 5% CO2 incubator. Isolation of the fibroblasts was done by lysis of the dermis in collagenase 1A 100U/ml (Sigma, Taufkirchen, Germany) for 3 h at 37°C in a 5% CO2 incubator. Isolated fibroblasts were grown in DMEM medium high glucose and L-Glutamin (Invitrogen), containing 10 % fetal calf serum (FCS;Biochrom, Berlin, Germany).

extract_protocol: Total RNA was isolated using the Nucleo Spin II RNA Mini Kit, (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions, including on-column digestion of DNA with RNase-free DNase I.

treatment_protocol: To mimic skin conditions of radiodermatitis and mucositis models were irradiated with 5 Gray (Gy). Afterwards, epidermal parts of the models were treated every second day with a dexpanthenol-containing ointment (DCO; Bepanthen® Wound Healing Ointment, Bayer Vital GmbH, Leverkusen, Germany) or liquid (DCL; Bepanthen® Lösung; Bayer Vital GmbH) in comparison to placebo-treated and untreated controls.

value: skin

tag: group

value: 5Gy-treated + dexpanthenol-containing ointment radiodermatitis


title: 7_3D28_5GY + DCL_d7

source_name: mucosal fibroblasts and keratinocytes

value: mucous membrane

value: 5Gy-treated +  dexpanthenol-containing liquid mucositis


title: 2_3D26_18_5GY-1_d7

value: 5Gy-treated radiodermatitis


title: 6_3D28_5GY-1_d7

value: 5Gy-treated mucositis


title: PP4

source_name: Flooding R1

value: Julior

value: Leaf tissue

value: 10 months old

value: Tolerant to flooding stress


title: 101: Patient 1

description: mRNA expression

source_name: Tumor sample

tag: disease state

value: Dermatofibrosarcoma protuberans (DFSP)

value: Tumor sample


title: Parental U2OS clone2

description:
Control
long non-coding RNAs
SAMPLE 2

source_name: Parental cell line

value: Parental U2OS

value: osteosarcoma

value: female


title: U2OS/ADM clone2

description:
Test
long non-coding RNAs
SAMPLE 5

value: adriamycin-resistant U2OS


title: Parental U2OS clone3

description:
Control
long non-coding RNAs
SAMPLE 3


title: 5_3D28_18_Kontrolle-2_d7

value: control mucositis


title: d1_ui_48h_S5_R1_001

tag: cells

value: CD4+ T cells

tag: inoculation

value: control

value: untreated


title: Parental U2OS clone1

description:
Control
long non-coding RNAs
SAMPLE 1


title: PP2

description: Plants under normal condition

source_name: Control R2


title: PQ

city: New York

first: Liza

middle: A.

last: Pon

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Base calling were conducted by the HiSeq Control Software
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Saccharomyces cerevisiae S288c reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_name feature in the annotation file. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
The Wald test was used to generate p-values and log2 fold changes. Genes with a p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: Saccharomyces cerevisiae S288c reference genome available on ENSEMBL
Supplementary_files_format_and_content: csv file show the comparison of gene expression between WT and PQ. The Wald test was used to generate p-values and Log2 fold changes.

organism: Saccharomyces cerevisiae

source_name: yeast cells treated with 2.5 mM for 8hr

growth_protocol: Cells were grown in glucose-based rich media (yeast extract/peptone/dextrose, YPD) to mid-log phase (optical density OD600 = 0.3-0.5)

extract_protocol:
RNA was extracted from PQ-treated and non-treated mid-log phase yeast cells using the RNeasy kit (Qiagen, Germantown, MD)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 2.5 mM PQ for 8 hrs in YPD

tag: phase

value: mid-log

value: 2.5 mM PQ for 8 hr


title: WT

source_name: yeast cells

tag: strain


title: d1_HIV_144h_EFV_S10_R1_001

value: EFV

tag: time point of rna extraction post inoculation

tag: donor


title: PP5

source_name: Flooding R2

value: Julior


title: TFKWCE_2

status: Public on May 18 2020

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
Tumor cholangiocyte
TFKWCE_2

hyb_protocol: Standard, as recommended by illumina

scan_protocol: Standard, as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.22.1). It was log2 transformed and quantile normalized. The normalized data table does not contain all the probes since the ones that do not follow the established criteria are filtered out. Only probes with a detection p-value lower than 0.01 in at least one sample are analzyed.

