title: BbRB50_Cu_Const  Rep2

city: Lille

first: Rudy

last: Antoine

address: 1, rue du Professeur Calmette

country: France

institute: CIIL

data_processing:
The RNAseq data of each sample were analyzed using Rockhopper v2.0.3 with the default parameters to calculate the RPKM value for each coding sequence with the Bordetella pertussis Tohama I NC_002929  or the Bordetella bronchiseptica NC_002927 genome annotations
Genome_build: Bordetella pertussis Tohama I NC_002929 and Bordetella bronchiseptica NC_002927
Supplementary_files_format_and_content: Excel files with RPKM values for each duplicated sample.

organism: Bordetella bronchiseptica

source_name: Bordetella bronchiseptica total RNAseq

growth_protocol: B. pertussis strains were grown on BG agar plates for 2 days at 37°C and then cultured in modified Stainer Scholte (SS) liquid medium at 37°C under agitation

extract_protocol:
Bacteria were pelleted, and total RNA was extracted using TriReagent (Invitrogen) following the manufacturer’s instructions. Genomic DNA was removed by DNase I treatment (Sigma Aldrich).
For each RNAseq sample, DNA-depleted total RNA was treated with the Ribo-Zero rRNA Removal Kit (Illumina) following the manufacturer’s recommendations. The rRNA-depleted RNA was then used to build the Illumina library using the TruSeq RNA Library Preparation Kit, followed by sequencing on an Illumina NextSeq 500 benchtop sequencer on SR150 high output run mode.

treatment_protocol: The bacterial cultures were stopped at mid exponential phase (OD600 =1.5) by adding 2 mL of a mixture of 5:95 phenol:ethanol (v:v) to 8 mL of bacterial suspensions.

tag: strains

tag: protocol

value: RNAseq

tag: culture conditions

value: strain was cultivated in SS media for 16 h in the presence of 2 mM CuSO4 to an OD600 nm = 1.5

value: Alex Rivera-Millot

value: November 2018


title: PT4-S1: Parental tumor 4 (sample 1)

status: Public on Oct 27 2020

type: genomic

city: Bethesda

first: Daniela

last: Hirsch

address: 50 South Drive

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description: aCGH

hyb_protocol: Combined samples were hybridized at 65 °C and 20 rpm for 24-48 hours to the CGH microarrays.

scan_protocol: Scanned with microarray scanner G2565BA (Agilent)

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Parental tumor

label_protocol: Parental tumor DNA was extracted from FFPE tissue and labeled with the Genomic DNA ULS Labeling Kit (Agilent); cell line DNA was enzymaticall labeled using the SureTag Labeling System (Agilent). Tumor and cell line DNA was labeled with Cy-3, genomic reference DNA (Promega) with Cy-5.

growth_protocol: Cell were cultured in DMEM - high glucose (CL1, CL2, CL3) or DMEM/KSFM (2:1; CL4) supplemented with fetal bovine serum (20% v/v), penicillin (100 U/ml) and gentamicin (2.5 mg/ml) at 37 °C in a humidified atmosphere of 5% CO2. Medium was replaced every third day.

extract_protocol: DNA was isolated using the DNeasy Blood and Tissue Mini Kit (Qiagen).

tag: gender

value: male

tag: tumor type

value: Pancreatic ductal adenocarcinoma

source_name: Genomic reference DNA


title: PT2-S2: Parental tumor 2 (sample 2)

description: aCGH

value: Colorectal adenocarcinoma


title: p14 Mertk WT-3

type: SRA

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description:
p14 Mertk WT-3
17-7

library_source: transcriptomic

data_processing:
align to genome with STAR
count reads mapping to genes with featureCounts
Genome_build: grcm38
Supplementary_files_format_and_content: gene counts, txt

molecule: total RNA

organism: Mus musculus

source_name: retinal pigmented epithelial cells

extract_protocol:
RNA was extracted with RNeasy qiagen kit per kit protocol starting at 2 hour post-light onset.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Library Prep. Briefly, total RNA  is used to purify the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. RNA is fragmented into small pieces. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Then, second strand cDNA is synthesized using DNA Polymerase I and RNase H. cDNA fragments then have a single "A" base added along with ligation of adapters. The products are then purified using magnetic beads and then PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

tag: strain

value: mixed c57Bl/6J and B6;129-Mertktm1Grl/J

tag: age

tag: tissue

value: retinal pigment epithelium

tag: Sex

value: female

tag: genotype/variation

value: Mertk WT


title: BbRB50_Cu_Const  Rep1


title: CL2: Derived cell line 2

description: aCGH

source_name: Cell line


title: CL1: Derived cell line 1

description: aCGH

value: Esophageal adenocarcinoma


title: B6-091_WT_LFD_Liver

city: Davis

first: Michael

middle: L

last: Goodson

state: CA

address: One Shields Ave

institute: University of California Davis

data_processing:
Base calling was done using Illumina Casava
Aligned to GRCM38 (mm10) genome using Tophat /Bowtie2
Transcript assemblies created using Cufflinks/cuffmerge v. 2.1.1
Differential gene expression computed using Cuffdiff
Genome_build: mm10/Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: Normalized count (FPKM) tables (_FPKM_matrix.txt) and differential gene expression lists (_gene_exp.diff) for HFD and LFD WT vs KO samples in Liver and eWAT

source_name: Liver

growth_protocol: Adult  NCoR-omega KO and C57BL/6N (WT) adult mice were fed HF (Research Diets Cat#D12492; 60% kcal fat) or LF (Research Diets Cat#D12450B;10%kcal fat) diet for 10 weeks.

extract_protocol:
Qiagen RNeasy Mini Kit
Nugen Encore Complete RNA-Seq Library System

treatment_protocol: LFD/HFD

value: Liver

value: 17 weeks

tag: diet

value: LFD

tag: genotype

value: WT


title: p14 Mertk KO-3

description:
p14 Mertk KO-3
17-6

value: Mertk KO


title: BbRB50_Tris_Const  Rep2

value: RNAseq

value: strain was cultivated in SS media for 16 h in the presence of 3.2 mM Tris pH5.5 to an OD600 nm = 1.5


title: p14 Mertk KO-2

description:
p14 Mertk KO-2
17-5


title: PT3: Parental tumor 3

description: aCGH


title: PT2-S1: Parental tumor 2 (sample 1)

description: aCGH


title: EOs_Gills_L_2

type: RNA

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Gene expression for gills of gilthead sea bream fed 0.5% EOs diet pool 2

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to S. aurata array (ID 024502, Agilent) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: For microarray analysis, a percentile shift normalization was carried out and then data were filtered by expression (standard deviation) among groups. Then, gene-level analysis was conducted in order to obtain the median of signal intensities from spots within a probe set. Statistical test (t-test unpaired) was done with GeneSpring software GX 14.3 to obtain the differentially expressed genes (p-value < 0.05) between control and treatments.

organism: Sparus aurata

source_name: diet with 0.5% essential oils

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: test animals: Gilthead sea bream (Sparus aurata) were obtained from an aquaculture company (Valencia, Spain) and transported to the on-grown facilities of IRTA in Sant Carles de La Ràpita (Tarragona, Spain).

extract_protocol: Total RNA was extracted from gills using  the RNeasy® Mini Kit (Qiagen, Germany). Total RNA was eluted in a final volume of 35 μL nuclease-free water and treated with DNAse using the DNA-freeᵀᴹ DNA Removal Kit according to manufacturer’s instructions (Invitrogen, Thermo Fisher Scientific, Lithuania). Total RNA concentration and purity were quantified using a Nanodrop-2000® spectrophotometer (Thermo Scientific, USA) and stored at -80 °C until analysis. Prior to hybridization with microarrays, samples were diluted to 133.33 ng/µL concentration and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Spain). All the RNA analysed in this study were selected by the criteria of a RIN value > 8.5.

treatment_protocol: All animal experimental procedures were conducted in compliance with the experimental research protocol approved by the Committee of Ethics and Animal Experimentation of the Institut de Recerca i Tecnologia Agroalimentàries and in accordance with the Guidelines of the European Union Council (86/609/EU) for the use of laboratory animals. After transport, fish received three treatments with hydrogen peroxide and two treatments with formaldehyde (150 ppm, during one hour each) to treat injuries and avoid the presence of any parasite. After the on-growing period of 105 days, 150 fish (BW = 40.26 ± 0.14 g) were randomly distributed in six aerated 450 L square-shaped tanks with smoothed corners, using an IRTAmar® recirculation system (5-10 % water replacement per day) under natural photoperiod. Water temperature (21-28 °C), oxygen (6.8 ± 1.7 mg/L) and pH (7.5 ± 0.01) were daily controlled, whereas salinity (35‰)as well as ammonia (0.13 ± 0.1 mg NH4+ L−1) and nitrite (0.18 ± 0.1 mg NO2- L−1) levels were weekly monitored.The nutritional assay was carried out in triplicate tanks with an initial density of 2 kg/m3 (25 fish per tank). Fish were fed both diets two times per day at the daily rate of 3.0% of the stocked biomass, which approached apparent satiation.  At day 65 of feeding, four fish were randomly selected from each tank, euthanized with anaesthetic (MS-222, Sigma-Aldrich) and their second gill arch from the right side was sampled and stored in RNAlater™, incubated overnight at 4 °C, and stored at -80 °C until analysed.

value: Gills

value: juveniles, 155 g


title: Sample 14-6_skin_non-lesional_treated

first: Astrid

middle: Haaskjold

last: Lossius

state: Oslo

address: Sognsvannsveien 20

department: Dermatology/Pathology

country: Norway

institute: University of Oslo

hyb_protocol: The final target were hybridized Clariom S human Array in Gene Chip Hybridization Oven. The arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G

data_processing: The data were processed with Transcriptomic Analysis Console (SST-RMA)

label: biotin

label_protocol: Fragmented and biotinylated ssDNA were prepared according to the standard Affymetrix protocol

growth_protocol: 4 mm skin biopsies were bisected and immidiately fixated in RNAlater

extract_protocol: RNA was isolated with Rneasy kit from Qiagen according to protocol

treatment_protocol: 1 & 4: untreated lesional skin; 2: untreated non-lesional skin; 3: nb-UVB x 3, 5: 6-8 weeks of treatment, lesional skin; 6: 6-8 weeks of treatment, non-lesional skin

tag: subject status

value: Atopic dermatitis (AD) patient

value: Female

tag: treatment

value: treated

value: Skin


title: BbRB50_Tris_Const  Rep1

value: Alex Rivera-Millot

value: November 2018


title: Sample 15-2_skin_non-lesional_untreated

value: untreated


title: p14 Mertk WT-2

description:
p14 Mertk WT-2
17-4

value: mixed c57Bl/6J and B6;129-Mertktm1Grl/J

value: retinal pigment epithelium

value: female

value: Mertk WT


title: PT1: Parental tumor 1

description: aCGH

value: male

value: Esophageal adenocarcinoma


title: EOs_Gills_L_3

description: Gene expression for gills of gilthead sea bream fed 0.5% EOs diet pool 3


title: Sample 14-5_skin_lesional_treated


title: pH55_2

city: GwangJu

first: JongHee

last: Lee

state: GwangJu

address: kimchiro 86

department: Advanced Process Technology and Fermentation Research Group

country: South Korea

institute: WIKIM

description: kimchi origin

data_processing:
bcl2fastq 1.8.4 software combines per-cycle BCL basecall files that generated Illumina sequencing instruments and translates them into FASTQ files. The raw FASTQ files were split into files containing about 20,000,000 reads and checked for quality using the FASTQC (v0.11.7). The reads were filtered (removing sequences that did not pass Illumina's quality filter) and trimmed based on the quality results by trimmomatic-0.36. Quality filtered reads were aligned to the reference-genome sequence using Bowtie2 (v 2.2.3). The sequence data for the reference genome was retrieved from the NCBI database (GCF_000203855.3, Lactobacillus plantarum WCFS1) . Qualityfiltered reads were aligned to the reference-genome sequence using Bowtie2. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM). The eggNOG (evolutionary genealogy of genes: Nonsupervised Orthologous Groups) database was used to cluster genes into functionally related groups and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database was used to analyze metabolic pathway.
Genome_build: Lactobacillus plantarum WCFS1 (CGF_000203855.3)
Supplementary_files_format_and_content: normalized counts

organism: Lactiplantibacillus plantarum

source_name: 3h after MRS pH 5.5 rep2

growth_protocol: Bacteria was cultivated with MRS media (pH 6.2)

extract_protocol: Total RNA were extracted and purified using the Bacterial RNA kit (qiagen) according to the protocol provided by the manufacturer.

