title: X12hUSA500phoU23

city: Shanghai

first: Yongpeng

last: Shang

address: Zhidao building, Dong'an road, Xuhui district

department: Department of Medical Microbiology And Parasitotology

institute: Fudan University

description: phoU2 deletion strain_rep3

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:S. aureus USA500 2395）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: NZ_CP007499.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Staphylococcus aureus

source_name: staphylococcus aureus

growth_protocol: In brief, S. aureus and derivative strains were diluted 1:200 into 20 mM TSB and incubated at 37°C. At the 4 h and 12 h, 8 ml bacteria were collected at 6,000 rpm and washed twice times with cold saline. With 0.5 ml 0.1-mm Zirconia-silica beads, cells were homogenized 5 rounds using Mini-Bead beater (Biospec, Bartlesville, OK, USA) at 4,800 rpm for 1 min, and cooling on ice for 1 min. Then the samples were centrifuged at 12,000 rpm, and RNA in the supernatant was extracted using the silica-based filter of Neasy Mini kit.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: staphylococcus aureus

value: grown for 12h

tag: genotype


title: WTQ_12wk_3mice_L2409

status: Public on Oct 19 2019

type: SRA

city: La Jolla

first: Theresa

last: Gaasterland

state: CA

address: 9600 Gilman Drive MS 0202

department: Scripps Institution of Oceanography

country: USA

institute: University of California San Diego

description: SCA7 repeat length, normal

library_source: transcriptomic

data_processing:
RNAseq: For each condition, combine 3 fastq files; reducing 12 files to 4 files (Unix "cat" command)
POOLED RNAseq: alignment to reference mm10 mouse genome (mm10 downloaded 8/21/2014; mapped with bowtie v0.12.7, up to 3 mismatches, 1 match site allowed)
POOLED RNAseq: sam output files converted to bam format (samtools view, sort, index commands; samtools 0.1.12a)
POOLED RNAseq: generated readcounts per sample, normalized by millions-of-reads-per-sample (cuffdiff v1.3.0)
POOLED RNAseq: extracted normalized readcounts for each sample into one table (boutique scripts)
POOLED RNAseq: set aside ncRNA, miRNA, rRNA genes, zero signal, low signal (boutique scripts)
POOLED RNAseq: calculated log2 ratios for pairwise comparisons: 12wk WTQ vs 92Q; 29wk WTQ vs 92Q (boutique scripts)
POOLED RNAseq: identified differential patterns, WTQ vs 98Q, across 2 time points (boutique scripts)
Genome_build: mm10 (downloaded 8/21/2014)
Supplementary_files_format_and_content: format: tab-separated txt; content: columns: geneID, normalized readcounts per pooled sample

molecule: total RNA

organism: Mus musculus

source_name: cerebellum

growth_protocol: Standard mouse colony conditions

extract_protocol:
Total RNA from the cerebellum of fxSCA7 92Q mice and wild-type littermates aged 12 and 29 weeks (n=3 per group) was isolated using TRIzol (Life Technologies) and purified using an RNeasy kit (Qiagen).  Samples were then sent to BGI Americas for deep sequencing on the Illumina HiSeqTM 2000 system (50SE).
Illumina TruSeq for RNA

tag: genotype/variation

value: wild type

tag: timepoint

value: 12 weeks

tag: pool

value: 3 mice


title: X12hUSA500phoU21

country: China

description: phoU2 deletion strain_rep1

tag: tissue

tag: age


title: SCNT_KDM5B_8C_replicate 1

city: Yangling

first: Chuan

last: Zhou

state: Shaanxi

address: 3 Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
bcl2fastq2 Conversion software (v2.16) was used for basecalling with the parameters bcl2fastq2-v2.16/bin/bcl2fastq --input-dir <runfolder-dir>/Data/Intensities/BaseCalls/ --output-dir <output-dir> --use-bases-mask Y*,Y*,Y*,Y*
Noise reads were removed in raw reads followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 20 is greater than 50% in a read).
The filtered reads were stored in FASTQ format and mapped with HISAT (v0.1.6-beta) to the bovine UMD3.1.1 reference genome with the parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
We used StringTie (v1.0.4) to reconstruct transcripts, and used CuffCompare (v2.2.1) to compare reconstructed transcripts to reference annotation. We then selected  'u','i','o','j' class code types as novel transcripts, and used CPC (v0.9-r2) to predict coding potential of novel transcripts. Complete reference consisted of coding novel   transcripts and reference transcripts.
Clean reads were mapped to the complete reference using Bowtie2 (v2.2.5). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) using RSEM (v1.2.12).
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript in different samples.

organism: Bos taurus

source_name: SCNT KDM5B eight-cell embryos

extract_protocol:
BFFs were digested with trypsin and washed three times with PBS. After centrifugation, the supernatant was discarded and the cell precifitate was stored at -80°C. Pools of 8 eight-cell embryos were washed in RNase-free PBS, then transferred into the lysis buffer immediately on ice. Samples were then centrifuged at 10000 rpm for 30 s at 4°C, and stored at -80°C.
Embryos for each sample were directly lysed and used for cDNA synthesis using SuperScript III (Thermo Fisher Scientific). cDNAs were amplified and fragmented with the NEBNext Ultra DNA Library Prep Kit (E7370, New England Biolabs) to construct  cDNA library. RNA sequencing was performed on the HiSeq4000 (Illumina) platform.

tag: breed

value: Holstein

tag: sample group

value: SCNT embryos

value: KDM5B overexpression

tag: tissue/cell type

value: eight-cell embryos


title: SCNT_8C_replicate 3

source_name: SCNT eight-cell embryos


title: X12hUSA500phoU13

description: phoU1 deletion strain_rep3


title: Scid.adh.2c2_FA_1%input-rep1

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

country: Japan

institute: Tokai University School of Medicine

library_source: genomic

data_processing:
ChIP-seq data were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.    RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).  Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf.  The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with –keepAll setting).  For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED-files  All genomic coordinates are relative to mm9 mouse assembly.

molecule: genomic DNA

source_name: Scid.adh.2c2 cells

growth_protocol: Scid.adh.2c2 cells (Dionne et al., 2005) were cultured in RPMI1640 with 10% fetal bovine serum (FBS, Sigma-Aldrich), sodium pyruvate (Gibco), non-essential amino acids (Gibco), Pen-Strep-Glutamine (Gibco) and 50 mM b-mercaptoethanol (Sigma-Aldrich).   An ILC2 cell line, ILC2/b6 (Zhang et al., 2017) was cultured in OP9 medium (a-MEM, 20% FBS, 50 mM b-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of IL-2, IL-7 and IL-33 (Pepro Tech Inc.).

extract_protocol:
ChIP-seq; Ten million of ILC2/b6 or Schd.adh.2c2 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Five μg per 107 cells of anti-Bcl11b Abs (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)), anti-Runx3 (kindly provided from Dr. Ditsa Levanon and Dr. Yoram Groner, Weizmann Institute of Science), anti-GATA3 (a mixture of sc-268, Santa Cruz and MAB26051, R&D) or anti-Runx1 (ab23980, Abcam) were hybridized to Dynabeads anti-Rabbit, Dynabeads anti-Mouse or Dynabeads Protein A/G (Invitrogen) and added to the diluted chromatin complex.  They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg/ml proteinase K).  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.
RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

tag: cell type

tag: chip (antibody)


title: Propionate feed (SP)

city: muang

first: Dome

last: Adoonsook

state: ChiangMai

address: Suthep

country: Thailand

institute: Dome

description:
Bacteria
processed data file: Classification.txt
processed data file: Propionate_feed_SP.report.pdf

data_processing:
Sequencing was carried out by using Illumina MiSeq sequencing on an Illumina MiSeq device (Illumina Inc., San Diego, CA, USA) with 600 cycles (300 cycles for each paired read and 12 cycles for the barcode sequence) according to the manufacturer’s instructions.
Sequence analysis was conducted using the 16S-based metagenomics workflow of MiSeq Reporter version 2.6.2.3 (Illumina).
Samples were gathered into a single library for sequencing on Illumina MiSeq sequencing system which generated paired 300 bp reads.
Sequences were then demultiplexed based on index sequences.
Genome_build: V3 and V4 regions of the 16S rRNA gene.
Supplementary_files_format_and_content: Classification.txt file includes Sample 1 Number 1SS (Glucose feed (SS)), Sample 2 Number 1SP (Glucose feed (SP)), Sample 3 number 2_1SS (Acetate feed (SS)), Sample 4 number 2_1SP (Acetate feed (SP)), Sample 5 number 7SS (Propionate feed (SS)) and Sample 6 number 8Ano (Propinate feed (SP)).

organism: wastewater metagenome

source_name: Sponge biomass

extract_protocol:
Fast-DNA SPIN kit for soil (MP Biomedicals, Solon, OH, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: sample type

value: Sponge biomass

tag: mbr system

value: Biofilm anoxic-oxic

tag: carbon source

value: Propionate


title: etv2_het_15som-1

city: Tampa

first: Saulius

last: Sumanas

state: FL

address: 560 Channelside Dr

department: Department of Pathology and Cell Biology

institute: University of South Florida

data_processing:
Sequencing was performed at 20M PE-150 read depth by Novogene Inc
Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters.
Genome_build: Zv9
Supplementary_files_format_and_content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq-normalized log-scaled RPKM values are provided

organism: Danio rerio

source_name: Whole embryos

growth_protocol: etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/-; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15-somite stage.

extract_protocol:
Bulk RNA was purified using RNA-quous 4-PCR kit (ThermoFisher).
Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene, Inc

treatment_protocol: 3 batches of heterozygous and homozygous embryos 15-20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.

value: Whole embryos

tag: line allele

value: Heterozygous

tag: embryo stage

value: 15 somite


title: X12hUSA500phoU12

description: phoU1 deletion strain_rep2

tag: strain


title: HuccT1 control3

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Total RNA was isolated from HuccT1 cells and analyzed miRNA expression by microarray.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Homo sapiens

source_name: HuccT1 control

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: HuccT1 and MMNK-1 cells were obtained and cultured as recommended by the supplier.

extract_protocol: RNA samples were extracted from cells using miRNeasy mini kit (Qigen).