label: Biotin

source_name: Cell line

label_protocol: Whole-Genome Gene Expression DASL®HT Assay Guide (Part#15018210 Rev. D)

growth_protocol: NHC, H69, EGI and TFK cell lines were cultured in collagen-coated plates: NHC, H69 and EGI cells in FLASK media (as described in DOI: 10.1136/gutjnl-2013-305281) and TFK cells in DMEM/F12+Glutamax media suplemented with FBS10%

extract_protocol: RNA was extracted from the described samples by  using miRCURY RNA Isolation kit - Biofluids (EXIQON; ref #300112). Quality control was performed with 2100 Bioanalyzer.

tag: disease

value: Tumor cholangiocyte


title: H69WCE_2

description:
Immortalized cholangiocyte
H69WCE_2

value: Immortalized cholangiocyte


title: NHCWCE_3

description:
Normal cholangiocyte
NHCWCE_3

value: Normal cholangiocyte

value: NHC


title: TFKWCE_1

description:
Tumor cholangiocyte
TFKWCE_1


title: TFKWCE_3

description:
Tumor cholangiocyte
TFKWCE_3


title: NHCWCE_2

description:
Normal cholangiocyte
NHCWCE_2


title: EGIWCE_2

description:
Tumor cholangiocyte
EGIWCE_2


title: EGIWCE_3

description:
Tumor cholangiocyte
EGIWCE_3


title: 1_3D26_18_Kontrolle-1_d7

value: skin

value: control radiodermatitis


title: EGIWCE_1

description:
Tumor cholangiocyte
EGIWCE_1


title: NHCWCE_1

description:
Normal cholangiocyte
NHCWCE_1


title: H69WCE_3

description:
Immortalized cholangiocyte
H69WCE_3


title: H69WCE_1

description:
Immortalized cholangiocyte
H69WCE_1


title: EV_H69

description:
Immortalized cholangiocyte
EV_H69

source_name: Cell line-derived Evs


title: EV_EGI1

description:
Tumor cholangiocyte
EV_EGI1


title: S_PSC_82

description:
PSC
S_PSC_82

source_name: Serum EVs

value: Primary Sclerosing Cholangitis


title: EV_TFK1

description:
Tumor cholangiocyte
EV_TFK1


title: O_UC_87

description:
UC
O_UC_87

source_name: Urine EVs

value: Ulcerative Colitis


title: O_CCA_78

description:
CCA
O_CCA_78

value: Cholangiocarcinoma


title: O_UC_88

description:
UC
O_UC_88


title: S_PSC_85

description:
PSC
S_PSC_85


title: EV_NHC

description:
Normal cholangiocyte
EV_NHC


title: S_PSC_81

description:
PSC
S_PSC_81


title: O_CCA_77

description:
CCA
O_CCA_77


title: O_CCA_73

description:
CCA
O_CCA_73


title: O_CCA_72

description:
CCA
O_CCA_72


title: S_PSC_84

description:
PSC
S_PSC_84


title: S_PSC_80

description:
PSC
S_PSC_80


title: O_CCA_69

description:
CCA
O_CCA_69


title: O_CCA_76

description:
CCA
O_CCA_76


title: O_CCA_59

description:
CCA
O_CCA_59


title: O_CCA_61

description:
CCA
O_CCA_61


title: O_CCA_60

description:
CCA
O_CCA_60


title: S_PSC_79

description:
PSC
S_PSC_79


title: O_CCA_74

description:
CCA
O_CCA_74


title: O_CCA_71

description:
CCA
O_CCA_71


title: O_CCA_67

description:
CCA
O_CCA_67


title: O_CCA_56

description:
CCA
O_CCA_56


title: O_CCA_65

description:
CCA
O_CCA_65


title: O_CCA_57

description:
CCA
O_CCA_57


title: O_CCA_51

description:
CCA
O_CCA_51


title: O_PSC_50

description:
PSC
O_PSC_50


title: O_PSC_51

description:
UC
O_PSC_51


title: O_CCA_55

description:
CCA
O_CCA_55


title: O_CCA_70

description:
CCA
O_CCA_70


title: O_UC_44

description:
UC
O_UC_44


title: O_UC_43

description:
UC
O_UC_43