treatment_protocol: Bacteria was cultivated until OD600 =0.5 and treated with MRS pH 5.5 or MRS pH 5.0

value: 3h after MRS pH 5.5


title: Q83X 2 CTC 2months PHA 543613

city: La Jolla

first: Alysson

middle: R.

last: Muotri

address: 2880 Torrey Pines Scenic Road MC 0695

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

data_processing:
A RNeasy Mini kit (Qiagen) was used to isolate RNA for library preparation (Illumina TruSeq RNA Sample Preparation Kit; San Diego, CA, USA) and sequencing (Illumina HiSeq2000, 50bp paired-end reads, 50 million high-quality sequencing fragments per sample, on average). Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture (OnRamp BioInformatics, Inc., San Diego, CA). Reads were trimmed using cutadapt, quality scores were assessed using FastQC, and reads were aligned to the Homo sapiens genome build hg19 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression using DESeq2 R library. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Gene clustering of differentially expressed genes was done using the Partitioning Around Medoids method using the fpc R library. Functional enrichment analysis of pathways, gene ontology, domain structure, and other ontologies was performed using several databases (HOMER, Interpro, NCBI, MSigDB, REACTOME, WikiPathways).
Genome_build: hg19
Supplementary_files_format_and_content: txt document, raw and normalized counts with annotations

source_name: stem cell-derived cortical organoids

growth_protocol: Differentiation was performed as previously described (Chailangkarn et al, 2016). After seven days, mTeSR1 used to feed PSCs was replaced with N2 medium [DMEM/F12 (Life Technologies, Carlsbad, CA, USA), 0.5x N2 (Life Technologies), 1% penicillin/streptomycin (P/S; Life Technologies), 1μM Dorsomorphin (Dorso; R&D Systems, Minneapolis, MN, USA), and 10µM SB431542 (SB; Stemgent, Cambridge, MA, USA)] for 1-2 days, after which embryoid bodies (EBs) were formed by scraping PSC colonies and culturing them in shaker suspension (95 rpm at 37°C) for eight days. EBs were dissociated and plated on a Matrigel-coated dish in N2B27 medium [N2 medium with 0.5x B27-Supplement (Life Technologies) and 20 ng/mL FGF-2]. Emerging rosettes were picked manually, dissociated in Accutase (Life Technologies), and seeded on poly-L-ornithine/laminin plates. Emergent NPCs were expanded and maintained in N2B27 medium with feeding on alternate days; all NPCs used for neurons were passage 5-20. FGF‑2 was withdrawn from the medium to induce neuronal differentiation, considered Day 0 of differentiation.

extract_protocol:
RNA was extracted using a RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. DNase-treated RNA was assessed with a NanoDrop1000 (ThermoScientific, Waltham, MA, USA). Total RNA was converted to cDNA and evaluated for RT-PCR array per the manufacturer’s instructions (Qiagen, Hilden, Germany).
A RNeasy Mini kit (Qiagen) was used to isolate RNA for library preparation (Illumina TruSeq RNA Sample Preparation Kit; San Diego, CA, USA) and sequencing (Illumina HiSeq2000, 50bp paired-end reads, 50 million high-quality sequencing fragments per sample, on average). Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture (OnRamp BioInformatics, Inc., San Diego, CA). Reads were trimmed using cutadapt, quality scores were assessed using FastQC, and reads were aligned to the Homo sapiens genome build hg19 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression using DESeq2 R library. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Gene clustering of differentially expressed genes was done using the Partitioning Around Medoids method using the fpc R library. Functional enrichment analysis of pathways, gene ontology, domain structure, and other ontologies was performed using several databases (HOMER, Interpro, NCBI, MSigDB, REACTOME, WikiPathways).

treatment_protocol: One-month old neurons were treated for two weeks at the drug. Neurospheres were treated as detailed above. One-month old cortical organoids were treated for one month with either Nefiracetam (1 µM) or PHA 543613 (1 µM) during every-other-day media changes. The concentration of the drugs was selected based on the specific Kd reported for each drug and from previous work on animal models and human neurons. The time points were strategically selected after we observed a cellular or functional phenotype in MECP2-KO neurons. Based on published work from our group, MECP2-KO neurons and neurospheres already show a distinct deficit after 4 weeks.

value: MECP2 mutant 2

tag: agent


title: pH55_1

description: kimchi origin

source_name: 3h after MRS pH 5.5 rep1


title: Q83X 1 CTC 2months PHA 543613


title: p14 Mertk WT-1

description:
p14 Mertk WT -1
17-30


title: p14 Mertk KO-1

description:
p14 Mertk KO - 1
17-29

value: Mertk KO


title: EOs_Gills_L_1

description: Gene expression for gills of gilthead sea bream fed 0.5% EOs diet pool 1

value: Gills

value: juveniles, 155 g


title: pH50_2

description: kimchi origin

source_name: 3h after MRS pH 5.0 rep2

value: 3h after MRS pH 5.0


title: Sample 14-3_skin_lesional_nb-UVB x 3

source_name: Skin_lesional_nb-UVB x 3

value: Atopic dermatitis (AD) patient

value: Female

value: nb-UVB x 3


title: Control_Gills_2

description: Gene expression for control group pool 2

source_name: control standard diet


title: Control_Gills_3

description: Gene expression for control group pool 3


title: Sample 14-2_skin_non-lesional_untreated

value: Skin


title: Sample 13-6_skin_non-lesional_treated

value: treated


title: Sample 14-1_skin_lesional_untreated

value: untreated


title: Sample 13-5_skin_lesional_treated


title: Q83X 2 CTC 2months Nefiracetam

value: Nefiracetam


title: pH50_1

description: kimchi origin

source_name: 3h after MRS pH 5.0 rep1


title: p14 Mertk WT Bai1 Tg neg. 4

description:
p14 Mertk WT Bai1 Tg neg. 4
12-63

value: mixed c57Bl/6J and B6;129-Mertktm1Grl/J

value: retinal pigment epithelium

value: female

value: Mertk WT Bai1 Tg neg


title: Q83X 1 CTC 2months Nefiracetam


title: Control_Gills_1

description: Gene expression for control group pool 1


title: p14 Mertk WT Bai1 Tg neg. 3

description:
p14 Mertk WT Bai1 Tg neg. 3
12-60


title: p14 Mertk WT Bai1 Tg pos. 3

description:
p14 Mertk WT Bai1 Tg pos. 3
12-61

value: Mertk WT Bai1 Tg pos


title: Q83X 2 CTC 2months untreated

value: MECP2 mutant 2


title: Sample 13-2_skin_non-lesional_untreated


title: con_1

description: kimchi origin

source_name: 3h after MRS  rep1

value: 3h after MRS


title: p14 Mertk WT Bai1 Tg neg. 2

description:
p14 Mertk WT Bai1 Tg neg. 2
12-58


title: Day0_2

city: Beijing

first: Xiaoxing

last: Liang

address: 18 Shuangqing Road

country: China

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences,

description:
hESCs-H1
mRNA
processed data file: core_table.xls

data_processing:
Base calling were conducted with BGISEQ-500.
Reads were filtered by Trimmomatic (v0.360), summarized with SOAPnuke (v1.4.0).
The clean data were alignment to the reference genome, GRCh3.p11 (hg38), and the expected counts were calculated by using Bowtie2 (v2.2.5).
Genome_build: GRCh3.p11 (hg38)
Supplementary_files_format_and_content: core_table.xls: Excel file includes FPKM values.

source_name: hESCs

growth_protocol: H1 were cultured in mTeSR1 medium. Single hESCs were seeding in microwell to form cell aggregates, then transferred into ultralow plates for 21-day EB differentiation.

extract_protocol:
Total RNA extraction was obtained with the RNeasy Plus Mini Kit (74136, QIAGEN, Germany) according to the guidance.
The cDNA library construction and sequencing were performed at Beijing Genomics Institute, using the BGISEQ-500 platform.

treatment_protocol: Cells were treated with 100 nM bisphenols or 0.01% DMSO (control) for 21 days.

tag: cell line

tag: original cell type

value: human embryonic stem cells

value: male

tag: time point

value: day 0


title: Sample 13-3_skin_lesional_nb-UVB x 3

value: Atopic dermatitis (AD) patient


title: Sample 13-4_skin_lesional_untreated

value: Female


title: p14 Mertk WT Bai1 Tg neg. 1

description:
p14 Mertk WT Bai1 Tg neg. 1
12-57


title: Day0_1


title: 904 2 CTC 2months PHA 543613

value: MECP2 mutant 1


title: 904 2 CTC 2months Nefiracetam


title: 904 1 CTC 2months PHA 543613


title: p14 Mertk WT Bai1 Tg pos. 2

description:
p14 Mertk WT Bai1 Tg pos. 2
12-53


title: p14 Mertk WT Bai1 Tg pos. 1

description:
p14 Mertk WT Bai1 Tg pos. 1
12-51


title: Control_1

source_name: hESCs EB differentiation

value: 21-day EB differentiation

value: DMSO


title: Control_2


title: con_2

description: kimchi origin

source_name: 3h after MRS  rep2


title: Sample 12-5_skin_lesional_treated

value: treated

value: Skin


title: 904 1 CTC 2months Nefiracetam

value: Nefiracetam


title: BPZ_2

value: BPZ


title: Sample 12-6_skin_non-lesional_treated


title: Q83X 1 CTC 2months untreated

value: untreated


title: Sample 12-3_skin_lesional_nb-UVB x 3

value: nb-UVB x 3


title: 904 2 CTC 2months untreated


title: Sample 12-4_skin_lesional_untreated


title: Sample 12-2_skin_non-lesional_untreated


title: BPZ_1


title: Sample 13-1_skin_lesional_untreated


title: BPS_2

value: BPS


title: Double+DC_node_steadystate_R2

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

data_processing:
A high read quality (mean score above 28) in all samples was confirmed using FastQC. Reads were aligned to the mouse genome (GRCm38) using Star (v2.6.0c) (Dobin et al. 2013) with the parameters --quantMode GeneCounts, --outFilterMultimapNmax 1 and --outFilterMatchNmin 35. The Star index was generated with the parameters --sjdbGTFfile (transcriptome version 93) and --sjdbOverhang 74. The mean alignment rate was above 85% per sample.  Read counting was performed by star using unstranded counting for both datasets. For both datasets normalised counts and differential expression values were generated using DESeq2 (Love et al. 2014) under default settings. Genes with an adjusted p-value of less than 0.01 and an absolute fold change of greater than 2 were considered significant.
The RNA-seq data was explored using Searchlight 2 (v2.0.0a) (Cole et al. n.d.) and R (version 3.4.4). Specifically, enrichment of gene ontologies was generated using a standard hypergeometric test with Benjamini-Hochberg multisample correction, and the gene-set database Gene Ontologies Molecular Function (GO_MF) (as downloaded from MsigDB collections (Subramanian et al. 2005).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include per gene read counts for each sample