tag: disease state

value: cholangiocarcinoma

tag: cell line


title: SCNT_8C_replicate 2


title: SCNT_8C_replicate 1


title: Propionate feed (SS)

description:
Bacteria
processed data file: Classification.txt
processed data file: Propionate_feed_SS.report.pdf

source_name: Suspended sludge

value: Suspended sludge


title: HuccT1 control2


title: HuccT1 control1


title: Acetate feed (SP)

description:
Bacteria
processed data file: Classification.txt
processed data file: Acetate_feed_SP.report.pdf

value: Acetate


title: WT_1st

city: Boston

first: Nikhil

last: Sharma

state: MA

address: 200 Longwood Avenue, Armenise 435

institute: Harvard University

data_processing:
Cell ranger was used to generate original count data which we imported into Seurat to additional information onto the raw read counts.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include counts for each transcript with cell identity information overlaid for clarity

source_name: dorsal root ganglia

extract_protocol:
DRGs were rapidly extracted, dissociated, and washed to remove any particulate matter
RNA libraries were prepared for sequencing using standard protocols

value: dorsal root ganglia


title: Scid.adh.2c2_aGATA3_ChIP-rep1

value: anti-GATA3 Ab (a mixture of sc-268, Santa Cruz Biotechnology and MAB26051, R&D Systems)


title: X12hUSA500phoU11

description: phoU1 deletion strain_rep1

value: staphylococcus aureus

value: grown for 12h

tag: genotype


title: IVF_8C_replicate 3

source_name: IVF eight-cell embryos

value: Holstein

value: IVF embryos


title: X12hUSA5003

description: The parent strain (the control strain)_rep3

value: wild type


title: Acetate feed (SS)

description:
Bacteria
processed data file: Classification.txt
processed data file: Acetate_feed_SS.report.pdf


title: X12hUSA500phoU22

description: phoU2 deletion strain_rep2


title: BFF_replicate 3

source_name: bovine fetal fibroblast

value: SCNT embryos

value: bovine fetal fibroblast (BFF)


title: BFF_replicate 2


title: IVF_8C_replicate 2

value: eight-cell embryos


title: IVF_8C_replicate 1


title: X12hUSA5002

description: The parent strain (the control strain)_rep2


title: BFF_replicate 1


title: X12hUSA5001

description: The parent strain (the control strain)_rep1


title: Glucose feed (SS)

description:
Bacteria
processed data file: Classification.txt
processed data file: Glucose_feed_SS.report.pdf

value: Biofilm anoxic-oxic

value: Glucose


title: Glucose feed (SP)

description:
Bacteria
processed data file: Classification.txt
processed data file: Glucose_feed_SP.report.pdf

value: Sponge biomass


title: Benign breast disease BC1053

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

description: Benign breast disease

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

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

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: Sex

value: Female


title: Muscle_FG-C_07

status: Public on Oct 18 2019

city: Nouzilly

first: Eva

last: Pampouille

address: UMR BOA

country: France

institute: INRA

description: Chicken issued from a fast-growing line with WS=0 and WB=0 visual notations

hyb_protocol: Transcriptome profiling was performed using a Custom Gene Expression 8x60K Gallus gallus array (Agilent). A total of 24 samples were analysed, corresponding to 3 slides. 600 ng of Cy3-labeled cRNA (specific activity > 6.0 pmol Cy3/μg of cRNA) were fragmented at 60°C for 30 minutes following the manufacturer’s instructions. Subsequently, Agilent Hybridization Buffer was added to the fragmentation mixture and hybridized to the arrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed according to the manufacturer’s recommendations.

scan_protocol: The slides were scanned on Agilent G2565CA Scanner System using one color scan setting for 8x60k array slide with a resolution of 3μm and a dynamic range of 20 bits.

data_processing: The scaned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE2_107_Sep09 protocol to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: Pectoralis major muscle, sampled 15 min postmortem

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared using 200ng of total RNA using the One-Color Low Imput Quick Amp Labeling kit (Agilent) following the recommended protocol. Specific activities and cRNA yields were determined using the NanoDrop ND-1000 (Thermo Fisher Scientific).

growth_protocol: Chickens were reared following standard rearing practices until 42 days of age, had ad libitum access to feed and water, at INRA UE1295 PEAT (Nouzilly, France)

extract_protocol: Samples of pectoralis major were collected fifteen minutes after slaughter and directly snap-frozen in liquid nitrogen for molecular analysis. All muscle samples were stored at - 80 °C until further analysis. Total RNA was extracted from pectoralis major muscle samples using RNeasy® Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Residual genomic DNA was removed by DNase I treatment (Qiagen, Valencia, CA, USA). RNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and their integrity was checked through the measure of RNA Integrity Number (RIN > 8) using RNA 6000 Nano chips run on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

tag: tissue

value: pectoralis major muscle

tag: genetic line

value: FG-C

tag: gender

value: female

value: 42 days


title: input 0-6 hr esc

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

data_processing:
Reads from fastq files were aligned to the dm6 genome.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of high-level H3K27me3 domains in 14-16 hr wt embryos.
Read numbers from the different H3K27me3 ChIP datasets were normalised based on the number of H3K27me3 molecules in each condition, as measured by mass spectrometry.
Pho peaks were identified using GenoGAM (Stricker et al., 2017).
Genome_build: dm6
Supplementary_files_format_and_content: Bedgraph files (for visualizing ChIP-seq datasets) contain the number of overlapping reads with 200 bp bins covering the 7 chromosomal arms of the Drosophila genome.
Supplementary_files_format_and_content: Bedgraph files (High Pho peaks and H3K27me3 domains) contain the position of the high Pho peaks and high-level H3K27me3 domains that were identified.

organism: Drosophila melanogaster

source_name: 0-6 hr old esc mat- zyg- embryos

growth_protocol: Drosophila embryos were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.

tag: developmental stage

value: 0-6 hr old embryo

tag: antibodies


title: Muscle_FG-C_08

tag: age


title: H3K27me3 ChIP 0-6 hr esc

value: H3K27me3 (Cell Signaling (C36B11))


title: input 0-6 hr wt

source_name: 0-6 hr old Oregon R embryos


title: Muscle_FG-WSWB_08

description: Chicken issued from a fast-growing line with WS=2 and WB=2 visual notations

value: FG-WSWB


title: H3K27me3 ChIP 0-6 hr wt


title: Muscle_SG_01

description: Chicken issued from a slow-growing line with WS=0 and WB=0 visual notations

value: SG

value: male


title: ChIP_FGO_Setd2_KO_H3K27ac_rep2

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

institute: Tsinghua University

description:
processed data file:
ChIP_FGO_Setd2_KO_H3K27ac.bed.gz

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome.

source_name: oocyte

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stageᔌᔘᔥᔱᔾᕊᕗᕣᕰᕼᖉᖕᖢᖮᖻᗇᗔᗠᗭᗹᘆᘒᘟᘫᘸᙄᙑᙝᙪᙶᚃᚏ᚜ᚨᚵᛁᛎᛚᛧᛳᜀᜌ᜙ᜥᜲ᜾ᝋ᝗ᝤᝰ᝽ញពអឯុៈ។១៭៺᠆᠓᠟ᠬᠸᡅᡑᡞᡪᡷᢃᢐᢜᢩᢵᣂᣎᣛᣧᣴᤀᤍᤙᤦᤲ᤿᥋ᥘᥤᥱ᥽ᦊᦖᦣ᦯ᦼᧈ᧕᧡᧮᧺ᨇᨓᨠᨬᨹᩅᩒᩞᩫ᩷᪄᪐᪝᪩᪶᫂᫏᫛᫨᫴ᬁᬍᬚᬦᬳᬿᭌ᭘᭥᭱᭾ᮊᮗᮣ᮰ᮼᯉᯕᯢᯮ᯻ᰇᰔᰠᰭ᰹᱆᱒ᱟᱫᱸᲄᲑᲝᲪᲶ᳃᳏᳨᳜

value: oocyte

value: FGO

tag: chip-antibody

value: H3K27ac (Active Motif, Cat.39133)


title: Muscle_FG-WSWB_03


title: Muscle_SG_08


title: Muscle_FG-C_06


title: ChIP_FGO_Setd2_KO_H3K27ac_rep1

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stageͤV_x0002__x0000_L_x0000_ͻW_x0002__x0000_N_x0000_ΐT_x0002__x0000_P_x0000_跀Μ_x0011__x0002__x0000_R_x0000_γJ_x0002__x0000_T_x0000_铀ο]_x0002__x0000_V_x0000_ϖᠣᠰᠾᡌᡚᡨᡶᢄᢒᢠ᢮ᢻᣉᣗᣥᣳᤁᤏᤝᤫ᤹᥆ᥔᥢ᥮᥻ᦉᦗᦥᦲᦿ᧋᧘᧤᧱᧽ᨊᨖᨣᨱᨾᩌᩚᩧ᩵᪂᪐᪞᪬᪹᫇᫕᫣᫱᫿ᬌᬙᬧ᬴ᭂ᭏᭜᭨᭵ᮂᮏᮜ᮪᮸ᯆᯔᯡᯯ᯽ᰉᰖᰢᰯ᰻᱈᱔ᱡᱭᱺᲆᲓᲠᲮ᲼᳉᳥᳗ᳳᴁᴏᴝᴫᴹᵇᵔᵢᵰᵾᶌᶚᶨᶶ᷄᷒ᷟᷭ᷻ḉḗḥḳṁ_x0000__x0000_


title: Muscle_FG-WSWB_05


title: Muscle_FG-WSWB_07


title: ChIP_FGO_Setd2_Con_H3K27ac_rep2

description:
processed data file:
ChIP_FGO_Setd2_Con_H3K27ac.bed.gz


title: Muscle_SG_07


title: Muscle_SG_05


title: Muscle_FG-WSWB_04


title: Muscle_FG-C_04


title: MEF_control_2

first: Yuxin

last: Fang

state: Beijing

address: Yiheyuan Road No.5

institute: Peking University

data_processing:
Library strategy: DNA-seq
Raw reads were first performed with adaptor and quality trimming using cutadapt1. Reads with quality values below 25 and reads shorter than 45 nt after trimming were excluded.
The processed reads were mapped to mouse reference genome (mm9) using bowtie2
Duplicate reads were marked by picard and removed. Non-reducdant reads aligned to the genome were converted to a bigwig format for visualization.
Peaks were called by model-based analysis of ChIP-Seq (MACS2) using non-redundant reads. For peaks called by enrich/input, p<0.001 was used as cutoff. While for peaks called by enrich/control, an easier cutoff, p<0.05, was used. Only the peaks called by two methods simultaneously were remained. Overlap of two biological replicates was defined as high-confidence peaks and was applied to further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: genomic regions identified as high-confidence peaks; bigwig with reads alignment

source_name: Mouse Embryonic Fibroblast

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco). Cells were cultured at 37℃ under 5% CO2.

extract_protocol:
Cells were harvested and genomic DNA was extracted with TIANamp Genomic DNA Kit (TIANGEN, DP304). 0.1 mM desferal (TargetMol, T1637) was added at each step to prevent further DNA oxidation during genomic DNA extraction. Genomic DNA was digested to 100-1000 bp with NEBNext dsDNA Fragmentase (NEB, M0348). DNA fragments were purified with 2×CMPure beads (CWbiotech, CW2508). 2 pg model sequences were spiked into each 10 μg genomic DNA fragments. Half of the DNA mixture was incubated with Fpg (NEB, M0240) at 37℃ for one hour for damage excision. DNA was purified with 2×CMPure beads. 100 ng DNA was separated from each sample as input. For each enrichment, 4 μg genomic DNA was incubated with 4.5 μM hOGG1 in 100 μL system with 1×NEBuffer1(NEB, B7001). To improve the enrichment fold, 20 μg empty vector plasmid pcDNA3.1 was added as blocking DNA in each enrichment system. The mixture was incubated at 37℃ for 40 min and enriched as procedures described above. After elution, DNA was purified with 2×CMPure beads.
NGS library construction was performed with VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme, NP604) following the manufacturer’s guidelines. Size selection was conducted after PCR amplification by using 0.55× and 0.2× VAHTS DNA clean beads (Vazyme, N411) to obtain 300-500 bp fragments.