title: O_UC_42

description:
UC
O_UC_42


title: O_CCA_63

description:
CCA
O_CCA_63


title: O_UC_36

description:
UC
O_UC_36


title: O_CCA_58

description:
CCA
O_CCA_58


title: O_CCA_75

description:
CCA
O_CCA_75


title: O_PSC_52

description:
PSC
O_PSC_52


title: O_PSC_46

description:
PSC
O_PSC_46


title: O_CCA_66

description:
CCA
O_CCA_66


title: O_PSC_49

description:
PSC
O_PSC_49


title: O_CCA_52

description:
CCA
O_CCA_52


title: O_UC_45

description:
UC
O_UC_45


title: O_UC_39

description:
UC
O_UC_39


title: OCtrl_34

description:
Healthy
OCtrl_34

value: Healthy


title: O_UC_41

description:
UC
O_UC_41


title: OCtrl_33

description:
Healthy
OCtrl_33


title: O_UC_38

description:
UC
O_UC_38


title: OCtrl_31

description:
Healthy
OCtrl_31


title: S_CCA_30

description:
CCA
S_CCA_30

source_name: serum Evs


title: OCtrl_32

description:
Healthy
OCtrl_32


title: S_CCA_25

description:
CCA
S_CCA_25


title: S_CCA_28

description:
CCA
S_CCA_28


title: S_CCA_23

description:
CCA
S_CCA_23


title: S_CCA_24

description:
CCA
S_CCA_24


title: S_CCA_27

description:
CCA
S_CCA_27


title: O_UC_40

description:
UC
O_UC_40


title: S_CCA_29

description:
CCA
S_CCA_29


title: S_CCA_22

description:
CCA
S_CCA_22


title: S_UC_18

description:
UC
S_UC_18


title: S_CCA_21

description:
CCA
S_CCA_21


title: S_CCA_26

description:
CCA
S_CCA_26


title: S_CCA_20

description:
CCA
S_CCA_20


title: S_ctrl_9

description:
Healthy
S_ctrl_9


title: S_UC_15

description:
UC
S_UC_15


title: S_UC_17

description:
UC
S_UC_17


title: O_PSC_48

description:
PSC
O_PSC_48


title: S_UC_11

description:
UC
S_UC_11


title: S_ctrl_8

description:
Healthy
S_ctrl_8


title: S_UC_13

description:
UC
S_UC_13


title: S_ctrl_6

description:
Healthy
S_ctrl_6


title: S_CCA_19

description:
CCA
S_CCA_19


title: S_UC_10

description:
UC
S_UC_10


title: S_ctrl_3

description:
Healthy
S_ctrl_3


title: Pool-10ab

city: London

first: Davide

last: Zecchin

address: Gower Street

institute: University College London

description: Please note that the raw (fastq) files uploaded here contain multiplexed data: The included README.txt file describes how the individual samples may be demultiplexed from each GEO sample.

data_processing:
Demultiplex each lane of sequencing using internal barcodes (nucleotides 1-6) & extract nuclotides 31-51 as the shRNA within the backone vector
Please see README.txt file for sample-barcode associations
Collapse reads to unique "tags" along with count of ocurrences of each tag in full file -- in-house software
Align tags to shRNA library using bwa 0.5.9, -n 4, -l 90, -k 4
Summarise number of reads mapping to each target, weighted by ocurrences of each tag - in-house code
Discard off-target reads (wrong pool or unmapped) and scale counts to maximum total reads aligned across all samples for that pool
Genome_build: MISSION Lentiplex Human Pooled shRNA library sequences (Sigma-Aldrich Cat. SHPH01)
Supplementary_files_format_and_content: _RawCounts.txt: tab delimited text file containing un-normalised counts of reads aligning to each feature

growth_protocol: MDA-MB-468 were grown in DMEM supplemented with 10% FBS and 1% pen/strep.