source_name: CD103+ CD11b+ dendritic cells

extract_protocol:
Cells were isolated from C57BL/6 mice that previously underwent complete mesenteric lymphadenectomy. ILCs were identified as live, single, CD45+ IL-7Rα+ lineage- (CD3, CD5, CD11b, CD11c, B220) cells and T cells as live, single, CD45+ CD11b- CD11c- B220- CD3+ CD5+ CD4+ CD44high CD25- cells. Cells for RNA seq were purified by flow cytometric sorting, collected into 350 μl RLT plus buffer (Qiagen) and stored at -80°C until further processing. Samples were sorted in quadruplicates and isolated cell types included migratory ILCs (n = 15) and T cells (n = 8) from afferent lymph of thoracic duct cannulated mice in steady state, ILCs (n = 4) and T cells (n = 4) from the colonic and small intestinal lamina propria at similar proportions, and migratory ILCs (n = 25) from afferent lymph of Salmonella infected mice that underwent thoracic duct cannulation. RNA was isolated according to the manufacturer’s protocol (RNAeasy plus micro kit, Qiagen). CD11b+ CD103- and CD11b+ CD103+ DCs (live, single, CD45+, CD64- MHCIIhigh CD11c+) were isolated from the small intestinal lamina propria of C57BL/6 mice after removal of Peyer’s Patches. The migratory DC counterparts were isolated by thoracic duct cannulations of mice that previously underwent complete mesenteric lymphadenectomy. RNA was isolated according to the manufacturer’s protocol (RNAeasy kit, Qiagen).
The ILC and T-cell sequencing libraries were prepared according to published protocols (Bar-Ephraim et al. 2017), using a TAKARA SMART-seq v4 ultra low input library preparation kit with 15 cycles of amplification, and were sequenced to a mean depth of 5.1 million read pairs per sample using an Illumina HiSeq 2500. The DC sequencing libraries were prepared using a TAKARA SMART-seq v4 ultra low input library preparation kit, and were sequenced to a mean depth of 37.5 million read pairs per sample using an Illumina HiSeq 4000. The read length for both libraries was 75bp.

treatment_protocol: C57BL/6 mice were either used at steady state or infected with Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344. For S. Typhimurium infections,  mice received 20 mg streptomycin (Sigma) in 100 μl PBS via oral gavage 24h before infection with Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344. S. Typhimurium was grown in luria broth (LB) at 37°C for 5h at 180 rpm. After incubation, the cultures were diluted 1:2 in LB and further kept in a static incubator overnight. The following day, bacterial cell density was adjusted to an OD600 of 0.75. Intact or lymphadenctomised mice received 5-8 x 107 colony forming units (CFU) bacteria in 100μl PBS via oral gavage.

tag: cell type

value: CD103+ CD11b+ dendritic cells

value: intestinal lymph node


title: 904 1 CTC 2months untreated


title: BPF_2

value: human embryonic stem cells

value: BPF


title: Sample 12-1_skin_lesional_untreated


title: CD103+DC_node_steadystate_R3

source_name: CD103+ dendritic cells

value: CD103+ dendritic cells


title: Sample 11-6_skin_non-lesional_treated

value: Atopic dermatitis (AD) patient


title: CD103+DC_node_steadystate_R2


title: BPF_1

value: male


title: C57BL/6 mice treated with insulin glargine 2

city: Pamplona

first: Pedro

last: Berraondo

address: Avenida Pio XII 55

department: Program of Immunology and Immunotherapy

country: Spain

institute: Cima Universidad de Navarra

hyb_protocol: A total of 2.3μg of biotinylated cRNA was fragmented and hybridized to Affymetrix Mouse Gene 1.0 ST array

scan_protocol: Arrays were scanned with  Affymetrix GeneChip Command Console (AGCC) Software

data_processing: Background correction and normalization were done using the Robust Multichip average algorithm.

source_name: Liver from C57BL/6

label_protocol: RNA (100ng) was used for generating biotinylated cRNA through single-round amplification using the MessageAmpIII RNA Amplification kit following the manufacturer’s recommendations (Ambion, ThermoFisher Scientific Inc.).

growth_protocol: 6 week-old C57BL/6 mice

extract_protocol: 6 hours later, livers were extracted and homogenized. RNA was obtained using Maxwell 16 LEV simplyRNA purification kit (Promega Madison, WI).

treatment_protocol: We administered subcutaneously saline, Albulin (55nmol/kg), Insulin-Apo (55nmol/kg) or insulin glargine (55nmol/kg) to wild type mice

value: insulin glargine (55nmol/kg)

tag: activation time

value: 6 hours


title: C57BL/6 mice treated with insulin glargine 3


title: BPE_2

value: 21-day EB differentiation

value: BPE


title: C57BL/6 mice treated with insulin glargine 1


title: CD103+DC_node_steadystate_R1


title: C57BL/6 mice treated with saline 3

value: saline


title: Sample 11-5_skin_lesional_treated

tag: gender

value: Female

value: treated

value: Skin


title: Sample 11-3_skin_lesional_nb-UVB x 3

value: nb-UVB x 3


title: C57BL/6 mice treated with saline 2


title: C57BL/6 mice treated with saline 1


title: BPE_1


title: CD11b+DC_node_steadystate_R3

source_name: CD11b+ dendritic cells

value: CD11b+ dendritic cells


title: Sample 11-2_skin_non-lesional_untreated

value: untreated


title: C57BL/6 mice treated with insulin-apolipoprotein A-I 3

value: Insulin-Apo (55nmol/kg)


title: Sample 11-4_skin_lesional_untreated


title: BPB_2

value: human embryonic stem cells

value: BPB


title: Double+DC_node_steadystate_R1

value: CD103+ CD11b+ dendritic cells

value: intestinal lymph node


title: BPS_1

value: male

value: BPS


title: Sample 11-1_skin_lesional_untreated

value: Atopic dermatitis (AD) patient


title: C57BL/6 mice treated with insulin-apolipoprotein A-I 2

value: 6 hours


title: BPB_1

value: 21-day EB differentiation


title: CD11b+DC_node_steadystate_R1


title: Sample 10-6_skin_non-lesional_treated


title: Double+DC_duct_steadystate_R1

value: intestinal lymph duct


title: C57BL/6 mice treated with insulin-apolipoprotein A-I 1


title: BPA_1

value: BPA


title: CD103b+DC_duct_steadystate_R4

value: CD103+ dendritic cells


title: CD11b+DC_node_steadystate_R2


title: BPA_2


title: BPAF_1

value: BPAF


title: Double+DC_gut_steadystate_R2

value: small intestlnal lamina propria


title: Double+DC_gut_steadystate_R3


title: miRNA_Psedoexfoliation (PXF)

city: Bhubaneswar

first: Munmun

last: Chakraborty

state: Odisha

address: MTC campus,Patia

department: Reasearch

country: India

institute: L.V Prasad Eye Institute

description:
Control
miRNA
SAMPLE 1

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.qiagen.com/in/shop/genes-and-pathways/data-analysis-centre-overview-page/
For the normalization it uses the average of four housekeeping miRNA's: RNU6-6P, SNORD61, SNORD68 and SNORD95
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.

label: SYBR Green

source_name: Human Peripheral mononuclear cells

label_protocol: The total RNA obtained after PBMC isolation was purified of erythrocytes by PBS wash and used for miRNA extraction using the miRNA extraction kit (Qiagen, Hilden, Germany) This was reverse transcribed using the miScript II RT Kit (Qiagen) with 400ng of cDNA and later loaded onto human fibrosis/human miFinder The thermal cycling conditions used were as follows: Stage 1(1 cycle): 95°C for 15min, Stage 2 (40cycles): 94°C for 15seconds, 55°C for 30seconds and 70°C for 30seconds.

extract_protocol: PBMC was extracted using ficol and miRNA was obtained from PBMC using Trizol reagent and following steps as mentioned in Qiagen miRNeasy mini kit protocol

tag: diagnosis

value: Psedoexfoliation (PXF)

value: Blood


title: miRNA_Ocular Hypertension (OHT)

description:
Test
miRNA
SAMPLE 2

value: Ocular Hypertension (OHT)


title: miRNA_Pigmentary PXF

description:
Test
miRNA
SAMPLE 3

value: Pigmentary PXF


title: miRNA_Classical PXF

description:
Test
miRNA
SAMPLE 2

value: Classical PXF


title: Double+DC_gut_steadystate_R1

value: CD103+ CD11b+ dendritic cells

tag: strain


title: C57BL/6 mice treated with albulin 2

value: Albulin (55nmol/kg)


title: Sample 10-1_skin_lesional_untreated

value: Female

value: untreated

value: Skin


title: Sample 10-4_skin_lesional_untreated

value: Atopic dermatitis (AD) patient


title: Sample 10-2_skin_non-lesional_untreated


title: C57BL/6 mice treated with albulin 1

value: 6 hours


title: C57BL/6 mice treated with albulin 3


title: Sample 10-3_skin_lesional_nb-UVB x 3

value: nb-UVB x 3


title: BPAF_2

value: human embryonic stem cells

value: male

value: 21-day EB differentiation


title: CD103+DC_gut_steadystate_R3

value: CD103+ dendritic cells

value: small intestlnal lamina propria


title: CD103b+DC_duct_steadystate_R3

value: intestinal lymph duct


title: miRNA_Psedoexfoliation Glaucoma (PXG)

description:
Test
miRNA
SAMPLE 3

value: Psedoexfoliation Glaucoma (PXG)

value: Blood


title: miRNA_Cataract

description:
Control
miRNA
SAMPLE 1

value: cataract


title: KT365: Aorta_Female_Control_rep 5

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

institute: Rutgers NJMS

description: gene expression from KT mice, healthy renal function

hyb_protocol: Biotin labeled RNA was hybridized to the miRNA 4.0 Array (ThermoFisher Scientific, Waltham, MA, #902412, Sanger miRBase v20) for 18 hours at 48°C using an Affymetrix® 450 Hybridization Oven (Affymetrix, Santa Clara, CA).  Arrays were washed and stained on an Affymetrix® 450 Fluidics Station (Affymetrix, Santa Clara, CA), using the Applied Biosystems™ GeneChip™ Hybridization, Wash, and Stain Kit (ThermoFisher Scientific, Waltham, MA, #900720).