tag: cell type

value: MEF

tag: enrichment

value: yes

tag: fpg treatment


title: Muscle_SG_03


title: MEF_enrich_2

value: no


title: Muscle_FG-WSWB_02


title: Muscle_FG-C_05


title: MEF_input_2


title: Muscle_FG-C_01


title: Muscle_SG_04


title: Muscle_FG-WSWB_01


title: Muscle_SG_02


title: Muscle_SG_06


title: Muscle_FG-C_02


title: MEF_control_1


title: MEF_input_1


title: MEF_enrich_1


title: Muscle_FG-C_03


title: 101231000132_R06C01

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged with BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Minfi preprocessIllumina was used to process samples (for background subtraction and colour correction).
Average Beta (after minfi::preprocessIllumina in R).

label: Cy5 and Cy103

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using the Masterpure system (Epicentre, USA) and quantified using a NanoPhotometer P300 (Implen, Germany). Bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

value: Buccal epithelial cells


title: 101231000132_R03C01

label: Cy5 and Cy100

value: Female


title: 101231000132_R05C01

label: Cy5 and Cy102


title: 101231000132_R06C02

label: Cy5 and Cy108


title: 101231000132_R02C02

label: Cy5 and Cy105


title: 101231000132_R03C02

label: Cy5 and Cy106


title: 101231000132_R04C01

label: Cy5 and Cy101


title: 101231000132_R01C02

label: Cy5 and Cy104


title: 101231000130_R05C02

label: Cy5 and Cy96


title: 101231000130_R06C02

label: Cy5 and Cy97


title: 101231000132_R02C01

label: Cy5 and Cy99


title: 101231000130_R03C02

label: Cy5 and Cy95


title: 101231000132_R01C01

label: Cy5 and Cy98


title: 101231000130_R02C02

label: Cy5 and Cy94


title: 101231000130_R01C02

label: Cy5 and Cy93


title: 101231000130_R06C01

label: Cy5 and Cy92


title: control_3

city: Sheffield

first: Allan

last: Lawrie

address: University of Sheffield

department: Infection Immunity and Cardiovascular Disease

country: United Kingdom

institute: University of Sheffield

description: Gene expression after 6hr stimulation with 0.2% FCS

scan_protocol: Protocol AgilentHD_GX_1Color on G2505C (Agilent Technologies, UK)

data_processing: Loess normalisation and data analysis was performed using the Linear Models for Microarray Data (LIMMA) package in R (http://www.r-project.org/).

source_name: control

label_protocol: mRNA labelling was performed as per manufacturers instructions (Agilent Technologies, UK)

growth_protocol: Cellswere synchronised with growth arrest media (DMEM, 0.2% FBS, penicillin and streptomycin) for 48hourspriortostimulation.Allexperimentationwasconductedat37°Cwith5%CO2with cells aged between passage 4-7

extract_protocol: total RNA was extracted using the Direct-zolTM RNA kit (Zymo Research)

treatment_protocol: Mock or 6hr stimulation with OPG

value: Pulmonary Artery Smooth Muscle Cells (PASMCs)


title: opg_1

description: Gene expression after 6hr stimulation with 50ng/ul OPG

hyb_protocol: performed as per manufacturers instructions (Agilent Technologies, UK)

source_name: opg


title: control_2


title: opg_2


title: control_1


title: 101231000130_R04C01

label: Cy5 and Cy90


title: 101231000130_R02C01

label: Cy5 and Cy88


title: 101231000130_R03C01

label: Cy5 and Cy89


title: opg_3


title: 101231000132_R04C02

label: Cy5 and Cy107


title: 101231000125_R02C02

label: Cy5 and Cy82


title: 101231000125_R05C02

label: Cy5 and Cy85


title: 101231000125_R04C02

label: Cy5 and Cy84


title: 101231000114_R05C02

label: Cy5 and Cy74


title: 101231000125_R06C01

label: Cy5 and Cy81


title: 101231000125_R06C02

label: Cy5 and Cy86


title: 101231000125_R04C01

label: Cy5 and Cy79


title: 101231000125_R03C02

label: Cy5 and Cy83


title: 101231000125_R01C01

label: Cy5 and Cy76


title: 101231000114_R06C02

label: Cy5 and Cy75


title: control_4


title: 101231000125_R02C01

label: Cy5 and Cy77


title: 101231000114_R03C02

label: Cy5 and Cy72


title: 101231000130_R05C01

label: Cy5 and Cy91


title: 101231000114_R01C02

label: Cy5 and Cy71


title: 101231000125_R03C01

label: Cy5 and Cy78


title: 101231000114_R04C02

label: Cy5 and Cy73


title: 101231000114_R03C01

label: Cy5 and Cy67


title: 101231000114_R05C01

label: Cy5 and Cy69


title: 101231000114_R04C01

label: Cy5 and Cy68


title: 101231000130_R01C01

label: Cy5 and Cy87


title: 101231000125_R05C01

label: Cy5 and Cy80


title: 101231000114_R02C01

label: Cy5 and Cy66


title: 101231000114_R01C01

label: Cy5 and Cy65


title: 101231000112_R06C02

label: Cy5 and Cy64


title: 101231000112_R05C02

label: Cy5 and Cy63


title: CD4+ Tcells_cKO_KDMRNA8

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

description: RNA from CD4+ T cells

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: txt file has count values for each Sample

source_name: Lymph node

growth_protocol:
Animals were maintained under standard conditions in a 12 h dark/12 h light cycle with access to food and water ad libitum.
[breeding protocol] CD4-specific Kdm6a-/- or Kdm6a-/y mice (cKO) were generated by crossing Kdm6af/f-CD4-Cre females with Kdm6af/y males.

extract_protocol:
RNA purification was performed using the Direct-zol™ RNA MicroPrep Plus kit following manufacturer’s instructions (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: Lymph node

value: CD4+ T cell

value: Male

value: cKO

tag: floxed allele

value: floxed/y Kdm6a

tag: cre


title: CD4+ Tcells_WT_KDMRNA9

description: RNA from CD4+ T cells

tag: strain

value: WT


title: 101231000112_R04C02

label: Cy5 and Cy62


title: 101231000112_R03C02

label: Cy5 and Cy61


title: CD4+ Tcells_cKO_KDMRNA7

description: RNA from CD4+ T cells


title: CD4+ Tcells_cKO_KDMRNA6

description: RNA from CD4+ T cells


title: 101231000112_R01C02

label: Cy5 and Cy59


title: CD4+ Tcells_WT_KDMRNA5

description: RNA from CD4+ T cells


title: 101231000112_R02C02

label: Cy5 and Cy60


title: 101231000112_R05C01

label: Cy5 and Cy57


title: CD4+ Tcells_WT_KDMRNA4

description: RNA from CD4+ T cells


title: CD4+ Tcells_cKO_KDMRNA2

description: RNA from CD4+ T cells


title: 101231000112_R06C01

label: Cy5 and Cy58


title: CD4+ Tcells_WT_KDMRNA3

description: RNA from CD4+ T cells


title: 101231000112_R03C01

label: Cy5 and Cy55


title: 101231000094_R06C02

label: Cy5 and Cy53


title: CD4+ Tcells_WT_KDMRNA1

description: RNA from CD4+ T cells


title: 101231000112_R04C01

label: Cy5 and Cy56


title: WT19

description:
RNA from auto antigen specific CD4+ T cells
Kdm6a.CD4_rawcounts.xlsx

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "Kdm6a.CD4_rawcounts.xlsx" has count values for each Sample

growth_protocol:
Animals were maintained under standard conditions in a 12 h dark/12 h light cycle with access to food and water ad libitum.
CD4-specific Kdm6a-/- or Kdm6a-/y mice (cKO) were generated by crossing Kdm6af/f-CD4-Cre females with Kdm6af/y males.
Lymph node cell suspensions were cultured at a concetnration of in complete RPMI medium with MOG 35-55 (25 ug/mL) for 18 hours.

value: floxed/floxed Kdm6a


title: WT10


title: WT14


title: 101231000112_R01C01

label: Cy5 and Cy54


title: KO7


title: 101231000094_R05C02

label: Cy5 and Cy52


title: KO12


title: 101231000094_R04C02

label: Cy5 and Cy51


title: 101231000094_R03C02

label: Cy5 and Cy50


title: KO3


title: 101231000094_R02C02

label: Cy5 and Cy49


title: KO2


title: 101231000094_R01C02

label: Cy5 and Cy48


title: 101231000094_R04C01

label: Cy5 and Cy46


title: 101231000094_R05C01

label: Cy5 and Cy47


title: 101231000094_R01C01

label: Cy5 and Cy44


title: 101231000094_R02C01

label: Cy5 and Cy45


title: 101231000077_R06C02

label: Cy5 and Cy43


title: 101231000077_R05C02

label: Cy5 and Cy42


title: 101231000077_R03C02

label: Cy5 and Cy40


title: 101231000077_R04C02

label: Cy5 and Cy41


title: 101231000077_R02C02

label: Cy5 and Cy39


title: 101231000077_R06C01

label: Cy5 and Cy38


title: Muscle_FG-WSWB_06

value: pectoralis major muscle

value: FG-WSWB

value: male

value: 42 days


title: 101231000077_R04C01

label: Cy5 and Cy36


title: 101231000077_R03C01

label: Cy5 and Cy35


title: 101231000077_R02C01

label: Cy5 and Cy34


title: mRNA_WT_2

city: Bethesda

first: Jon

middle: R.

last: Lorsch

state: MD

address: BG 49 RM 2C08, 49 Convent Dr.

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development,

institute: National Institutes of Health

data_processing:
The ribosome profiling and mRNA sequencing data were processed as described in Ingolia, N.T. (2010). Genome-wide translational profiling by ribosome footprinting.  Methods Enzymol. 470, 119–142. Breifly, the sequnce linker and the first nucleotide of each read were removed using fastx_toolkit/0.0.13 (fastx_clipper and fastx_trimmer, respectively). Ribosome RNAs were removed using bowtie/2-2.2.5  alignment agains year ribosome RNA sequences.The non-rRNA reads were mapped to yeast geneome sacCer3 (http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz)using TopHat/2.0.13.
Wiggle files were produced from the alignment files using RiboSeq (https://github.com/ingolia-lab/RiboSeq), Two replicates of mRNA or foot-print alignment files were merged for generating two wiggle files, each for genes on the Watson or Crick strand. The total reads on both strands were summed and a normalization factor q was calculated as 1000,000,000/(total reads on W+C strands). Wiggle files were then regenerated by multiplying all reads by the factor q, yielding the number of reads per 1000 million total reads (rpkm).
Genome_build: yeast geneome sacCer3
Supplementary_files_format_and_content: WIG

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were generally grown to an OD600 of ~ 0.7  in synthetic complete medium at 30°C,without treatment with cycloheximide before harvesting.