extract_protocol:
Genomic DNA was extracted and shRNA inserts were retrieved by PCR amplification
PCR primers contained Indexes and adaptors for deep sequencing: P5_Illuseq, P7 and barcodes.

treatment_protocol:
MDA-MB-468 cells were infected the whole-genome shRNA library, MISSION Lentiplex Pooled shRNA library from Sigma (SHPH01). The library was divided in 10 pools (treated individually) and the infection was done in triplicate.
Selected cells were treated with vehicle control, 250 nM AZD8186, 250 nM GDC0941 or 450 nM MK2206 for 12 days. One fraction of cells was frozen at time 0 (before drug treatment).


title: S_ctrl_7

description:
Healthy
S_ctrl_7


title: Pool-6ab


title: Pool-56c


title: Pool-910c


title: Pool-78c


title: Pool-9ab


title: Pool-34c


title: Pool-7ab


title: papillary

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: papillary predominant adenocarcinoma

extract_protocol:
Total RNAs were extracted from the cells with miRNeasy FFPE Kit (QIAGEN), according to the manufacturer’s protocol.
NGS library preparation was performed using the TruSeq RNA Access Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: papillary predominant adenocarcinoma


title: OCtrl_35

description:
Healthy
OCtrl_35


title: Pool-5ab


title: Pool-4ab


title: Pool-12c


title: treatment 3-1

city: Duarte

first: Haiqing

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

data_processing:
Basecalls performed using CASAVA version 1.8
The ChiP-Seq sequence reads were mapped to Homo sapiens genome assembly GRCh37 (hg19) using open source DNA-seq alignment tool BWA version 0.7.15
only keep the high quality unique alignments using SAM Tag (XA:Z and SA:Z) as filter
remove the duplicated alignments caused by PCR duplication using SAMTools (ver 0.1.19) ; the unmapped reads and the reads that is not the primary alignment are also removed using SAMTools based on the alignment quality tag (-F 4 -F 256).
ChiP-Seq peak calling was performed using MACS2 (v2.1.2) with broad option to detect the H3K4me3 binding sites with FDR<0.005 cutoff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for ChIP-seq Peaks

source_name: Melanoma_glutamine supplemented diet

growth_protocol: Tumor TM00702 was purchased from The Jackson Lab and propagated in NSG mice. Briefly, tumors were sectioned into 5 mm^3 pieces, and engrafted subcutaneously in 5 weeks old NSG mice.

extract_protocol:
10 mg of frozen tumor tissue was used for ChIP and pull down using H3K4me3
ChIP-seq libraries were prepared with Kapa DNA HyperPrep Kit (Cat No. KK 8700, Kapa) according to the manufacturer's protocol; A 10 cycles of PCR was performed on 5-10 ng of immunoprecipitated DNA to produce the final sequencing library. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.

treatment_protocol: When tumor reached a volume of 50 mm^3, mice were placed in to 2 groups receiving either control or glutamine supplemented diet. Tumors were collected at the end of the study and used for pull down with HeK4me3 antibody and ChIP-seq analysis.

tag: tumor model

value: Melanoma PDX TM00702 model (Jackson Lab)

value: H3K4me3 Millipore 17-614

value: melanoma


title: treatment 3-2


title: S_ctrl_2

description:
Healthy
S_ctrl_2


title: Pool-3ab


title: S_ctrl_1

description:
Healthy
S_ctrl_1


title: S_UC_14

description:
UC
S_UC_14


title: treatment 2-2


title: Pool-2ab


title: lepidic

source_name: lepidic predominant adenocarcinoma

value: lepidic predominant adenocarcinoma

tag: sample type

value: FFPE tissue specimen


title: treatment 2 input

tag: tissue


title: TRIM11 KO

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

description: KO

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh37 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: raw read count

source_name: nasopharyngeal carcinoma cell lines

growth_protocol: 10% FBS in DMEM

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions

tag: cell type

value: nasopharyngeal carcinoma cell lines

tag: passages

tag: cell line

value: TRIM11 KO


title: treatment 1 input

tag: chip antibody