scan_protocol: The arrays were scanned using the Affymetrix® Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: CEL files were generated using the Affymetrix data extraction protocol in the Affymetrix GeneChip® Command Console® Software (Affymetrix, Santa Clara, CA, USA). The resulting CEL files were analyzed using the Partek Genomics Suite 7.0 (Partek Inc., St. Louis, MO), including the Robust-Multi-array Average algorithm to correct for microarray background and to normalize miRNA expression profiles on a log scale. This was followed by Partek Genomic’s ANOVA analysis to determine the miRNAs of whose abundance differed significantly between control and Klotho homozygous mutant mice. Minimal significance was defined as a p value of 0.05.

label_protocol: 400 ng of total RNA was labeled with biotin using the Applied Biosystems™ FlashTag™ Biotin HSR RNA Labeling Kit (ThermoFisher Scientific, Waltham, MA, the # 902446)

growth_protocol: Control and Klotho homozygote mice were fed regular chow and euthanized at 51 + 3.4 days of age.  After weaning, Klotho homozygotes received softened chow on the floor of the cage.

extract_protocol: RNA was extracted using the miRNeasy Mini Kit (Qiagen Inc., Germantown, MD, # 217004). The RNA quality was checked using Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: On the day of necropsy, mice were killed with an inhalation overdose of isoflurane.  Immediately thereafter, the heart was perfused via the left ventricle with phosphate buffered saline (PBS, pH 7.3), to remove excess blood. The aorta including the ascending aorta, arch and descending thoracic aorta was removed.  After cutting at the surface of the heart, the aorta was rinsed in PBS, blot dried and weighed. The aorta was snap-frozen in liquid nitrogen and stored at -80◦C.  Frozen tissues were ground in liquid nitrogen using a mortar and pestle.


title: CD103+DC_gut_steadystate_R2


title: UPR_Pseudoexfoliation Glaucoma(PXG)

description:
Test
SAMPLE 3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
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.

label: SYBR green

source_name: Human peripheral mononuclear cells

label_protocol: PCR assays was performed using the RT2 profilerUnfolded Protein Response PCR array plates  (QIAGEN) following the Manufacturer’s instructions. Reverse transcription was performed from 2.1 µg total RNA using the RT2 First Strand Kit (QIAGEN). Quantitative real-time PCR were performed (Applied Biosciences, Life Technologies) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA extraction from isolated PBMC was done with QIAzol® Lysis reagent (QIAGEN).

value: Pseudoexfoliation Glaucoma(PXG)

value: Human blood


title: KT364: Aorta_Female_Control_rep 4

description: gene expression from KT mice, diseased renal function leading to hyperphosphatemia and vascular calcification

value: Female


title: Sample 10-5_skin_lesional_treated

value: treated


title: Sample 9-5_skin_lesional_treated

value: Male

value: Skin


title: Sample 9-6_skin_non-lesional_treated

value: Atopic dermatitis (AD) patient


title: CD103+DC_gut_steadystate_R1


title: CD11b+DC_gut_steadystate_R3

value: CD11b+ dendritic cells


title: CD11b+DC_gut_steadystate_R2


title: UPR_Pseudoexfoliation(PXF)

description:
Control
SAMPLE 1

value: Pseudoexfoliation(PXF)


title: B6-093_WT_LFD_Liver

source_name: Liver

value: male

value: Liver

tag: age

value: 17 weeks

value: LFD

value: WT


title: KT358: Aorta_Female_Control_rep 3

tag: tissue

value: aorta

tag: molecule subtype

value: microRNA


title: Sample 9-3_skin_lesional_nb-UVB x 3

value: nb-UVB x 3


title: KT296: Aorta_Male_Control_rep 6

tag: Sex


title: Lsd1Δ/+ rep2

city: atlanta

first: David

middle: J

last: Katz

state: ga

address: 615 Michael st

department: Cell Biology

institute: Emory University

data_processing:
FASTQ files were quality assessed using FASTQC (v.0.11.7), trimmed using Trimmomatic (v.0.36.5) and minimum QC score of 20 and minimum read length of 36bp.
Paired-end reads were subsequently mapped to the GRCm38 genome using HISAT2 (v.2.1.0). Unmapped, unpaired and multiply mapped reads were removed using Filter SAM or BAM (v.1.1.2).
Assignment of transcripts to GRCm38 genomic features was performed using Featurecounts (v.1.6.0.6) and the Ensembl GRCm38.93 gtf file
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) ((46)). For all datasets, a cutoff of adjusted p-value < 0.1 and abs (log2 fold change) > 0.58 was applied
Genome_build: GRCm38.93
Supplementary_files_format_and_content: tab-delimited text files include raw count data for each sample

source_name: Hippocampus

extract_protocol:
hippocampi were dissected and snap frozen with liquid nitrogen in 1mL Trizol, and stored at -80°C. For RNA isolation, samples were thawed at 37°C then kept on ice prior to homogenization with Polytron homogenizer with a 5 second pulse. After a 5 minute incubation at room temperature, one tenth the sample volume of 1-bromo-3chloropropane was added, mixed by inversion and incubated for 3 minutes at room temperature. Samples were then centrifuged at 13,000 X g for 15 minutes at 4°C to separate the aqueous and organic layers. As much of the aqueous layer was recovered as possible, then RNA was precipitated with isoproponal. Pellets were then washed with 75% ethanol and resuspended in 50μL of dionized water.
RNA library preparation and sequencing were performed by HudsonAlpha Genomic Services Lab. RNA was Poly(A) selected and 300bp size selected

value: hippocampus

value: Lsd1 heterozygote


title: UPR_Classical Pseudoexfoliation(Cl PXF)

description:
Test
SAMPLE 2

label_protocol: PCR assays was performed using the RT2 profiler Fibrosis Pathway PCR array plates  (QIAGEN) following the Manufacturer’s instructions. Reverse transcription was performed from 2.1 µg total RNA using the RT2 First Strand Kit (QIAGEN). Quantitative real-time PCR were performed (Applied Biosciences, Life Technologies) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

value: Classical Pseudoexfoliation(Cl PXF)

value: Human blood


title: CD11b+DC_gut_steadystate_R1

value: small intestlnal lamina propria


title: KT357: Aorta_Female_Klotho_Homozygote_rep 2

value: Female

value: Klkl/kl


title: UPR_Pigmentary Pseudoexfoliation(Pig PXF)

description:
Test
SAMPLE 3

value: Pigmentary Pseudoexfoliation(Pig PXF)


title: KT297: Aorta_Male_Control_rep 7

value: Male

value: Kl+/kl


title: Sample 9-4_skin_lesional_untreated

value: Atopic dermatitis (AD) patient

value: untreated

value: Skin


title: Sample 9-2_skin_non-lesional_untreated


title: UPR_Cataract

description:
Control
SAMPLE 1

value: Cataract


title: Sample 9-1_skin_lesional_untreated


title: Sample 8-6_skin_non-lesional_treated

value: treated


title: stationary phase ChIP-seq

city: Taipei

first: San-Chi

last: Chang

address: 1 Sec. 4, Roosevelt Road

department: Department of Agricultural Chemistry

country: Taiwan

institute: National Taiwan University

description: IP DNA

library_source: genomic

data_processing:
Raw QC was demonstrated with CLC Genomics Workbench v9.0
Sequence reads were trimed with CLC Genomics Workbench v9.0
Transcription factor ChIP-Seq Analysis in CLC Genomics Workbench v9.0 was used for peak finding
Bedtools v2.17.0 to conduct comparison
Genome_build: Alignments made to an unpublished genome sequence. The FASTA file with the genome sequence is available on the series page.
Supplementary_files_format_and_content: Wig files for mapping and peak region.

organism: Vibrio parahaemolyticus

source_name: stationary phase (IP DNA 6h)

growth_protocol: FLAG-OpaR/VP93 was grown to late-log phase (OD600 3) and stationary phase (OD600 4.2).

extract_protocol:
ChIP DNA was then purified using the Agencourt AMPure XP PCR Purification Kit (Beckman Coulter).
Libraries for the ChIP-seq were prepared using the Ovation Ultralow library system V2 1–96 (NuGEN).

treatment_protocol: Bacterial culture was mixed with 1% formaldehyde for 20 min at 25 °C. Cross-linking was ceased using 0.5 M glycine. Lysed cells were sonicated using the Bioruptor Pico (Diagenode) for 20 cycles to generate 300 to 500 bp DNA fragment.

value: Vibrio parahaemolyticus no. 93

tag: growth phase

value: stationary

value: FLAG-OpaR


title: Sample 8-5_skin_lesional_treated


title: UPR_Ocular Hypertension(OHT)

description:
Test
SAMPLE 2

value: Ocular Hypertension(OHT)


title: PS19;Lsd1Δ/+ rep2

value: hippocampus

tag: genotype

value: PS19 tg; LSD1 +/-

value: PS19 transgene, Lsd1 heterozygote


title: KT295: Aorta_Male_Klotho_Homozygote_rep 5

value: aorta

value: microRNA


title: KT289: Aorta_Male_Klotho_Homozygote_rep 4

value: Klkl/kl


title: late-log phase ChIP-seq

description: IP DNA

source_name: late-log phase-(IP DNA 3h)

value: late-log


title: Sample 8-4_skin_lesional_untreated

tag: subject status

value: Male


title: KT278: Aorta_Male_Control_rep 5

value: Kl+/kl


title: PS19;Lsd1Δ/+ rep1

tag: treatment


title: stationary phase input

description: input

source_name: stationary phase (input 6h)


title: Sample 8-2_skin_non-lesional_untreated

value: Atopic dermatitis (AD) patient

value: untreated


title: Sample 8-3_skin_lesional_nb-UVB x 3

source_name: Skin_lesional_nb-UVB x 3

value: nb-UVB x 3

value: Skin


title: KT276: Aorta_Male_Klotho_Homozygote_rep 3


title: Sample 8-1_skin_lesional_untreated


title: PS19 rep2

value: PS19 tg ; LSD1 +/+

value: PS19 transgene


title: late-log phase input

description: input

source_name: late-log phase-(input 3h)

value: Vibrio parahaemolyticus no. 93

value: FLAG-OpaR


title: Lsd1Δ/+ rep1

value: hippocampus

value: Lsd1 heterozygote


title: PS19 rep1


title: plasma-Male-6 [M06]

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

data_processing:
Filtering and statistical analysis of the OA miRNA profiling data were performed in R/Bioconductor. Data were first filtered according to cycle threshold (Ct< 25), amplification score (AmpScore >/= 1.24) and quantification cycle confidence (Cqconf >/= 0.8) provided by the ExpressionSuite software (ThermoFisher Scientific). Only miRNAs expressed in >80% of samples were included in the study. Missing data points were imputed (Bioconductor package “Non-detects” and the data was normalised to the geometric mean (GM) as implemented in Bioconductor package “HTqPCR”. Differential expression analysis was then performed by applying a Student’s t-test to the normalized Ct values between the two conditions. The p-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg. Fold changes (FC) were calculated as FC = 2−∆Ct, where ∆Ct = CtmiRNA − GM.
the normalized.txt contains DeltaCt normalized signal.

label: FAM

source_name: plasma, Male

label_protocol: Pre-amplifications were performed and miRNA expression was quantified using TaqMan OpenArray Human miRNA Panels in the QuantStudio™ 12 K Flex Real-Time PCR system, allowing for 754 miRNAs to be quantified per sample.