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer containing 500 µg/ml cycloheximide. Total mRNA isolated from whole cell extract using miRNeasy minikt (Qiagen). Total RNA fragmentation, Size selection,  linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223. Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to to remove ribosome contamination after linker ligation step.
RNA-Seq

tag: genotype/variation

value: MATa ura3-52 leu2-3 leu2-112 trp1{delta}-63 his4-301(ACG) sui1{delta}::hisG pJCB101 (sc LEU2 SUI1)


title: mRNA_sui1-L96P_2

value: MATa ura3-52 leu2-3 leu2-112 trp1{delta}-63 his4-301(ACG) sui1{delta}::hisG pPMB03 (sc LEU2 sui1-L96P)


title: 101231000077_R01C01

label: Cy5 and Cy33


title: mRNA_sui1-L96P_1


title: mRNA_WT_1


title: wt 24hr 1mM Cu  TOTAL DNA cf REC-seq with 2u

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
genomic DNA
mutants_processed_data_report.txt

data_processing:
Library strategy: REC-Seq
After adapter and quality trimming using Trim Galore (v0.5.0), eccSEQ data was mapped to yeast genome R64-2-1 with 2μ sequence J01347.1 included as an additional chromosome using Bowtie2 (v2.3.2; with more stringent parameters: --no-mixed --score-min L,0,-0.2 --no-unal -X 2000). To avoid apparent enrichment of repetitive regions (https://sequencing.qcfail.com/articles/deduplicating-ambiguously-mapped-data-makes-it-look-like-repeats-are-enriched/) the resulting BAM files were subjected to de-duplication based on exact sequence identity of the first 50 bp of both Read1 and Read 2 using a custom script (available on request). These de-duplicated by sequence files were then imported into SeqMonk v1.44.0 for analysis (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), where they were additionally de-duplicated based on alignment position (chromosome, start and end). Reads were quantified in 20bp bins and normalised based on the total read count in each library. For 3xCUP1/Δ libraries, counts were performed in 100 bp bins and data from replicate sets compared using the edgeR statistical filter implemented in SeqMonk [79]. For mutant analysis, counts were performed in 250bp bins, and REC-seq samples normalised based on 2micron read counts in total DNA and REC-seq samples.
Genome_build: R64-2-1 with 2μ sequence J01347.1
Supplementary_files_format_and_content: Normalised log2-transformed read counts in bins spanning the genome, excluding ribosomal DNA, mitochondrial DNA and UBC9 locus. Bin sizes are 20bp (cu and gal), 100bp (3xcup1) or 250bp (mutants).

source_name: Cells aged 24 hours in SD media

growth_protocol: Experiments were performed in synthetic complete media (2% glucose, 0.67% yeast nitrogen base with ammonium sulfate, complete amino acid mix), to which CuSO4 was added from a 1 M stock solution as required. Or cells were grown in YP media (2% peptone, 1% yeast extract) with sugar at 2% final volume, pre-cultures for experiments in YP were grown in YP with 2% raffinose. In all cases, cells were grown at 30°C with shaking at 200 rpm.

extract_protocol:
Percoll gradients (1-2 per sample depending on final OD) were formed by vortexing 1.16ml Percoll (Sigma P1644) with 42 µl 5 M NaCl, 98 µl water in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Cells were defrosted, washed with 25 ml cold PBSE and re-suspended in a minimal amount of PBSE and layered on the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g to pellet the cells, which were then re-suspended in 1ml PBSE (re-uniting samples split across two gradients). 25 µl Streptavidin magnetic beads were added (Miltenyi Biotech 1010007) and cells incubated for 15 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. 50 µl cells were set aside for quality control, while 1 μl 10% Triton X-100 was added to the remainder which were then pelleted by centrifugation and frozen or processed directly for DNA extraction. Cell pellets were re-suspended in 50 µl 0.34 U/ml lyticase (Sigma L4025) in 1.2 M sorbitol, 50 mM EDTA, 10 mM DTT and incubated at 37° C for 45 min. After centrifugation at 1,000 g for 5 min, cells were gently re-suspended in 80 µl of 0.3% SDS, 50 mM EDTA, 250 μg/ml Proteinase K (Roche 3115801) and incubated at 65° C for 30 min. 32 µl 5 M KOAc was added after cooling to room temperature, samples were mixed by flicking, and then chilled on ice for 30 min. After 10 min centrifugation at 20,000 g, the supernatant was extracted into a new tube using a cut tip, 125 µl phenol:chloroform pH 8 was added and samples were mixed on a wheel for 30 min. Samples were centrifuged for 5 min at 20,000 g, the upper phase was extracted using cut tips, and precipitated with 250 μl ethanol. Pellets were washed with 70% ethanol, air-dried and left overnight at 4° C to dissolve in 20 µl TE.
All reagents from NEB except where noted otherwise. 20 μl genomic DNA isolated from aged cells as above was diluted to 155 μl final volume containing 1x CutSMART and 0.75 μl RNase T1 (Fermentas), and incubated 15 min at room temperature before splitting into 3x 49 μl and 1x 3μl aliquots (the latter was diluted to 16 μl for total DNA isolation). The 49 μl aliquots were digested with 1 μl EagI-HF, PvuI-HF or 0.5μl PvuII-HF for 4 hours at 37 °C, 0.5 μl additional enzyme was added to the PvuII digest every hour. For mutant analysis, PvuII was replaced with SmaI and this digestion was performed at 25 °C. 6 μl 10 mM ATP, 1 μl 10x CutSmart, 1 μl Exonuclease V and 1 μl Exonuclease I were added to each digest and incubated over night at 37 °C before extraction with phenol chloroform and ethanol precipitation in the presence of 1 µl GlycoBlue (Life Technologies). DNA pellets were dissolved in 45 μl 0.1x TE, then 6 μl 10x CutSmart, 6 μl 10 mM ATP, 1 μl Exonuclease V, 1 μl Exonuclease I and 1 μl same restriction enzyme as previous day were added and samples again incubated over night at 37 °C before extraction with phenol chloroform and ethanol precipitation. For SmaI digestions, the enzyme and CutSmart were added first and digestion performed for 4 hours at 25 °C before addition of other components and shift to 37 °C for overnight incubation. Pellets were dissolved in 33 μl 0.1x TE and the 3 aliquots combined, precipitated again with ethanol and pellets dissolved in 16 μl 0.1x TE.
Exonuclease treated and total DNA samples were incubated at 37 °C for 45 min with 2 μl NEBNext DNA fragmentase  and 2 μl fragmentase buffer, then 5 μl 0.5 M EDTA was added followed by 25 μl water and samples were purified using 50 μl AMPure beads and eluted with 25.5 μl 0.1x TE. 3.5 μl NEBNext Ultra II end prep buffer and 1.5 μl  NEBNext Ultra II end prep enzyme were mixed in and samples incubated 30 min at 20 °C then 30 min at 65 °C. After addition of 1.25 μl 1:25 diluted NEBNext adaptor, 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix samples were incubated 15 min at 20 °C, then 1.5 μl USER enzyme was added and incubated 15 min at 37 °C. Samples were cleaned with 44 μl AMPure beads, eluted with 30 μl 0.1x TE, then cleaned again with 27 μl AMPure beads and eluted with 22.5 μl 0.1x TE.
1.25 μl library was amplified with 0.4 μl each NEBNext index and universal primers and 5μl NEBNext Ultra II PCR mix in 10 μl total volume using recommended cycling conditions with 8 cycles for total samples, 16 cycles for 48 hour aged samples and 18 cycles for 24 hour samples. These test amplifications were cleaned with 9 μl AMPure beads, eluted with 1.5 μl 0.1x TE and 1 μl run on a Bioanalyzer to determine the optimal cycle number for the final amplification. Library yield was aimed to be 2 pM, the test amplification should be equivalent to a 1:4 dilution of the final library. The remaining library (21 μl) was then amplified in a 50 μl reaction containing 2 μl each NEBNext index and universal primers and 25 μl NEBNext Ultra II PCR mix using the calculated cycle number, cleaned with 45 μl AMPure beads, eluted with 25 μl 0.1x TE, then cleaned again with 22.5 μl AMPure beads and eluted with 10.5 μl 0.1x TE.

treatment_protocol: 0.25x107 cells per sample were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 100 µl PBS and re-suspended in 100 μl PBS, then inoculated in required media at 2x104 cells/ml and allowed to recover for 2 hours at 30° before addition of 1µM β-estradiol (Sigma E2758) and CuSO4 as required. For ageing in YPD or YPGal, the same protocol was followed but no recovery period was included – as previously noted this prevents culture saturation without detectable contamination of young cells by 24-48 hours [31]. Cells were harvested by repeated centrifugation for 1 min, 4600 rpm in 50 ml tubes and immediately fixed by resuspension in 70% ethanol and storage at -80°C.

value: MEP


title: WT TAC3

city: suita

first: yuto

last: nakamura

address: yamada-oka, 2-2

department: metabolic medicine

institute: Osaka university

description: gene expression data from wild-type or ADAM12 knockout mice under TAC surgery

hyb_protocol: Following fragmentation, 5.2 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip mouse ClariomD arrays (GeneChip Hybridization Oven 640). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System (Work station: DELL PRECISION 490).

data_processing: The data have been normalized with Expression Console from Affymetrix and annotation and analyses have been performed with TAC.3 software from Affymetrix.

label: biotin

source_name: Heart in two weeks after transverse aortic constriction (TAC) surgery, biological replicate 3 of wild-type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChipTM WT PLUS Reagent Kit User Guide, 2017, Thermo Fisher Scientific).

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

value: 10 weeks

value: wild-type

value: Heart

tag: condition

value: TAC


title: A12KO sham1

source_name: Heart in two weeks after sham operation, biological replicate 1 of ADAM12 knockout

tag: genotype

value: ADAM12 knockout

value: sham operation


title: A12KO TAC1

source_name: Heart in two weeks after transverse aortic constriction (TAC) surgery, biological replicate 1 of ADAM12 knockout


title: WT TAC2

source_name: Heart in two weeks after transverse aortic constriction (TAC) surgery, biological replicate 2 of wild-type


title: WT sham3

source_name: Heart in two weeks after sham operation, biological replicate 3 of wild-type


title: 101178130031_R06C02

label: Cy5 and Cy32

value: Buccal epithelial cells

value: Female


title: A12KO TAC3

source_name: Heart in two weeks after transverse aortic constriction (TAC) surgery, biological replicate 3 of ADAM12 knockout


title: WT sham1

source_name: Heart in two weeks after sham operation, biological replicate 1 of wild-type


title: WT TAC1

source_name: Heart in two weeks after transverse aortic constriction (TAC) surgery, biological replicate 1 of wild-type


title: A12KO sham2

source_name: Heart in two weeks after sham operation, biological replicate 2 of ADAM12 knockout


title: 101178130031_R04C02

label: Cy5 and Cy30


title: A12KO sham3

source_name: Heart in two weeks after sham operation, biological replicate 3 of ADAM12 knockout


title: 101178130031_R03C02

label: Cy5 and Cy29


title: 101231000077_R05C01

label: Cy5 and Cy37


title: WT sham2

source_name: Heart in two weeks after sham operation, biological replicate 2 of wild-type


title: wt_24hr_TOTAL_DNA

description:
genomic DNA
cu_and_gal_processed_data_report.txt


title: 101178130031_R01C02

label: Cy5 and Cy28


title: wt_24hr_REC-seq_with_2u

description:
other
mutants_processed_data_report.txt


title: wt_24hr_REC-seq

description:
other
cu_and_gal_processed_data_report.txt


title: wt 24hr TOTAL DNA cf REC-seq with 2u


title: 101178130031_R06C01

label: Cy5 and Cy27


title: wt_24hr_no_rDNA_removal


title: wt_24hr_1mM_Cu_REC-seq_with_2u

description:
other
mutants_processed_data_report.txt


title: wt_24hr_1mM_Cu_TOTAL_DNA


title: wt_24hr_1mM_Cu_REC-seq


title: 101178130031_R05C02

label: Cy5 and Cy31


title: wt_24hr_1mM_Cu_no_rDNA_removal


title: spt3_24hr_REC-seq_with_2u

description:
other
mutants_processed_data_report.txt

value: MEP spt3


title: 101178130031_R01C01

label: Cy5 and Cy22


title: A12KO TAC2

source_name: Heart in two weeks after transverse aortic constriction (TAC) surgery, biological replicate 2 of ADAM12 knockout


title: 101130760029_R05C02

label: Cy5 and Cy20

source_name: buccal swab genomic DNA


title: 101178130031_R05C01

label: Cy5 and Cy26


title: 101130760029_R04C02

label: Cy5 and Cy19


title: sae2_24hr_TOTAL_DNA

value: MEP sae2


title: sae2_24hr_REC-seq_with_2u

description:
other
mutants_processed_data_report.txt


title: 101130760029_R03C02

label: Cy5 and Cy18


title: sae2_24hr_1mM_Cu_TOTAL_DNA


title: 101130760029_R01C02

label: Cy5 and Cy16


title: sae2_24hr_1mM_Cu_REC-seq_with_2u

description:
other
mutants_processed_data_report.txt


title: 101178130031_R04C01

label: Cy5 and Cy25


title: 101178130031_R03C01

label: Cy5 and Cy24


title: Pgal1-3HA_48hr_YPGal_TOTAL_DNA

source_name: Cells aged 48 hours in YPGal media

value: MEP [Pgal1-3HA cup1]/CUP1


title: 101178130031_R02C01

label: Cy5 and Cy23


title: spt3_24hr_TOTAL_DNA


title: 101130760029_R05C01

label: Cy5 and Cy14


title: Pgal1-3HA_48hr_YPD_TOTAL_DNA

source_name: Cells aged 48 hours in YPD media


title: Pgal1-3HA_48hr_YPGal_REC-seq


title: 101130760029_R06C02

label: Cy5 and Cy21


title: 101130760029_R04C01

label: Cy5 and Cy13


title: mus81_24hr_REC-seq_with_2u

description:
other
mutants_processed_data_report.txt

value: MEP mus81


title: Pgal1-3HA_48hr_YPD_REC-seq


title: mus81_24hr_TOTAL_DNA


title: mus81_24hr_1mM_Cu_TOTAL_DNA


title: 101130760029_R06C01

label: Cy5 and Cy15


title: mus81_24hr_1mM_Cu_REC-seq_with_2u

description:
other
mutants_processed_data_report.txt


title: 101130760029_R03C01

label: Cy5 and Cy12


title: 101130760020_R05C02

label: Cy5 and Cy9


title: 101130760029_R02C02

label: Cy5 and Cy17


title: 3xCUP1_24hr_3_REC-seq

description:
other
3xCUP1_processed_data_report.txt

value: MEP 3xCUP1/cup1


title: rse1#1

city: DAEGU

first: JAE

middle: HO

last: LEE

address: 333, Techno jungang-daero, Hyeonpung-myeon, Dalseong-gun

department: NewBiology

country: South Korea

institute: DGIST

data_processing:
Illumina HiSeq generated raw images using HiSeq Control Software v2.2 for the system control and base calling using Real Time Analysis v1.18-integrated primary analysis software.
The BCL (base calls) binary files were converted into FASTQ format using Illumina package bcl2fastq (v1.8.4).
Quality control and preprocessing of metagenomic data were performed using FastQC (v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The Trimmomatic (v0.32.3) (Bolger et al., 2014) was used to trim the adapter sequences and low-quality sequences. Remaining reads were aligned to the Arabidopsis thaliana Ler-0 genome using TopHat (v2.0.9) (Trapnell et al., 2009). The Ler-0 genome was reconstructed from Arabidopsis thaliana Col-0 genome based on the VCF (variant call format) file for Ler-0 obtained from the 1001 Genomes Project (https://1001genomes.org/) website. PCR duplicates were removed using Picard (v1.119; http://broadinstitute.github.io/picard/), 'MarkDupicates' and only uniquely mapped reads were counted using HTSeq (v0.6.1) (Anders et al., 2015).
The differential expression analysis was performed using DESeq2 (Love et al., 2014) and the P-values were determined using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). The differentially expressed genes(DEGs) were identified as the ones that have the adjusted P-value <0.05.
Genome_build: Arabidopsis thaliana Ler-0 genome reconstructed from Arabidopsis thaliana Col-0 reference genome (TAIR10).
Supplementary_files_format_and_content: tab-delimited text file including read counts processed by HTSeq-count.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf

growth_protocol: Arabidopsis plants were grown in soil in growth chambers at 22°C ± 2°C. The photoperiod was 16-h light/8-h dark.

extract_protocol:
Total RNA was extracted using plant RNA mini prep kit (ZYMO RESEARCH)
RNA purity was determined by assaying 1 µL of total RNA extract on a NanoDrop8000 spectrophotometer (Thermo Scientific). Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA integrity number value. mRNA sequencing libraries were prepared according to manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit). mRNA was purified and fragmented from total RNA (1 ug) using poly-T oligo-attached magnetic beads and two rounds of purification. Cleaved RNA fragments primed with random hexamers were reverse transcribed into first-strand cDNA using reverse transcriptase, random primers and dUTP in place of dTTP. (The incorporation of dUTP quenches the second strand during amplification because the polymerase does not incorporate past this nucleotide.) A single adenine base was added to these cDNA fragments and was followed by adapter ligation. The products were purified and enriched with PCR to create the final strand-specific cDNA library. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent). After qPCR using SYBR Green PCR Master Mix (Applied Biosystems), the index-tagged libraries were combined in equimolar amounts within a single pool.

value: leaf


title: rse1#2


title: 101130760020_R04C02

label: Cy5 and Cy8


title: Ler#3

value: Ler


title: 101130760020_R03C02

label: Cy5 and Cy7


title: 3xCUP1_24hr_300uM_Cu_3_REC-seq

description:
other
3xCUP1_processed_data_report.txt

source_name: Cells aged 24 hours in SD media


title: Ler#2


title: 3xCUP1_24hr_300uM_Cu_2_REC-seq

description:
other
3xCUP1_processed_data_report.txt


title: Ler#1


title: 101130760029_R01C01

label: Cy5 and Cy11


title: 3xCUP1_24hr_300uM_Cu_1_REC-seq

description:
other
3xCUP1_processed_data_report.txt


title: 101130760020_R06C01

label: Cy5 and Cy5


title: 101130760020_R01C02

label: Cy5 and Cy6


title: 101130760020_R06C02

label: Cy5 and Cy10


title: 3xCUP1_24hr_2_REC-seq

description:
other
3xCUP1_processed_data_report.txt


title: 101130760020_R04C01

label: Cy5 and Cy4


title: 101231000114_R06C01

label: Cy5 and Cy70


title: 3xCUP1_24hr_1_REC-seq

description:
other
3xCUP1_processed_data_report.txt


title: OVCAR8 Plastic 62

city: Bloomington

first: Anirban

middle: K

last: Mitra

state: IN

address: 915 E 3rd St

institute: Indiana University School of Medicine - Bloomington

data_processing:
Reads were adapter trimmed and quality filtered using Trimmomatic ver. 0.33, with the cutoff threshold for average base quality score set at 20 over a sliding window of 3 bases. Reads shorter than 20 bases post-trimming were excluded.
Cleaned reads mapped to human genome GRCh38 with gencode v25 annotation using Tophat2 ver 2.1.0. Number of reads mapping to annotated genes counted using htseq-counts ver. 0.5.4p1.
Significantly differentially expressed genes at 5% FDR with at least 2 fold change were called using DESeq2 ver. 1.12.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read counts aligned to the GRCh38 gencode v25 annotated genes. Counts generated using the software htseq-counts ver. 0.5.4p1

source_name: Ovarian cancer cells

extract_protocol:
Total RNA was isolated using Qiagen miRNeasy kit (Cat# 217004).
The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005).

tag: cell line

value: Ovarian cancer cells

tag: culture method

value: plastic culture dish

tag: passage


title: rse1#3

tag: tissue


title: 3_DMSO

city: Nantes

first: Julie

last: Gavard

address: 8 quai Moncousu

institute: INSERM

description:
Harford-Wright et al 2017 BRAIN
3_3708Nantes_GSC9-4hr-DMSO-3_RNASeq_hs_i10

data_processing:
Sequencing: Standard Illumina software base-calling and quality-control filtering was applied
The reads are mapped to the genome using the STAR algorithm (v2.5.2b) with default settings.
Read counts in gene features were determined using Subread (v1.5.2)
Differential anaysis was performed using DESeq2 (v1.24.0)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files

source_name: human glioblastoma cells from patient #9

growth_protocol: in NS34 medium as described in Harford-Wright et al., Brain 2017

extract_protocol:
Cell pellets were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA library kit.