extract_protocol: Plasma was obtained from the study participants, RNA was isolated using the miRNeasy Serum/Plasma kit (Qiagen) and reverse transcribed using pre-defined Megaplex™ pool RT-primers.

tag: bal total cell count (per ml)

tag: neutrophil elastase levels

tag: il-8 concentration pg/ml

tag: haemophilus spp.

value: Yes

tag: escherichia spp.

value: No

tag: staphyloccus spp.

tag: antibiotictx


title: WT rep2

value: wild type

value: control


title: WT rep1


title: plasma-Male-2 [M02]

tag: gender


title: plasma-Male-5 [M05]


title: plasma-Male-4 [M04]


title: plasma-Male-3 [M03]


title: KT272: Aorta_Female_Klotho_Homozygote_rep 1

value: aorta

value: Female

value: Klkl/kl

value: microRNA


title: KT271: Aorta_Female_Control_rep 2

value: Kl+/kl


title: KT269: Aorta_Male_Klotho_Homozygote_rep 2

value: Male


title: KT270: Aorta_Female_Control_rep 1


title: Sample 7-6_skin_non-lesional_treated

value: Atopic dermatitis (AD) patient

value: treated

value: Skin


title: KT274: Aorta_Male_Control_rep 4


title: plasma-Male-1 [M01]


title: KT268: Aorta_Male_Control_rep 2


title: plasma-Female-6 [F06]

source_name: plasma, Female


title: plasma-Female-5 [F05]


title: Female control replicate 4

city: Houston

first: Geoffrey

last: Preidis

state: TX

address: 1102 Bates Avenue

department: Gastroenterology, Hepatology & Nutrition

institute: Baylor College of Medicine

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the mm10 genome using HISAT2.
Aligned reads were quantified using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: Female control

extract_protocol:
RNA was exptracted from frozen liver tissue using the Rneasy kit from Qiagen with the Dnase treatment kit amendment.
Sequencing libraries were prepared using the Illumina Truseq stranded total RNA kit

treatment_protocol: Dams with 8-day-old pups were randomized to receive irradiated purified control diet (15% fat, 20% protein, 65% carbohydrate) or isocaloric LPLFD (5% fat, 7% protein, 88% carbohydrate) to induce malnutrition. On day-of-life 21, pups were weaned to their dams’ diet for another 5 weeks.

tag: condition

value: liver

value: 8 weeks

value: female


title: Female control replicate 5

tag: age


title: KT267: Aorta_Male_Control_rep 1

tag: tissue


title: Female control replicate 3


title: Sample 7-5_skin_lesional_treated


title: KT273: Aorta_Male_Control_rep 3

tag: molecule subtype


title: KT266: Aorta_Male_Klotho_Homozygote_rep 1

tag: Sex


title: plasma-Female-4 [F04]


title: Female control replicate 2


title: plasma-Female-3 [F03]


title: Sample 7-4_skin_lesional_untreated

value: untreated


title: Sample 7-3_skin_lesional_nb-UVB x 3

value: nb-UVB x 3


title: Female control replicate 1


title: Sample 7-1_skin_lesional_untreated


title: Female malnourished replicate 5

source_name: Female malnourished

value: malnourished


title: mouse, organoid 2

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

institute: CNAG

description: single-cell RNA-seq

data_processing:
cell_ranger-3.1.0
Genome_build: human: GRCh38-3.0.0, mouse: mm10-3.0.0
Supplementary_files_format_and_content: barcodes.tsv: cell barcodes
Supplementary_files_format_and_content: features.tsv: gene names
Supplementary_files_format_and_content: matrix.mtx: count matrix

source_name: mouse colorectal cancer

extract_protocol: none provided by the submitter

tag: cell type

value: cancer section

tag: cancer type

value: colorectal cancer

tag: protocol

value: 10X Chromium 3' RNA-seq


title: mouse, T cells

description: single-cell RNA-seq and TCR calling

value: T cells

value: 10X Chromium 5' RNA-seq + TCR


title: mouse, organoid 1

description: single-cell RNA-seq


title: Sample 7-2_skin_non-lesional_untreated

tag: subject status

value: Female

tag: treatment


title: GV16_3

first: Linqing

last: Miao

state: Beijing

address: No.5 Zhongguancun South St, Haidian District

department: Advanced Innovation Center

institute: Beijing Institute of Technology

description: MOG immunization with GV16 treatment

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include gene counts and FPKM values for each Sample

source_name: Retina

extract_protocol:
Retinas were removed and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: retina

value: 13 weeks

tag: genotype

value: wild type

value: MOG immunization with GV16 treatment


title: Female malnourished replicate 4


title: plasma-Female-1 [F01]

tag: bal total cell count (per ml)

tag: neutrophil elastase levels

tag: il-8 concentration pg/ml

tag: haemophilus spp.

value: No


title: GV16_2

description: MOG immunization with GV16 treatment


title: GV16_1

description: MOG immunization with GV16 treatment


title: Sample 6-6_skin_non-lesional_treated

value: Atopic dermatitis (AD) patient

tag: gender

value: treated

value: Skin


title: Sample 6-4_skin_lesional_untreated

value: untreated


title: Sample 6-5_skin_lesional_treated


title: Female malnourished replicate 3

tag: condition

value: liver

value: 8 weeks

value: female


title: Female malnourished replicate 1

value: malnourished

tag: age


title: Sample 6-3_skin_lesional_nb-UVB x 3

value: nb-UVB x 3

tag: tissue


title: Sample 6-2_skin_non-lesional_untreated


title: Sample 5-6_skin_non-lesional_treated

value: Male


title: GB20_3

description: MOG immunization with GB20 treatment

value: MOG immunization with GB20 treatment


title: Sample 6-1_skin_lesional_untreated

value: Female


title: Sample 5-5_skin_lesional_treated


title: Female malnourished replicate 2


title: Male control replicate 4

source_name: Male control

value: control

value: male


title: GB20_2

description: MOG immunization with GB20 treatment

value: retina

value: 13 weeks

value: wild type


title: plasma-Female-2 [F02]

value: No

tag: escherichia spp.

tag: staphyloccus spp.

value: Yes

tag: antibiotictx


title: GB20_1

description: MOG immunization with GB20 treatment


title: Male control replicate 3


title: Sample 5-4_skin_lesional_untreated

value: Atopic dermatitis (AD) patient

value: Skin


title: MOG_3

description: MOG35-55 peptide immunization

value: MOG35-55 peptide immunization


title: Sample 5-2_skin_non-lesional_untreated

value: untreated


title: Sample 5-3_skin_lesional_nb-UVB x 3


title: MDA-MB-468_MeCP2_sh3, 3-L002

city: Lubbock

first: Kevin

last: Pruitt

state: Texas

address: 3601 4th Street

department: Immunology & Molecular Microbiology

institute: Texas Tech University Health Sciences Center

description:
Lane (flow cell): L002
Samples_RPKM.xlsx
468_NTC_vs_468_MeCP2_sh3.xlsx

data_processing:
The RNA-Seq reads were normalized by RPKM and assembled by mapping reads directly to the annotated human reference genome using the DNASTAR SeqMan software (DNASTAR, Inc., Madison, WI).
Differential gene expression levels were quantified using Fisher’s Exact Test Signal Search in the DNASTAR ArrayStar software package (DNASTAR, Inc., Madison, WI).
Differentially expressed genes were filtered if they met the criterion for a two-fold change, a p-value that was less than .05 at a 95 % confidence interval.
Genome_build: GRCh38
Supplementary_files_format_and_content: Samples_RPKM.xlsx: RPKM values
Supplementary_files_format_and_content: 468_NTC_vs_468_MeCP2_sh*.xlsx: For each comparison, genes were sorted based on fold change. The results were ported into Excel spreadsheets where the log2 of the fold change for each gene was calculated.

growth_protocol: Cells were cultured in RPMI 1640 (Gibco), supplemented with 1% pen-strep and 10% fetal bovine serum from GIBCO at 37℃ in 5% CO2.

extract_protocol:
Total RNA was isolated using the Aurum™ Total RNA Mini Kit (Bio Rad).
Library preparation and sequencing were performed at Center for Biotechnology & Genomics of Texas Tech University. RNA quality was determined using RNA Screen Tape (Agilent). Ribosomal RNA depletion was achieved using NEB Next rRNA Depletion Kit (Human/Mouse/Rat) (NEB # E6310X). RNA fragmentation, double stranded cDNA and adaptor ligation was generated using NEBNext Ultra II Directional RNA Library Prep according to the manufacturer’s protocol (NEB # E7760L). PCR enriched libraries were quantified by Qubit and equimolar indexed libraries (different samples had different indexes for multiplexing) were pooled. Pooled libraries were quantitatively checked using the Agilent Tapestation 2200 and quantified using Qubit. The libraries were then diluted to 200 pM and spiked with 2% phiX libraries (Illumina control). The transcriptome sequencing was performed on the barcoded stranded RNA-Seq libraries using Illumina NovaSeq 6000 SP flow cell, paired-end reads (2 × 50 bp).

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: shRNA

value: sh3 MeCP2

tag: genotype/variation

value: MecP2 KD

tag: experimental group


title: Male control replicate 2

value: liver

value: 8 weeks


title: MDA-MB-468_MeCP2_sh3, 3-L001

description:
Lane (flow cell): L001
Samples_RPKM.xlsx
468_NTC_vs_468_MeCP2_sh3.xlsx


title: MOG_2

description: MOG35-55 peptide immunization

tag: strain

tag: genotype

tag: protocol


title: Male control replicate 1


title: Sample 5-1_skin_lesional_untreated

tag: subject status

value: Male

tag: treatment


title: Sample 4-6_skin_non-lesional_treated

tag: gender

value: treated


title: MDA-MB-468_MeCP2_sh3, 2-L002


title: Male Malnourished replicate5

source_name: Male Malnourished

tag: condition

value: malnourished

value: male


title: MOG_1

description: MOG35-55 peptide immunization

value: retina

tag: age

value: 13 weeks


title: Male Malnourished replicate4

tag: tissue


title: SHAM_3

description: sham control

value: wild type

value: sham control


title: MDA-MB-468_MeCP2_sh3, 1-L002


title: Sample 4-5_skin_lesional_treated

value: Atopic dermatitis (AD) patient


title: SHAM_2

description: sham control


title: MDA-MB-468_MeCP2_sh3, 1-L001


title: Sample 4-4_skin_lesional_untreated

value: Skin


title: Male Malnourished replicate2


title: MDA-MB-468_MeCP2_sh1, 3-L002

description:
Lane (flow cell): L002
Samples_RPKM.xlsx
468_NTC_vs_468_MeCP2_sh1.xlsx

value: sh1 MeCP2


title: Male Malnourished replicate1


title: MDA-MB-468_MeCP2_sh1, 2-L002


title: CD1_tail

city: Toronto

first: Cynthia

last: Hawkins

state: Ontario

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

description:
normal tail
123.mediastinal.vcf.gz
1327.lung.vcf.gz
161.mediastinal.vcf.gz