treatment_protocol: vehicle (DMSO) or mepazine (MPZ, 20 μM, 4 hours)

value: glioblastoma cells


title: 2_DMSO

description:
Harford-Wright et al 2017 BRAIN
2_3708Nantes_GSC9-4hr-DMSO-2_RNASeq_hs_i9


title: 4_MPZ

description:
Harford-Wright et al 2017 BRAIN
4_3708Nantes_GSC9-4hr-MPZ-1_RNASeq_hs_i11


title: 5_MPZ

description:
Harford-Wright et al 2017 BRAIN
5_3708Nantes_GSC9-4hr-MPZ-2_RNASeq_hs_i12


title: 6_MPZ

description:
Harford-Wright et al 2017 BRAIN
6_3708Nantes_GSC9-4hr-MPZ-3_RNASeq_hs_i13


title: 1_DMSO

description:
Harford-Wright et al 2017 BRAIN
1_3708Nantes_GSC9-4hr-DMSO-1_RNASeq_hs_i8


title: OVCAR8 Plastic 61


title: 101130760020_R02C01

label: Cy5 and Cy3

tag: gender


title: OVCAR8 3D 62

value: 3D omentum culture


title: 101070190151_R06C02


title: OVCAR8 Plastic 4


title: OVCAR8 3D 61


title: OVCAR8 3D 4


title: 101070190151_R05C02


title: OVCAR4 Plastic 4


title: 101070190151_R04C02


title: 101130760020_R03C01


title: OVCAR4 Plastic 6


title: OVCAR4 3D 42


title: OVCAR4 Plastic 42


title: OVCAR4 3D 6


title: 101070190151_R02C02


title: 101070190151_R03C02


title: Kuramochi plast 8

value: Kuramochi


title: OVCAR4 3D 4


title: 101070190151_R01C02


title: 22: MIFko_D7

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: All samples were checked for RNA quality prior to hybridization by Agilent 2100 Bioanalyzer (Agilent).

scan_protocol: Data were generated at the Wellcome Trust Clinical Research Facility (WTCRF) located at Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU. A total of 24 Illumina MouseWG6_V2_0_R3_11278593_A arrays were QC analyzed using the arrayQualityMetrics Bioconductor package to identify sub-standard and/or outlier arrays, which were not included in this data deposition.

data_processing: IlluminaIDs were converted to nuIDs using the lumi Bioconductor package, probe features filtered to include only those with detection call p value greater than zero, and the remainder normalised using VST/VSN.

source_name: Duodenal tissue

label_protocol: RNA amplification and biotinylation prior to array hybridization was performed using the Illumina TotalPrep RNA Amplification kit (Ambion) according to manufacturer’s instructions.

growth_protocol: Wild type BALB/c or MIF-deficient mice were infected with H. polygyrus for 3 or 7 days with tissues from the duodenum then collected and stored in RNA Later (Ambion) prior to processing. Duodenal tissues from uninfected BALB/c and MIFdeficient mice were also taken and stored (4 mice per group for each condition).

extract_protocol: Total RNA from tissues was extracted by firstly placing tissue in RLT buffer (Invitrogen) and then homogenized using a Tissue Lyser II (Qiagen) set for 2min at 25Hz. RNA isolation was performed with the RNeasy mini kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Tissues were extracted directly as detailed below.

value: duodenum

tag: day

value: MIFko

tag: infectionstatus

value: Heligmosomoides polygyrus Infected


title: Kuramochi plast 2


title: Kuramochi plast 4


title: 20: MIFko_D3


title: 15: MIFko_D0


title: Kuramochi 3D 4


title: 101070190151_R05C01

value: Buccal epithelial cells

tag: age


title: 101070190151_R06C01

value: Female


title: Kuramochi 3D 2

tag: cell type


title: 13: MIFko_D0


title: 23FT

source_name: FALLOPIAN TUBE

value: FALLOPIAN TUBE

value: NORMAL TISSUE

tag: ethnicity

value: Non-Hispanic

tag: race

value: White


title: 14: MIFko_D0


title: 19: MIFko_D3


title: 23P

source_name: OVARY TUMOR

value: OVARY TUMOR

value: SEROUS SURFACE PAPILLARY CARCINOMA


title: 7: BALB/c_D3

value: BALB/c


title: 24: MIFko_D7


title: 22P

value: PAPILLARY SEROUS AND ENDOMETRIOID ADENOCARCINOMA


title: 101070190151_R03C01


title: 22FT


title: 101070190151_R02C01


title: Kuramochi 3D 8

value: Ovarian cancer cells


title: 21P

value: SEROUS CARCINOMA


title: 101070190151_R01C01


title: 12: BALB/c_D7


title: 20P


title: 20FT


title: 19P

value: ENDOMETRIOID ADENOCARCINOMA


title: 19FT


title: 6: BALB/c_D3


title: 101231000131_R05C02


title: 5: BALB/c_D3


title: 2: BALB/c_D0


title: 18P

value: PAPILLARY SEROUS ADENOCARCINOMA


title: 17P

value: MIXED CLEAR CELL, ENDOMETRIOID AND PAPILLARY SEROUS CARCINOMAS


title: 101231000131_R04C02


title: 23: MIFko_D7

value: duodenum

value: MIFko


title: 16P

value: CLEAR CELL ADENOCARCINOMA, NOS


title: 101231000131_R03C02

value: Buccal epithelial cells

value: Female


title: M14B

source_name: OMENTUM

value: OMENTUM

value: PAPILLARY SEROUS CARCINOMA

tag: tumor type

value: Metastasis tumor


title: 16FT

value: FALLOPIAN TUBE

value: NORMAL TISSUE

value: Non-Hispanic

value: White


title: 101231000131_R01C02


title: 18: MIFko_D3

value: Heligmosomoides polygyrus Infected


title: 17FT


title: 21FT


title: M14A

source_name: OVARY

value: OVARY

value: Primary tumor


title: 101231000131_R06C01


title: 10: BALB/c_D7

value: BALB/c


title: 101231000131_R06C02


title: 9: BALB/c_D7


title: M13B

value: PAPILLARY SEROUS CYSTADENOCARCINOMA


title: 18FT


title: M13A


title: M12A


title: M12B


title: M10B


title: M10A


title: 1: BALB/c_D0

value: duodenum


title: M9A

value: SEROUS CARCINOMA


title: 4: BALB/c_D0


title: 101231000131_R03C01


title: M8B

value: SEROUS ADENOCARCINOMA


title: 21: MIFko_D7

value: MIFko


title: 101231000131_R02C01

value: Buccal epithelial cells

value: Female


title: M7B

value: OMENTUM

value: PAPILLARY SEROUS CARCINOMA


title: 101231000131_R05C01


title: 101231000131_R01C01


title: 101231000124_R06C02


title: 17: MIFko_D3


title: M7A


title: 101231000124_R05C02


title: 11: BALB/c_D7


title: M6A


title: M5B

value: PAPILLARY SEROUS ADENOCARCINOMA

value: Metastasis tumor


title: M2B

value: Unknown


title: M5A

value: Non-Hispanic

value: White


title: 101231000131_R04C01


title: M9B


title: 3: BALB/c_D0

value: Heligmosomoides polygyrus Infected


title: 16: MIFko_D0


title: M6B


title: M2A

value: OVARY

value: Primary tumor


title: 8: BALB/c_D3

value: BALB/c


title: 24: MIM

scan_protocol: Data were generated at the Wellcome Trust Clinical Research Facility (WTCRF) located at Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU. A total of 24 Illumina MouseWG6_V2_0_R3_11278593_A arrays were QC analyzed using the arrayQualityMetrics Bioconductor package to identify sub-standard and/or outlier arrays, which have not been included in this data submission.

source_name: mesenteric lymph nodes

growth_protocol: Wild type BALB/c or MIF-deficient mice were infected with H. polygyrus for 5 days with tissues from the duodenum (Duo) and mesenteric lymph nodes (MLN) then  and stored in RNA Later (Ambion) prior to processing. Duodenal tissues from uninfected BALB/c and MIFdeficient mice were also taken and stored (4 mice per group for each condition).

value: mesenteric lymph nodes

tag: treatment

value: MIM

value: MIFKO


title: 101231000124_R02C02


title: 101231000124_R01C02


title: M1B

source_name: PERITONEUM

value: PERITONEUM

value: SEROUS SURFACE PAPILLARY CARCINOMA


title: M8A

value: SEROUS ADENOCARCINOMA


title: piRNA day_0_3D - donor#3 - replicate#2

city: Davos Platz

first: Martin

middle: J

last: Stoddart

address: Clavadelerstrasse 8

country: Switzerland

institute: AO Research Institute Davos

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_41

data_processing:
Illumina NextSeq 500 raw sequencing read datathat passed the Illumina chastity filter were used for the following analysis. Trimmed reads (with 5’,3’-adaptor bases removed) were aligned to the piRBase, which is a manually curated resource of piRNAs. The maximum mismatch <= 2 reads are kept. The alignment statistical analysis was applied to retain the valid sequences for piRNA expression profiling and differential expression analysis. Hierarchical clustering, scatter plots and classification analysis were performed for the differentially expressed piRNAin R or Perl environment for statistical computing and graphics.
Raw data files in FASTQ format were generated by the Illumina sequencer. To examine the sequencing quality, the quality score plot of each sample was plotted.
After Illumina quality control, the sequencing reads were 5', 3'-adaptor trimmed, filtered for >=15 nt by cutadapt software, and aligned to piRBase (a manually curated resource of piRNAs) using NovoAlign software (v2.07.11) [3].The maximum mismatch <= 2 reads to the piRBase were kept.
After passing the Solexa CHASTITY filtering and 3'-adapter filter, the 3'-adapter trimmed reads were formatted into a non-redundant FASTA file where the copy number and sequence were recorded for each unique read. A bar graph is used to show the sequence read length distribution.
The piRNAs, which total number of sequence reads larger than five, were kept for normalization. The piRNA expression levels were measured and normalized as tag counts per million of total aligned piRNA reads (TPM/CPM). When comparing two groups of profile differences (such as disease versus control) use the normalized tag number of piRNAs, including the tag count of each sample, the "fold change" (i.e. the ratio of the group averages) between the groups for each piRNA is computed. piRNAs having fold changes >= 1.5 or fold changes <= 0.67 are selected as the differentially expressed piRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file with known expression (Reads Count)

source_name: Human mesenchymal stromal cells from bone marrow (vertebra)

growth_protocol: MSCs were seeded at an initial cell density of 3x103 cells/cm2 and grown in α-MEM with 10% MSC-qualified FBS, 100 U/mL penicillin, 100 μg/mL streptomycin and 5 ng/ml basic Fibroblast Growth Factor. Cultures were maintained at 37°C/5% CO2, and the medium was refreshed every second day.

extract_protocol:
Total RNA was isolated from day 0 2D and 3D samples collected in TRIreagent following manufacturer's instructions. Briefly, 100 µl of 1-Bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO, USA) were added to TRIreagent, mixed thoroughly and the samples were centrifuged at 12000 g for 15 min at 4°C. The recovered aqueous phase was mixed with 500 µl of 2-propanol (Sigma-Aldrich) and precipitation of RNA was carried out overnight at -20°C for enhanced recovery of small RNA species. RNA pellet was then washed with 75% EtOH (Sigma-Aldrich) and resuspended in 20 µl of DEPC-treated H2O. Total RNA concentration was measured with NanoDrop 1000 (Thermo Fisher) and purity was assessed by evaluation of the A260/280 and A260/230 ratios.
Total RNA of each sample was used to prepare the piRNA-sequencing library, which included the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~142-153bp PCR amplified fragments (corresponding to ~24-35 nt small RNAs). The libraries are qualified and quantified using Agilent BioAnalyzer2100. The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq follow the manufacturer’s instructions.

treatment_protocol: Cells were further expanded in the same expansion medium. When the cells were 70% confluent, cells were collected for RNA extraction. Monolayer of cells in triplicate, grown in 25 cm2 flasks (day 0 2D), were lysed directly with 1 ml of TRIreagent. The other cells were detached with 0.05% Trypsin-EDTA and counted. For each donor, three different aliquots of 1x106 cells each (day 0 3D) were lysed in 1 ml of TRIreagent within 30 minutes from trypsinization.

value: 55 years

tag: Sex

value: Female

tag: cell status

value: trypsinized cells


title: piRNA day_0_3D - donor#3 - replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_40


title: 101231000124_R06C01

value: Buccal epithelial cells


title: 101231000124_R05C01


title: 20: BIM

value: BIM

value: Balb/c


title: piRNA day_0_3D - donor#2 - replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_39

value: 80 years

value: Male


title: piRNA day_0_3D - donor#2 - replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_38


title: piRNA day_0_3D - donor#1 - replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_24

value: 59 years


title: 101231000124_R04C02


title: 101231000124_R04C01


title: 12: MUD

source_name: duodenal gut tissue

value: duodenum

value: MUD

value: Uninfected


title: piRNA day_0_2D - donor#3 - replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_20

value: monolayer adhesion


title: piRNA day_0_2D - donor#3 - replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_21


title: piRNA day_0_3D - donor#1 - replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_23


title: 4: BUD

value: BUD


title: piRNA day_0_2D - donor#2 - replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_6


title: 101231000124_R02C01


title: piRNA day_0_2D - donor#1 - replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_3


title: piRNA day_0_2D - donor#1 - replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_2


title: 8: BID

value: BID

value: Heligmosomoides polygyrus Infected


title: 101231000124_R01C01


title: miRNA day_0_3D - donor#3 - replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_41

data_processing:
Raw sequencing data generated from Illumina NextSeq 500 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis, we determine whether the results can be used for subsequent data analysis. If so, the expression profiling, differentially expressed miRNA are calculated. The novel miRNA are also predicted.  Hierarchical Clustering, miRNA Target analysis, Target Gene Ontology (GO), Target Pathway Analysis, scatter plots and volcano plots are performed for the differentially expressed miRNA in R or Python environment for statistical computing and graphics.
Raw data files in FASTQ format were generated from the Illumina sequencer. To examine the sequencing quality, the quality score plot of each sample was plotted.
After quality control, the reads were 3’-adaptor trimmed and filtered ≤15 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with bowtie software.
The expression level (Reads count) of miRNA were calculated using mirdeep2.
Differentially expressed miRNAs analyses were performed with R package edgeR. Fold change (cutoff 1.5), p-value ( 0.05) and CPM ( 1 mean in one group) were used for filtering differentially expressed miRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file with known expression (Reads Count)

extract_protocol:
Total RNA was isolated from day 0 2D and 3D samples collected in TRIreagent following manufacturer's instructions. Briefly, 100 µl of 1-Bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO, USA) were added to TRIreagent, mixed thoroughly and the samples were centrifuged at 12000 g for 15 min at 4°C. The recovered aqueous phase was mixed with 500 µl of 2-propanol (Sigma-Aldrich) and precipitation of RNA was carried out overnight at -20°C for enhanced recovery of small RNA species. RNA pellet was then washed with 75% EtOH (Sigma-Aldrich) and resuspended in 20 µl of DEPC-treated H2O. Total RNA concentration was measured with NanoDrop 1000 (Thermo Fisher) and purity was assessed by evaluation of the A260/280 and A260/230 ratios.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3’-adaptor ligation; 2) 5’-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 135~155 bp PCR amplified fragments (corresponding to 15~35 nt small RNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq per the manufacturer’s instructions. Agilent 2100 Bioanalyzer was used for assessment of the quality of sequencing library. Library concentration was determined by qPCR method.


title: 19: BIM

value: mesenteric lymph nodes


title: miRNA day_0_3D - donor#2 - replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_39


title: miRNA day_0_3D - donor#3 - replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_40

value: 55 years


title: miRNA day_0_3D - donor#2 - replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_38


title: 101231000093_R06C02

value: Female


title: 23: MIM

value: MIM

value: MIFKO


title: 15: MID

value: MID


title: 101231000124_R03C01

value: Buccal epithelial cells


title: 101231000093_R05C02


title: miRNA day_0_3D - donor#1 - replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_24

value: trypsinized cells


title: miRNA day_0_3D - donor#1 - replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_23

value: Male


title: 7: BID

value: Balb/c


title: 101231000093_R04C02


title: miRNA day_0_2D - donor#3 - replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_21


title: piRNA day_0_2D - donor#2 - replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
Sample_5

value: 80 years


title: miRNA day_0_2D - donor#3 - replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_20


title: 11: MUD

value: duodenum

value: MUD


title: 101231000093_R03C02


title: miRNA day_0_2D - donor#2 - replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_6

value: monolayer adhesion


title: miRNA day_0_2D - donor#1 - replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_3

value: 59 years


title: 101231000093_R02C02


title: 22: MIM


title: miRNA day_0_2D - donor#1 - replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_2


title: 14: MID


title: 101231000093_R01C02


title: 18: BIM

value: BIM


title: DU145_shE2F1_3

city: Nanning

first: Qingniao

last: Zhou

state: Guangxi

address: 22 Shuangyong road

institute: Guangxi Medical Universtiy

data_processing:
RNA-seq alignment (1.1.1) in Illumina BaseSpace platform was used for processing data.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR aligner in RNA-seq alignment application.
Reads Per Kilobase of exon per Megabase of library size (RPKM) estimation of reference genes and transcripts using Cufflinks 2, assembly of novel transcripts with Cufflinks 2.
Variant calling (SNVs and small indels) with the Isaac Variant caller, Manta is used for Optional fusion calling.
Genome_build: hg38
Supplementary_files_format_and_content: text files include RPKM values for each Sample

growth_protocol: PC3 and DU145 were cultured at 37 ℃ in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using  AxyPrep TM Multisource Total RNA Miniprep Kit (Corning Incorporated; NY, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Prostate cancer

value: Prostate cancer cells

value: E2F1 knockdown


title: 101231000093_R06C01

value: Female


title: DU145_shE2F1_2

tag: genotype


title: DU145_shE2F1_1

tag: cell line


title: DU145_vector_2

value: vector


title: 101231000093_R05C01


title: DU145_vector_3


title: DU145_vector_1


title: 101231000093_R04C01


title: 101231000093_R03C01


title: PC3_shE2F1_3


title: miRNA day_0_2D - donor#2 - replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
Sample_5


title: PC3_vector_3


title: PC3_shE2F1_1


title: PC3_vector_2


title: 101231000093_R02C01


title: PC3_vector_1


title: 101231000093_R01C01


title: 6: BID

value: BID

value: Heligmosomoides polygyrus Infected


title: 10: MUD

value: MIFKO

value: Uninfected


title: 17: BIM

value: mesenteric lymph nodes


title: 21: MIM

value: MIM


title: 13: MID

value: MID


title: 101231000088_R06C02

value: Buccal epithelial cells


title: 101231000088_R05C02


title: 101231000088_R04C02


title: 2: BUD

value: duodenum

value: BUD

value: Balb/c


title: 9: MUD

value: MUD


title: 101231000088_R02C02


title: 101231000088_R01C02


title: 5: BID


title: 101231000088_R06C01


title: 101231000088_R05C01


title: 101231000088_R04C01


title: 101231000088_R03C01


title: 101231000088_R01C01


title: Tbr2 conditional knockout _ embryonic cortex stage E16_replicate 6 [re-analysis]

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

institute: INSERM U839

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadArray Reader used to capture images with default setting.

data_processing: Illumina GenomeStudiov2011.1 were used to obtain raw signal intensities. Background substracted signal intensity for the detected probes (Detection p value<0.05) were used for analysis. Probes detected in one array and not in other were not considered during analysis. Further, outlier probes were removed and data were quantile normalized (Bolstad BM et al., 2003) along with our microarray gene expression data of E13 and E16 (GSE45450) and Tbr2 conditional knockout data (GSE121180).

label: biotin

label_protocol: Biotinylated cRNA were prepared by using Illumina TotalPrep-96 RNA amplification kit from Ambion # 4393543

extract_protocol: Total RNA was extracted from FACS isolated Tbr2 lineage neurons (GFP+) by using  mirVana kit (ambion) following manufacturer's protocol

value: embryonic cortex stage


title: 16: MID


title: Tbr2 conditional knockout _ embryonic cortex stage E16_replicate 4 [re-analysis]


title: 101231000078_R06C02


title: 101231000088_R03C02


title: Tbr2 conditional knockout _ embryonic cortex stage E16_replicate 2 [re-analysis]


title: 101231000078_R05C02


title: Tbr2 conditional knockout _ embryonic cortex stage E13_replicate 5 [re-analysis]

description:
Tbr2 lineage neurons_postnatal day 2_replicate 5
GFPplus_7_BS


title: Tbr2 conditional knockout _ embryonic cortex stage E16_replicate 3 [re-analysis]


title: Tbr2 conditional knockout _ embryonic cortex stage E16_replicate 5 [re-analysis]


title: Tbr2 conditional knockout _ embryonic cortex stage E16_replicate 1 [re-analysis]


title: Tbr2 conditional knockout _ embryonic cortex stage E13_replicate 4 [re-analysis]

description:
Tbr2 lineage neurons_postnatal day 2_replicate 4
GFPplus_6_BS


title: 101231000078_R03C02


title: 101231000078_R02C02


title: 101231000078_R04C02


title: 1: BUD


title: Tbr2 conditional knockout _embryonic cortex stage E13_replicate 1 [re-analysis]

description:
Tbr2 lineage neurons_postnatal day 2_replicate 1
GFPplus_2_BS


title: Tbr2 conditional knockout _ embryonic cortex stage E13_replicate 2 [re-analysis]

description:
Tbr2 lineage neurons_postnatal day 2_replicate 2
GFPplus_3_BS


title: 101231000078_R01C02


title: 101231000078_R06C01


title: E16 embryo_rep3 [re-analysis]

source_name: E16 embryo_rep3

value: E13 embryo


title: Tbr2 conditional knockout _ embryonic cortex stage E13_replicate 3 [re-analysis]

description:
Tbr2 lineage neurons_postnatal day 2_replicate 3
GFPplus_5_BS


title: 101231000078_R05C01

source_name: buccal swab genomic DNA


title: 101231000078_R04C01


title: E16 embryo_rep4 [re-analysis]

source_name: E16 embryo_rep4


title: E16 embryo_rep5 [re-analysis]

source_name: E16 embryo_rep5


title: E16 embryo_rep2 [re-analysis]

source_name: E16 embryo_rep2


title: E16 embryo_rep1 [re-analysis]

source_name: E16 embryo_rep1


title: 101231000078_R02C01


title: 101231000078_R03C01


title: 101231000076_R06C02


title: 101231000078_R01C01


title: E13 embryo_rep6 [re-analysis]

source_name: E13 embryo_rep6


title: E13 embryo_rep5 [re-analysis]

source_name: E13 embryo_rep5


title: 101231000076_R04C02


title: E13 embryo_rep3 [re-analysis]

source_name: E13 embryo_rep3


title: 101231000076_R03C02


title: 101231000076_R01C02


title: 101231000076_R02C02


title: 101231000076_R06C01


title: AVJ-E13.5-ATAC

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
ATAC-seq: reads were mapped to mm9 build of the mouse genome using BWA (Li et al., 2009) using default settings, generating BAM and SAM files
To generate the bed file, peaks were called on the SAM file using the OccuPeak method (de Boer et al., 2014). Excess ratio threshold was put at >3.5
Genome_build: mm9
Supplementary_files_format_and_content: BED file (peaks called)

source_name: Venus+ E14.5 atrioventricular junction

growth_protocol: Animal care was in accordance with guidelines from the European Union and Amsterdam University Medical Centers. Tbx3Venus mice were maintained on a FVB/NJ background commercially obtained from Jackson laboratory (stock number 100800).