data_processing:
Sequencing quality was checked with FastQC
Reads were trimmed with Trimmomatic v0.32
Reads were aligned to GRCm38 v68 with bwa-mem v0.7.8, processed with GATK v.3.6.0, and duplicates marked with Picard v2.5.0.
Gene-level read counts were done with HTSeq
Somatic mutations were called with Varscan v2.3.8 and Mutect2 and annotated with SnpEFF v4.3k
Genome_build: GRCm38 v68
Supplementary_files_format_and_content: vcf files contain somatic variants per-sample

source_name: normal tail

extract_protocol:
Genomic DNA was extracted with DNeasy kit and quality verified with Bioanalyzer
SureSelect Mouse All Exon Kit (Agilent)

value: WT

tag: developmental stage

value: adult

value: normal tail


title: MDA-MB-468_MeCP2_sh1, 3-L001

description:
Lane (flow cell): L001
Samples_RPKM.xlsx
468_NTC_vs_468_MeCP2_sh1.xlsx

value: Breast cancer cell line

value: MecP2 KD


title: Sample 4-1_skin_lesional_untreated

data_processing: The data were processed with Transcriptomic Analysis Console (SST-RMA)

extract_protocol: RNA was isolated with Rneasy kit from Qiagen according to protocol

value: untreated


title: H2B-4KA-2

city: New Haven

first: Hong-Yeoul

last: Ryu

state: CT

address: 266 Whitney Ave

department: MB&B

institute: Yale

data_processing:
Low quality reads were trimmed, and adaptor contamination was removed using Trim Galore (v0.5.0).
Trimmed reads were mapped to the S. cerevisiae genome (sacCer3) using HISAT2 (v2.1.0) (Kim et al., 2015).
Gene expression levels were quantified using StringTie (v 1.3.3b) (Pertea et al., 2015) with gene models from SGD and previous ncRNA datasets (Neil et al., 2009; Xu et al., 2009).
Differentially expressed genes were identified using DESeq2 (v 1.22.1) (Love et al., 2014).
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

source_name: Yeast cells

extract_protocol:
Yeast strains, WT (MHY10244), set3Δ (MHY10869) and H2B-4KA (MHY10883), were grown in SD-Trp media until reaching mid-log phase (OD600 of 0.8 to 1.0). The 1.0 OD600 equivalent of cells was used for RNA preparation using the RNeasy Mini Kit (Qiagen, 74104). Contaminating DNA was removed from the samples using the DNA-free™ DNA Removal Kit according to the manufacturer’s protocol (Ambion, AM1906).
RNA samples were submitted to YCGA, and the libraries were constructed by YCGA protocols (https://medicine.yale.edu/keck/ycga/Images/9_tcm240-21599.pdf). The libraries underwent 101-bp paired-end sequencing using an Illumina HiSeq 2500 according to Illumina protocols.


title: WT-2


title: K358_tail

description:
normal tail
358.lymphoma.vcf.gz


title: MDA-MB-468_MeCP2_sh3, 2-L001

value: sh3 MeCP2


title: H2B-4KA-1


title: Sample 4-2_skin_non-lesional_untreated

first: Astrid

last: Lossius

address: Sognsvannsveien 20

institute: University of Oslo

value: Male


title: Sample 3-6_skin_non-lesional_treated

value: Female

value: treated


title: Sample 4-3_skin_lesional_nb-UVB x 3

value: nb-UVB x 3


title: Male Malnourished replicate3

value: malnourished

value: liver

value: 8 weeks

value: male


title: MDA-MB-468_MeCP2_sh1, 2-L001


title: Sample 3-5_skin_lesional_treated

value: Atopic dermatitis (AD) patient

value: Skin


title: MDA-MB-468_MeCP2_sh1, 1-L002

value: sh1 MeCP2


title: K358_lymphoma

description:
lymphoma
358.lymphoma.vcf.gz

source_name: lymphoma

value: adult

value: lymphoma


title: SHAM_1

description: sham control

value: retina

value: 13 weeks

value: wild type

value: sham control


title: Sample 3-4_skin_lesional_untreated

value: untreated


title: WT-1


title: set3Δ-2

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ssd1 htb1-1 htb2-1 set3<delta>::kanMX4 [pRS314-FLAG-HTB1]


title: set3Δ-1


title: KP161_lymphoma

description:
lymphoma
161.mediastinal.vcf.gz


title: K1327_lung_carcinoma

description:
lung carcinoma
1327.lung.vcf.gz

source_name: lung carcinoma

value: lung carcinoma


title: MDA-MB-468_NTC, 3-L002

description:
Lane (flow cell): L002
Samples_RPKM.xlsx
468_NTC_vs_468_MeCP2_sh1.xlsx
468_NTC_vs_468_MeCP2_sh3.xlsx

value: Breast cancer cell line

value: Non-target control (NTC)

value: WT


title: Sample 3-3_skin_lesional_nb-UVB x 3

value: Female

value: nb-UVB x 3


title: K123_lymphoma

description:
lymphoma
123.mediastinal.vcf.gz


title: Mut7

description: rawCountMatrix.txt

data_processing:
Sequencing quality was checked with FastQC
Reads were aligned to GRCm38 v68 with STAR 2.5.0 and duplicates marked with Picard v2.5.0
Gene-level read counts were done with HTSeq
Genome_build: GRCm38 v68
Supplementary_files_format_and_content: rawCountMatrix.txt contains raw gene-level counts

source_name: brain

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy kit and sample quality confirmed with Bioanalyzer.
TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold

value: mid/hind-brain


title: IP-Set3-TAP-WT-1

data_processing:
ChIP-seq reads were trimmed using the Trim Galore (v0.5.0; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors
The trimmed reads were then aligned to aligned to the yeast reference genome (sacCer3) using BWA (v0.7.17) (Li 2013).
Peaks were called using MACS2 (v2.1.1) (Feng, Liu et al. 2012)
The normalized bedGraph files were generated using MACS2 ("-B --SPMR") and then converted to bigwig files using the bedGraphToBigWig program downloaded from the website of UCSC Genome Browser.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig

extract_protocol:
ChIP experiments were performed as described previously (Ryu & Ahn, 2014; Ryu et al, 2016). TAP-tagged Set3 proteins were precipitated with IgG-Sepharose beads (GE Healthcare, 17-0969-01). Formaldehyde was added to a final concentration of 1% for 20 min. Cross-linking was quenched by addition of glycine to 240 mM. Cells were collected by centrifugation, washed in 1× TBS, and lysed with glass beads in FA lysis buffer (50 mM HEPES-KOH at pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS, 1 mM PMSF). Chromatin was sheared by sonication, therefore the average fragment size was between 200 and 700 bp.
Approximately 5-10 ng of DNA is cleaned up using Ampure XP SPRI beads (Beckman Coulter Genomics). The DNA is then end-repaired, A-tailed, adapter ligated and PCR enriched (8-10 cycles) using the KAPA Hyper Library Preparation kit (KAPA Biosystems, Part#KK8504). Indexed libraries that meet appropriate cut-offs are quantified by qPCR using the Library Quantification Kit (KAPA Biosystems, Part#KK4854) and inserts size distribution by using the Caliper LabChip GX system. Samples with a yield of ≥0.5 ng/l are used for sequencing.

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ssd1 htb1-1 htb2-1 SET3-TAP::HIS3MX6 [pRS314-FLAG-HTB1]

tag: chip antibody


title: IP-Set3-TAP-H2B 4KA-2

value: IgG-Sepharose beads (GE Healthcare, 17-0969-01)


title: IP-Set3-TAP-H2B 4KA-1


title: MDA-MB-468_NTC, 2-L001

description:
Lane (flow cell): L001
Samples_RPKM.xlsx
468_NTC_vs_468_MeCP2_sh1.xlsx
468_NTC_vs_468_MeCP2_sh3.xlsx


title: Sample 3-1_skin_lesional_untreated

value: Atopic dermatitis (AD) patient

value: Skin


title: MDA-MB-468_NTC, 2-L002


title: MDA-MB-468_NTC, 1-L001


title: INPUT-Set3-TAP-WT-1


title: WT5

description: rawCountMatrix.txt


title: MDA-MB-468_MeCP2_sh1, 1-L001

value: sh1 MeCP2

value: MecP2 KD


title: MDA-MB-468_NTC, 1-L002


title: Sample 2-5_skin_lesional_treated

value: treated


title: Mut6

description: rawCountMatrix.txt


title: INPUT-Set3-TAP-WT-2


title: INPUT-Set3-TAP-H2B 4KA-2


title: Sample 3-2_skin_non-lesional_untreated


title: IP-Set3-TAP-WT-2


title: WT4

description: rawCountMatrix.txt

value: wild type


title: Sample 2-6_skin_non-lesional_treated


title: WT6

description: rawCountMatrix.txt


title: ovarian

description: single-cell RNA-seq

source_name: ovarian cancer

value: cancer section

tag: cancer type

value: ovarian adenocarcinoma

value: 10X Chromium 3' RNA-seq


title: Sample 2-1_skin_lesional_untreated

value: untreated


title: MDA-MB-468_NTC, 3-L001

tag: cell line

value: Breast cancer cell line

value: Non-target control (NTC)


title: Mut5

description: rawCountMatrix.txt


title: Sample 2-4_skin_lesional_untreated

value: Female


title: Sample 2-2_skin_non-lesional_untreated


title: liver metastasis, patient 2, CD45 enriched

description: single-cell RNA-seq

source_name: liver metastasis

tag: cell type

value: cancer section, CD45+ enriched

value: liver metastasis from uveal melanoma


title: T09_2

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

data_processing:
Clustering and sequencing (Novogene Experimental Department):The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500  platform ( GPL17021)  and 125 bp/150 bp paired-end reads were generated
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20,Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level:HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis:Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
Supplementary_files_format_and_content: Excel, fastq

source_name: Gut, duodenum

extract_protocol:
RNA quantification and qualification: RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA,USA) .RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer(Life Technologies, CA, USA).RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: duodenum

value: T09- 50mg/kg/day

value: 8-12wks of age


title: Sample 1-6_skin_non-lesional_treated

value: Atopic dermatitis (AD) patient

value: Male

value: Skin


title: INPUT-Set3-TAP-H2B 4KA-1


title: uveal melanoma

description: single-cell RNA-seq

source_name: uveal melanoma cancer

value: uveal melanoma


title: T09_3


title: IP-HA-SUMO-H2B-WT-2

data_processing:
ChDIP-seq reads were trimmed using the Trim Galore (v0.5.0; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors
The trimmed reads were then aligned to aligned to the yeast reference genome (sacCer3) using BWA (v0.7.17) (Li 2013).
Peaks were called using MACS2 (v2.1.1) (Feng, Liu et al. 2012)
The normalized bedGraph files were generated using MACS2 ("-B --SPMR") and then converted to bigwig files using the bedGraphToBigWig program downloaded from the website of UCSC Genome Browser.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig

extract_protocol:
ChDIP assays were carried out as described previously (Nathan et al., 2006; Ryu et al., 2019). Preparation of chromatin fragments and elution steps were performed as described above for ChIP experiments. After overnight immunoprecipitation with anti-Flag agarose beads (Sigma, A2220) at 4°C, elution was performed with triple-Flag peptide (Sigma, F3290). While 5% of the elute was used as INPUT, the remaining 95% was incubated with anti-HA-conjugated agarose (Thermo Scientific, 26182) overnight at 4°C and then washed with FA lysis buffer four times. N-ethylmaleimide (NEM; Sigma, E3876) was added to buffers at a final concentration of 20 mM to prevent SUMO deconjugation.
Approximately 5-10 ng of DNA is cleaned up using Ampure XP SPRI beads (Beckman Coulter Genomics). The DNA is then end-repaired, A-tailed, adapter ligated and PCR enriched (8-10 cycles) using the KAPA Hyper Library Preparation kit (KAPA Biosystems, Part#KK8504). Indexed libraries that meet appropriate cut-offs are quantified by qPCR using the Library Quantification Kit (KAPA Biosystems, Part#KK4854) and inserts size distribution by using the Caliper LabChip GX system. Samples with a yield of ≥0.5 ng/l are used for sequencing.
ChDIP-seq