extract_protocol:
Tbx3Venus/+ hearts were dissected from embryonic day (E) 12.5-E14.5 embryos and AV conduction system tissues were isolated by microdissection. Tissue samples were dissociated into a single cell suspension using 0.05% Trypsin/EDTA (ThermoFisher Scientific, 25300-054) for 15 minutes at 37°C. Dissociated cells were resuspended in DMEM (ThermoFisher Scientific, 31966-021) supplemented with 10% FBS (ThermoFisher Scientific, 10270-106) and fluorescence activated cell sorting (FACS) performed selecting for cells with Venus fluorescence. Approximately 75.000 Venus+ cells were collected and used as input for assay for transposase-accessible chromatin (ATAC)-sequencing.
Venus+ cells were washed in PBS and lysed in cold lysis buffer (10mM Tris.Cl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) Igepal CA-630). Transposition reaction on the nucleus extract was performed as described using the Nextera DNA Library Prep kit (Illumina, FC-121-1030) for 30 minutes, followed by cleanup using the MinElute PCR Purification Kit (Qiagen, 28004). Transposed DNA fragments were amplified using NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs, M0541) with custom barcoded PCR primers (sequences as described in Buenrostro et al., 2013). The amplified library was purified using the MinElute PCR Purification Kit (Qiagen, 28004).  Pooled libraries sequenced on a NextSeq 500 system (Illumina) with 76 bp single-end reads.

treatment_protocol: No treatment conducted

tag: strain

value: FVB/NJ

value: Embryonic day 14.5

value: Atrioventricular junction (AVJ)


title: 101231000076_R05C02

value: Female


title: 101231000076_R05C01


title: NCoR1 KD CpG Rep2

city: Bhubaneswar

first: Sunil

middle: Kumar

last: Raghav

state: Odisha

address: Nalco Square

department: Infectious Disease Biology

country: India

institute: Institute of Life Sciences

description:
CpG activation (NCoR1 KD)
Emp_CpG_NCoR1_CpG.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were checked for quality using FastQC v0.11.5, then mapped to mm10 whole genome using TopHat v2.1.0 with defult parameters
Fragment Per Kilobase of exon per Megabase of library size (FPKM) and differential expression were calculated using cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output

source_name: CpG activation (NCoR1 KD)

growth_protocol: The CD8α+ DC lines were grown in IMDM medium supplemented with 10% FBS and antibiotic solution (Gibco), 5x10-5M 2-mercaptoethanol,sodiumbicarbonate, hepes. The cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
The cells were thawed by placing the plates/tubes on ice. Total RNA was isolated using RNeasy plus kit (Qiagen) according to vendor recommended protocol. RNA concentration was estimated by nanodrop (Thermo)
2 ug of total RNA was used to isolate mRNA through magnetic beads using mRNA isolation kit (PolyA mRNA isolation Module, NEB) followed by RNA-seq library preparation using mRNA library preparation kit (NEB) strictly following the vendor recommended protoco.l

treatment_protocol: DCs were plated in 6 well plates at a density of 5 x 10^6 cells/ml overnight. Cells were challenged with different activation media containing TLR9 agonist CpG-B, TLR3 agonist pIC for different time points. cells were washed in the plate once with PBS followed by addition of RNA-later (RLT) buffer (Qiagen) for lysis of cells. The plates were then stored at -80oC until further RNA isolation and processing of samples.

tag: genotype/variation

value: NCoR1 KD

tag: cell line genetic background strain

value: Dendritic cell


title: NCoR1 KD CpG Rep1


title: 101231000076_R04C01

data_processing:
Minfi preprocessIllumina was used to process samples (for background subtraction and colour correction).
Average Beta (after minfi::preprocessIllumina in R).

tag: tissue

tag: gender


title: E13 embryo_rep2 [re-analysis]

source_name: E13 embryo_rep2


title: NCoR1 KD Uns Rep2

description:
Unstimulated (NCoR1 KD)
Emp_Uns_NCoR1_Uns.txt

source_name: Unstimulated (NCoR1 KD)


title: E13 embryo_rep1 [re-analysis]

source_name: E13 embryo_rep1


title: Neurons (GFPpositive) _postnatal day2_replicate 3

source_name: tissue: Brain cortex, cell type: neurons

value: Postnatal day 2

value: Neurons (GFPpositive)

value: Brain cortex


title: Neurons (GFPpositive) _postnatal day2_replicate 5


title: Neurons (GFPpositive) _postnatal day2_replicate 2


title: Neurons (GFPpositive) _postnatal day2_replicate 1


title: NCoR1 KD Uns Rep1


title: 101231000076_R03C01


title: M1A

source_name: OVARY

value: OVARY

value: SEROUS SURFACE PAPILLARY CARCINOMA

value: Primary tumor

value: Non-Hispanic

value: White


title: 101231000076_R02C01

value: Buccal epithelial cells


title: Neurons (GFPpositive) _postnatal day2_replicate 4


title: E13 embryo_rep4 [re-analysis]

source_name: E13 embryo_rep4


title: 101231000076_R01C01


title: 24uv4_L_4: 24hour_MONDNJ_LPS_rep4

city: Oxford

first: Andrew

middle: Cameron

last: Sayce

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

scan_protocol: Standard Illumina scan protocol using iScan system

data_processing: Bead-level data were processed in Illumina GenomeStudio analytical software to generate mappings and probe-level intensities. Probe-level data was imported into R Bioconductor v2.14 using the lumi package. Data were normalised using neqc protocol. Inclusion criteria for further analysis required a detection p-value <0.01 for at least 1 of the 48 samples for a given probe. This analysis identified 21,705 expressed probes for further evaluation.

label: Biotin

source_name: Monocyte-derived macrophage, MON-DNJ treated, LPS treated, 24 hours

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by centriguation through Ficoll-Paque PLUS density gradient. Monocytes were isolated by adherence to tissue culture plates coated in 2% bovine gelatin, transferred to 6 well plates seeded at 3x10^6 cells, and cultured in X-VIVO 10 supplemented with 1% (v/v) donor-autologous heat-inactivated human plasma and 25 ng/mL recombinant human interleukin-4 for 3 days at 37°C, 5% CO2 to differentiate into macrophages.

extract_protocol: Samples were washed in 37°C PBS containing calcium and magnesium once followed by lysis in TRIzol reagent for 5 minutes. Samples were applied to a Direct-zol RNA Mini-prep column (Zymo Research) and treated according to manufacturer's instructions to collect total RNA.

treatment_protocol: At 3 days, media was removed, and infectious stimuli diluted in X-VIVO 10 (or X-VIVO 10 only) were added to samples. Infection (or mock-infection) occurred at room temperature (20°C) with rocking for 90 minutes. Mock-media and DENV-media were removed at 90 minutes and replaced with MON-DNJ or control media containing 1% autologous plasma. LPS treatments were diluted to a final concentration of equivalent drug and autologous plasma. Treatmentwith drug or control was continued such that total time of treatment including the 90 minute infection was 6 hours or 24 hours.

value: Monocyte-derived macrophage

tag: time point

value: 24 hours p.i.

tag: drug treatment

value: MON-DNJ, 25 μM

tag: infection

value: LPS, S. enterica, 200 ng/mL pulse, 100 ng/mL sustained

tag: replicate


title: 101178130143_R06C02

source_name: buccal swab genomic DNA

extract_protocol: Genomic DNA was extracted using the Masterpure system (Epicentre, USA) and quantified using a NanoPhotometer P300 (Implen, Germany). Bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

tag: age


title: Input

data_processing:
Basecalls performed using integrated primary analysis software called RTA (Real TimeAnalysis. v1.18) for PU.1 datasets.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.6 with --qc-filter -P -t  -q
Uniquely aligned reads were taken for downstream analysis
peaks were called using findPeaks form HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files were generated using HOMER tool and further converted to BigWig using bedGraphToBigWig

source_name: DC1940 cell line

extract_protocol:
Cell pellets were treated with different chromatin extraction buffer supplemented with protease and phosphatase inhibitors (Roche)  then clarified from sonicated nuclei and histone-DNA complexes were isolated with respective antibodies. 50 µl blocked protien A sepharose beads were added to each sample and incubated for 2.5h at 4°C to pull down the respective antibody-chromatin complexes. The beads were then washed with different washing buffers. Protein-bound chromatin complexes were eluted from beads for 30 min using elution buffer followed by reverse-crosslinked by incubating the eluted supernatant at 65°C overnight. Next day DNA was purified from the reverse cross-linked chromatin by proteinase-K and RNase digestion followed by purification using PCR purification kit (Qiagen).
For ChIP-seq library preparation, 30 µl ChIP-DNA was processed for library preparation according to ChIP-seq library preparation recommended protocol (NEB)

treatment_protocol: DCs were plated in 15 cm plates at a density of 30 x 106 cells/ml overnight. cells were then challenged with different activation media containing TLR9 agonist CpG-B, TLR3 agonist pIC for different time points. the cells were cross-linked using 1% formaldehyde (sigma) for 10 min at room temperature followed by quenching the reaction using 2.5 M glycine (sigma) for 10 min. The plates were placed on ice and the cells were scraped and collected in 50 ml conical tubes. The cells were then washed three times using cold 1 x PBS and cell pellets were stored at -80°C.

value: wildtype

tag: cell type

tag: chip antibody


title: NCoR1 ChIPseq 0hr

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.6 with --qc-filter -P -t  -q. Uniquely aligned reads were taken for downstream analysis
peaks were called using findPeaks form HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files were generated using HOMER tool and further converted to BigWig using bedGraphToBigWig


title: Empty CpG Rep2

description:
CpG activation (Control)
Emp_CpG_NCoR1_CpG.txt

source_name: CpG activation (Control)


title: 24uv4_L_2: 24hour_MONDNJ_LPS_rep2