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ssd1 htb1-1 htb2-1 smt3<delta>::HIS3 [pRS314-FLAG-HTB1, pRS425-GPD-HA-SMT3]


title: Sample 1-5_skin_lesional_treated

value: treated


title: IP-HA-SUMO-H2B-WT-1

value: anti-HA-conjugated agarose (Thermo Scientific, 26182)


title: T09_1


title: liver metastasis, patient 1, CD45 enriched

description: single-cell RNA-seq

value: 10X Chromium 3' RNA-seq


title: Vehicle4

value: Vehicle 0.5% Carboxy-methylcellulose


title: IP-HA-SUMO-H2B-set1-2

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ssd1 htb1-1 htb2-1 smt3<delta>::HIS3 set1<delta>::kanMX4 [pRS314-FLAG-HTB1, pRS425-GPD-HA-SMT3]


title: liver metastasis, patient 1

description: single-cell RNA-seq

value: cancer section


title: Vehicle3


title: IP-HA-SUMO-H2B-set1-1


title: Sample 2-3_skin_lesional_nb-UVB x 3

source_name: Skin_lesional_nb-UVB x 3

value: Female

value: nb-UVB x 3


title: Inu_6

city: Davis

first: saumya

last: wickramasibnghe

address: One Shields AVE

department: Food Science and Technology

institute: University of California Davis

description: DNAse reated totla RNA

data_processing:
Demultiplexed sequence files were processed using the CLC-Bio Genomics Workbench (CLC Bio, Denmark). Reads were trimmed (maximum of 2 ambiguous base pairs) and deleted if the quality scores were below 0.5
Edited reads were aligned to fasta files generated for L.agilis YZ050 genome at IMG
Reads Per Kilobase per Million mapped reads (RPKM) values were automatically calculated by CLC-Bio Genomics Workbench by using information on the gene length, total and unique gene reads aligning to a specific locus tag.
Genome_build: L.agilis YZ050 genome at IMG
Supplementary_files_format_and_content: Matrix table with raw gene counts and RPKM for every gene and every sample

organism: Ligilactobacillus agilis

source_name: Bacterial cells

growth_protocol: Ligilactobacillus agilis inoculated into basal MRS media supplemented with 1% inulin or 1% glucose in five biological replicates, sample collection at mid log phase

extract_protocol:
Bacterial cells were immediately pelleted and resuspended in 1ml of RNAprotect Bacteria Reagent. Cells were pre-lysed  lysozyme and mutanolysin. Then, Total RNA is extracted using the RNeasy mini kit (Qiagen Inc, Valencia). Total RNA samples were DNase treated twice .Ribosomal RNA depletion was carried using RiboMinus Transcriptome Isolation Kit, bacteria (Thermo Fisher, Waltham, MA) on 1 μg of total RNA.
Barcode indexed RNA-seq libraries were generated from 20 ng ribo-depleted RNA using the Kapa Hyper Stranded RNA-seq kit (KapaBiosystems, Cape Town, South Africa)

treatment_protocol: treatment is MRS medai supplemented with 1% inulin, control is MRA media supplemented with 1% glucose

value: Grown on 1% Inulin


title: INPUT-Flag-H2B-WT-2

value: anti-Flag agarose beads (Sigma, A2220)


title: brain metastasis

description: single-cell RNA-seq and TCR calling

source_name: brain metastasis

value: CD45+ and CAFs

value: glioblastoma metastasis from NSCLC

value: 10X Chromium 5' RNA-seq + TCR


title: Sample 1-4_skin_lesional_untreated

value: Atopic dermatitis (AD) patient

value: Male

value: untreated


title: Inu_5

description: DNAse reated totla RNA


title: Vehicle2

value: duodenum

value: 8-12wks of age


title: U2OS_M_rep2

city: Urbana

first: Prasanth Kumar

middle: Vijayan

last: Kannanganattu

state: Illinois

address: 601S, Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

description: M

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
RNA-seq reads were aligned to human reference genome GRCh38 assembly using HISAT2
raw gene counts were first analyzed by HTSEQ-Count
Genome_build: GRCh38
Supplementary_files_format_and_content: Individual files include gene count information are presented in txt format

source_name: U2OS cells

growth_protocol: U2OS cells were grown in DMEM, high glucose medium with 10% FBS.

extract_protocol:
Total RNA was extracted using TRNaeasy minikit from Qiagen
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), polyadenylated mRNAs were captured with oligodT beads.

treatment_protocol: Cells were synchronized to mitosis by treatment with 50 ng/ml nocodazole for 12 hr. To collect cells in G1 phase, mitotic cells were shaken off and released in fresh medium for 3.5 hr. G1/S-boundary, S-phase and G2-phase samples were collected by double thymidine block and release. G1/S samples were collected after the second block. Cells were then released in fresh medium for 4 hr to be collected as S-phase samples and 8 hr to be collected as G2-phase samples.

value: M synchronised cell


title: Sample 1-3_skin_lesional_nb-UVB x 3

value: Skin


title: INPUT-Flag-H2B-WT-1

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ssd1 htb1-1 htb2-1 smt3<delta>::HIS3 [pRS314-FLAG-HTB1, pRS425-GPD-HA-SMT3]


title: Vehicle1

value: Vehicle 0.5% Carboxy-methylcellulose


title: Inu_3

description: DNAse reated totla RNA


title: INPUT-Flag-H2B-set1-2

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 ssd1 htb1-1 htb2-1 smt3<delta>::HIS3 set1<delta>::kanMX4 [pRS314-FLAG-HTB1, pRS425-GPD-HA-SMT3]


title: U2OS_G2_rep2

value: G2 synchronised cell


title: Sample 1-1_skin_lesional_untreated


title: INPUT-Flag-H2B-set1-1


title: liver metastasis, patient 2

description: single-cell RNA-seq

value: cancer section

value: liver metastasis from uveal melanoma

value: 10X Chromium 3' RNA-seq


title: Inu_2

description: DNAse reated totla RNA

value: Grown on 1% Inulin


title: Inu_1

description: DNAse reated totla RNA


title: U2OS_G2_rep1


title: U2OS_S_rep2

description: S

value: S synchronised cell


title: Glu_6

description: DNAse reated totla RNA

value: Grown on 1% glucose


title: nrl-KO

city: Wuhan

first: Fei

last: Liu

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
The scRNA-seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome (GRCz11 from Ensembl), generate feature-barcode matrices, and perform clustering and gene expression analysis.
Seurat (Butler, et al., 2018) was used for quality control, gene expression normalization, principal component analysis (PCA), and cell clustering. In brief, cells with a clear outlier number of genes (potential multiplets) and a high percentage of mitochondrial genes (potential dead cells) were excluded by “FilterCells” function. A global-scaling normalization method “LogNormalize” was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs, a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p-value genes were used to identify the unsupervised cell clusters. t-SNE (t-distributed Stochastic Neighbor Embedding) was used to visualize and explore the distribution of cells in a low-dimensional space (2D-plot).
For every single cluster, differentially expressed genes (up-regulated) were identified by the likelihood-ratio test using “FindAllMarkers” function in Seurat package, compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram.
GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes.
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts for every gene and cell in WT group
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts for every gene and cell in nrl-KO group
Supplementary_files_format_and_content: Tab-delimited text files showing the cell clustering results
Supplementary_files_format_and_content: Tab-delimited text files showing the marker genes for each cell cluster

organism: Danio rerio

source_name: Retinal single-cell suspension

extract_protocol:
Three retinas from WT and nrl-KO zebrafsih were dissociated. The single-cell suspensions were examined to ensure compliance with the requirements, and then loaded onto the 10x Genomics Chromium Single Cell system using the 3' Reagent Kits (v3 chemistry). Approximately 10,000 live cells were loaded per sample.
Single-cell GEM generation, barcoding, and libraries preparation were performed according to the user guides.

value: Retinal single-cell suspension

value: AB

value: 5 months post fertilization

value: nrl-KO


title: WT

value: wild type


title: U2OS_S_rep1

description: S


title: nrl-R2

data_processing:
Quality control, mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The high-quality clean data were generated by Trimmomatic (v0.30) and aligned to the reference genome of zebrafish via software Hisat2 (v2.0.1).
Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq (v0.6.1). Differential expression analysis was performed by DESeq Bioconductor package. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, the threshold of p-values was set to <0.05 to detect differentially expressed genes.
GO and KEGG enrichment analysis: GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG), which was used to enrich significant differential expression gene in KEGG pathways.
Genome_build: GRCz11 from Ensembl
Supplementary_files_format_and_content: Tab-delimited text files including the raw counts and FPKM values for each Sample
Supplementary_files_format_and_content: Tab-delimited text files showing the foldchanges and p-values of the differentially expressed genes

source_name: Retina

extract_protocol:
For each RNA sample, three eyes (lens removed) from different zebrafish were homogenized in RNAiso Plus reagent (Takara, Cat# 9108). Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies) and NanoDrop (Thermo Fisher Scientific). RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA-seq.
The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.

value: Retina

value: 2 months post fertilization


title: Glu_3

description: DNAse reated totla RNA


title: Glu_5

description: DNAse reated totla RNA


title: WT-R2


title: U2OS_G1S_rep1

value: G1/S synchronised cell


title: Glu_2

description: DNAse reated totla RNA


title: U2OS_G1_rep2

value: G1 synchronised cell


title: U2OS_M_rep1

description: M

value: M synchronised cell


title: WT-R1


title: Sample 1-2_skin_non-lesional_untreated

value: Atopic dermatitis (AD) patient

value: Male

value: untreated

value: Skin


title: SHR8

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

description: Gene expression data from SK-ES1 shRING1B cell line

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Ewing sarcoma cell line

label_protocol: 30ng of total RNA from each sample was processed and labelled according to manuals GeneChip  WT PLUS Reagent kit (P/N 703174 Rev. 2) (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: RNA was extracted following Qiagen protocol

value: Ewing sarcoma cell line

tag: type

value: RI


title: SHR6


title: SHR4

description: Gene expression data from A673 shRING1B cell line


title: SHR5

description: Gene expression data from SK-ES1 shGFP cell line

value: GI

value: shGFP


title: SHR7


title: SHR3

description: Gene expression data from A673 shGFP cell line


title: nrl-R1

value: AB


title: SHR2


title: U2OS_G1_rep1


title: U2OS_G1S_rep2


title: SHR1


title: UKN1_sat_a_VPA_4mM_D12_32NS_202

status: Public on Oct 26 2020

city: Berlin

first: Johannes

last: Meisig

address: Chariteplatz 1

department: Institut für Pathologie

country: Germany

institute: Charite Universitätsmedizin

description: Gene expression data from H9 human embryonic stem cells

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: Microarrays were analyzed using RMA (Robust Multi-array Analysis) as available in the bioconductor R  package oligo

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 4mM VPA from 96-144h

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer

growth_protocol: According to Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).

extract_protocol: Total RNA has  been isolated with  Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

treatment_protocol: H9 hESCs were differentiated for up to 6 days in the presence and absence of valproic acid into neuroepithelia progenitors (NEP)  (Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).

value: female

tag: state

value: differentiated state

value: H9 human embryonic stem cells


title: UKN1_sat_a_VPA_2mM_D12_32NS_203

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 2mM VPA from 96-144h


title: UKN1_sat_a_untr_D12_31NS_200

source_name: hESCs have been incubated with culturing medium for 144h


title: UKN1_sat_a_untr_D12_TW_212


title: UKN1_sat_a_VPA_0,6mM_D12_31NS_199

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 0.6mM VPA from 96-144h


title: UKN1_sat_a_VPA_0,6mM_D12_32NS_205


title: UKN1_sat_a_untr_D12_32NS_206


title: UKN1_sat_a_VPA_1mM_D12_TW_210

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 1mM VPA from 96-144h


title: UKN1_sat_a_VPA_2mM_D12_TW_209


title: UKN1_sat_a_VPA_4mM_D12_TW_208


title: UKN1_sat_a_VPA_5mM_D12_TW_207

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 5mM VPA from 96-144h


title: UKN1_sat_a_VPA_1mM_D12_32NS_204


title: Dreser_4.9

source_name: hESCs have been incubated with 0.6 mM VPA for 144h


title: Dreser_4.3

source_name: hESC maintenance culture

value: undifferentiated


title: Dreser_4.6

source_name: hESCs have been incubated with 0.6 mM VPA for 72h


title: UKN1_sat_a_VPA_4mM_D12_31NS_196


title: UKN1_sat_a_VPA_0,6mM_D12_TW_211


title: Dreser_4.2

source_name: hESCs have been incubated with culturing medium for 72h


title: Dreser_3.11

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 0.6mM VPA from 24-72h


title: UKN1_sat_a_VPA_5mM_D12_31NS_195


title: Dreser_3.12

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 0.6mM VPA from 72-144h


title: Dreser_4.1


title: UKN1_sat_a_VPA_1mM_D12_31NS_198


title: UKN1_sat_a_VPA_2mM_D12_31NS_197


title: Dreser_4.11


title: Dreser_4.10

source_name: hESCs have been incubated with culturing medium for 144h and were exposed to 0.6mM VPA from 24-96h


title: Dreser_3.10


title: UKN1_sat_a_VPA_5mM_D12_32NS_201


title: Dreser_3.9

source_name: hESCs have been incubated with 0.6 mM VPA  for 144h


title: Dreser_2.12


title: Dreser_2.7

source_name: hESCs have been incubated with 0.6 mMVPA for 96h


title: Dreser_3.7


title: Glu_1

description: DNAse reated totla RNA

source_name: Bacterial cells

value: Grown on 1% glucose


title: Dreser_3.6

source_name: hESCs have been incubated with 0.6 mMVPA for 72h


title: Dreser_3.4_2

source_name: hESCs have been incubated with 0.6 mMVPA for 24h


title: Dreser_3.2


title: Dreser_3.5

source_name: hESCs have been incubated with 0.6 mMVPA for 48h


title: Dreser_2.11


title: Dreser_3.3


title: Dreser_3.1

source_name: hESCs have been incubated with culturing medium for 144h


title: Dreser_2.9


title: Dreser_2.6


title: Dreser_2.4


title: Dreser_2.1


title: Dreser_1.11


title: Dreser_2.10


title: Dreser_2.5


title: Dreser_1.6


title: Dreser_1.10


title: UKN1_sat_c_untr_D12_27NS_170


title: Dreser_1.3


title: Dreser_1.9


title: Dreser_2.2


title: Dreser_2.3


title: UKN1_sat_c_untr_D12_25NS_168


title: UKN1_sat_c_untr_D12_27NS_167


title: UKN1_sat_c_untr_D12_26NS_169


title: Dreser_1.2


title: Dreser_1.1


title: UKN1_sat_c_untr_D12_25NS_165

source_name: hESCs have been incubated with 0.025 mM VPA for 144h


title: UKN1_sat_c_VPA_25muM_D12_26NS_163


title: UKN1_sat_c_VPA_25muM_D12_25NS_162


title: UKN1_sat_c_untr_D12_26NS_166


title: UKN1_sat_c_VPA_25muM_D12_27NS_164


title: UKN1_sat_c_VPA_350muM_D12_26NS_157

source_name: hESCs have been incubated with 0.35 mM VPA for 144h


title: UKN1_sat_c_VPA_150muM_D12_26NS_160

source_name: hESCs have been incubated with 0.15 mM VPA for 144h


title: UKN1_sat_c_VPA_350muM_D12_27NS_158


title: UKN1_sat_c_VPA_550muM_D12_26NS_151

source_name: hESCs have been incubated with 0.55 mM VPA for 144h


title: UKN1_sat_c_VPA_450muM_D12_27NS_155

source_name: hESCs have been incubated with 0.45 mM VPA for 144h


title: UKN1_sat_c_VPA_150muM_D12_27NS_161


title: UKN1_sat_c_VPA_650muM_D12_25NS_147

source_name: hESCs have been incubated with 0.65 mM VPA for 144h


title: UKN1_sat_c_VPA_450muM_D12_25NS_153


title: UKN1_sat_c_VPA_800muM_D12_26NS_145

source_name: hESCs have been incubated with 0.8 mM VPA for 144h


title: UKN1_sat_c_VPA_1000muM_D12_25NS_141

source_name: hESCs have been incubated with 1 mM VPA for 144h


title: UKN1_sat_c_VPA_1000muM_D12_26NS_142


title: UKN1_sat_c_VPA_1000muM_D12_27NS_143


title: UKN1_sat_c_VPA_550muM_D12_25NS_150


title: UKN1timecourse_ND_72h_Exp4

source_name: hESCs have been incubated with culturing medium for 72h


title: UKN1_sat_c_VPA_800muM_D12_27NS_146


title: UKN1_sat_c_VPA_350muM_D12_25NS_156


title: UKN1_sat_c_VPA_150muM_D12_25NS_159


title: UKN1_sat_c_VPA_550muM_D12_27NS_152


title: UKN1_sat_c_VPA_650muM_D12_27NS_149


title: UKN1timecourse_ND_120h_Exp4

source_name: hESCs have been incubated with culturing medium for 120h


title: UKN1_sat_c_VPA_650muM_D12_26NS_148


title: UKN1_sat_c_VPA_450muM_D12_26NS_154


title: UKN1timecourse_ND_144h_Exp4


title: UKN1timecourse_ND_96h_Exp4

source_name: hESCs have been incubated with culturing medium for 396h


title: UKN1timecourse_ND_48h_Exp4

source_name: hESCs have been incubated with culturing medium for 48h


title: UKN1_sat_c_VPA_800muM_D12_25NS_144


title: UKN1timecourse_ND_36h_Exp4

source_name: hESCs have been incubated with culturing medium for 36h


title: UKN1timecourse_ND_16h_Exp4

source_name: hESCs have been incubated with culturing medium for 16h


title: UKN1timecourse_ND_60h_Exp4

source_name: hESCs have been incubated with culturing medium for 60h


title: UKN1timecourse_ND_6h_Exp4

source_name: hESCs have been incubated with culturing medium for 6h


title: UKN1timecourse_ND_0h_Exp4

source_name: hESCs have been incubated with culturing medium for 0h


title: UKN1timecourse_ND_72h_Exp3


title: UKN1timecourse_ND_d-3_Exp4

source_name: hESC maintenance culture


title: UKN1timecourse_ND_120h_Exp3


title: UKN1timecourse_ND_3h_Exp4

source_name: hESCs have been incubated with culturing medium for 3h


title: UKN1timecourse_ND_10h_Exp4

source_name: hESCs have been incubated with culturing medium for 10h


title: UKN1timecourse_ND_24h_Exp4

source_name: hESCs have been incubated with culturing medium for 24h


title: UKN1timecourse_ND_24h_Exp3


title: UKN1timecourse_ND_16h_Exp3


title: UKN1timecourse_ND_144h_Exp2

source_name: hESCs have been incubated with culturing medium for 144h


title: UKN1timecourse_ND_48h_Exp3


title: UKN1timecourse_ND_120h_Exp2


title: UKN1timecourse_ND_10h_Exp3


title: UKN1timecourse_ND_0h_Exp3


title: UKN1timecourse_ND_144h_Exp3


title: UKN1timecourse_ND_36h_Exp2


title: UKN1timecourse_ND_36h_Exp3


title: UKN1timecourse_ND_6h_Exp3


title: UKN1timecourse_ND_96h_Exp3


title: UKN1timecourse_ND_60h_Exp3


title: UKN1timecourse_ND_3h_Exp3


title: UKN1timecourse_ND_d-3_Exp3


title: UKN1timecourse_ND_10h_Exp2


title: UKN1timecourse_ND_16h_Exp2


title: UKN1timecourse_ND_60h_Exp2


title: UKN1timecourse_ND_48h_Exp2


title: UKN1timecourse_ND_3h_Exp2


title: UKN1timecourse_ND_0h_Exp2


title: UKN1timecourse_ND_6h_Exp2


title: UKN1timecourse_ND_96h_Exp2


title: UKN1timecourse_ND_24h_Exp2


title: UKN1timecourse_ND_72h_Exp2


title: SEM_Input_BRD4_DMSO90

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling and annotation using Homer v4.7

source_name: ChIP seq Input for BRD4 in DMSO-treated SEM cells

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (EZH2). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

value: Leukemia cell line (SEM)

value: DMSO for 90 min

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

value: input


title: SEM_Input_MED26

source_name: ChIP seq Input for MED26 in SEM cells


title: SEM_BRD4_DMSO90

source_name: BRD4 ChIP-seq in DMSO-treated SEM cells


title: SEM_MED12

source_name: MED12 ChIP-seq in SEM cells


title: SEM_MED26

source_name: MED26 ChIP-seq in SEM cells


title: SEM_Input_BRD2_BRD3

source_name: ChIP seq Input for BRD2 and BRD3 in SEM cells


title: SEM_BRD3

source_name: BRD3 ChIP-seq in SEM cells


title: UKN1timecourse_ND_24h_Exp1


title: UKN1timecourse_ND_48h_Exp1

source_name: hESCs have been incubated with culturing medium for 48h


title: UKN1timecourse_ND_120h_Exp1

source_name: hESCs have been incubated with culturing medium for 120h


title: UKN1timecourse_ND_96h_Exp1

source_name: hESCs have been incubated with culturing medium for 396h


title: UKN1timecourse_ND_36h_Exp1

source_name: hESCs have been incubated with culturing medium for 36h


title: SEM_BRD2

source_name: BRD2 ChIP-seq in SEM cells


title: UKN1timecourse_ND_72h_Exp1

source_name: hESCs have been incubated with culturing medium for 72h