title: S3_C_3 (bicolor leaf development)

description: Bicolor leaf during development proceeded as follows: S1, leaves are red; S2, red appears at the leaf center, although the margins are green; and S3, the leaf center is red while the margins are green. Samples of the red center at S3.

value: the red center at S3


title: MF33_flg22_rep3 (MAE030)

status: Public on Mar 27 2021

type: SRA

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.20.0 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC
Trimmomatic was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using HISAT2
The featureCounts function from the subread package was used to count reads that mapped to protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were germinated on Johnson medium solidified with 1% bacto-agar. Plates were kept in the vertical position for seven days in a growth chamber under a 16-hour light/8-hour dark regime at 21oC day/18oC night. The resulting seedlings were then submitted to the treatments.

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings according to Logemann, J. et al. Anal. Biochem. 163, 16–20 (1987). PMID: 2441623.
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

treatment_protocol: Seven-day old seedlings were transferred to Johnson medium with or without 1 µM of flg22 (in the presence of a commensal strain; 10e5 cfu/mL). Plates were kept in a growth chamber under a 9-hour light/15-hour dark regime at 21oC day/18oC night. The entire eedlings was harvested for RNA extraction 12 days after the transfer to the treatment plates.

tag: ecotype

tag: bacteria presence

tag: treatment

tag: time

tag: experiment


title: 7

city: Shanghai

first: Jing

last: Yang

state: Shanghai

address: No. 1508 Longhang Road  Jinshan District

department: Pediatrics

country: China

institute: Jinshan Hospital of Fudan University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10/hg19 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: Genome_build: mm10/hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

tag: strain

tag: age

value: 8.71 weeks

tag: genotype/variation


title: 199

value: wild type


title: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+ ZH_7263

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

description: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+

data_processing:
bcl2fastq v2.20 was used for base calling and demultiplexing
Reads were trimmed for adaptors using fastp v 0.20.0
Reads were aligned using STAR v 2.7.4a
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include raw values for each sample

source_name: Distal convoluted tubule

extract_protocol:
β-mercaptoethanol-containing RNA Lysis buffer was added to 1000 Biosorter-sorted DCT fragments. RNA was isolated using NucleoSpin® RNA/Protein Kit (Macherey-Nagel, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Recombination of Cre was induced by the oral gavage of tamoxifen (2mg/animal/day in ethanol – sunflower oil mixture with a ratio of 1:9, respectively) for five consecutive days. Experiments were performed 3 weeks after induction.

tag: genotype

value: Control


title: MF33_flg22_rep2 (MAE029)


title: S3_C_2 (bicolor leaf development)

city: Shenyang City

first: jie

last: ren

address: Dongling Road NO.120

institute: Shenyang Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to brassica_oleracea ensemble v38 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM. estimate the expression levels of all transcripts. software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: brassica_oleracea ensembl v38 (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Brassica oleracea

source_name: Brassica oleracea L. var. acephala

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

tag: tissue

value: leaf

tag: leaf developmental stage


title: HMJ5-379

city: Huntington

first: Sandrine

last: Pierre

state: West Virginia

address: 1676 Third Avenue

department: MIIR

country: USA

institute: Marshall University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes log2FoldChange, padj, gene name
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from cardiac tissue using Trizol® reagent (Life Technologies, Carlsbad, CA, USA) and the RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
RNA-seq was performed by Novogene (Sacramento, CA, USA) using the Illumina NovaSeq 6000 system.

tag: strain background

value: Na/K-ATPase a1s/sa2s/s (sensitive)

value: 3 months

value: Heart


title: MF33_flg22_rep1 (MAE028)


title: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+ ZH_7285

description: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+


title: 6


title: MF33_Mock_rep3 (MAE027)

value: Mock


title: MF33_Mock_rep2 (MAE026)


title: S3_C_1 (bicolor leaf development)


title: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+ ZH_7284

description: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+

value: KO


title: 158

value: 11.14 weeks


title: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+ ZH_7282

description: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+


title: S2_2 (bicolor leaf development)

description: Bicolor leaf during development proceeded as follows: S1, leaves are red; S2, red appears at the leaf center, although the margins are green; and S3, the leaf center is red while the margins are green. Samples of whole leaf without veins at S2.

value: whole leaf without veins at S2


title: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+ ZH_7281

description: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+


title: 146

value: 11.29 weeks


title: MF40_Mock_rep1 (MAE031)


title: 156


title: MF33_Mock_rep1 (MAE025)


title: S2_1 (bicolor leaf development)


title: MF29_flg22_rep3 (MAE024)


title: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+ ZH_7286

description: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+


title: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+ ZH_7232

description: Cnb1fl wt, NCCcre Tg/+, TOMATO Tg/+


title: MF29_flg22_rep2 (MAE023)


title: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+ ZH_7231

description: Cnb1fl Tg/Tg, NCCcre Tg/+, TOMATO Tg/+


title: S1_3 (bicolor leaf development)

description: Bicolor leaf during development proceeded as follows: S1, leaves are red; S2, red appears at the leaf center, although the margins are green; and S3, the leaf center is red while the margins are green. Samples of whole leaf without veins at S1.

value: whole leaf without veins at S1


title: HEK293T_rep3_eEndoV

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

data_processing:
Library strategy: Slic-seq
Adapter seqeucnes were trimmed by using trim_galore
fastuniq is used to remove PCR duplication. Then use seqtk trimfq '-e 10' or '-b 6 -e 10' remove random sequences added in library construction
Clean reads were mapped to genome by using HISAT2; with parameter "--mp 4,2 --rna-strandness RF --no-softclip --no-mixed --no-discordant".
Peak detection within genes. To search for enriched peaks in the treated samples, we scanned each gene using sliding windows of 100 nt with 50 nt overlaps. The total number of reads per window was calculated for each dataset. The number of reads for each window in treated and control was determined using HTSeq 0.12.4(-s no -m union --nonunique all parameters)
A custom python script was used to parse the pileup format into a tabular format summarizing the mutation at each position.
Genome_build: hg38 and mm10

organism: Homo sapiens

source_name: HEK293T cell line

growth_protocol: HEK293T cells were cultured in DMEM medium without sodium pyruvate (Dulbecco’s Modified Eagle Medium, HyClone) supplemented with 10% FBS (Cegrogen) and 1% penicillin/streptomycin (Genview). The cells were maintained at 37 ℃ under a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from cell lines or mouse tissues with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25 (NEB)
Fragmented RNA was first subjected to end repair by T4 PNK. For the treated sample, the RNA was treated with periodate followed by Endonuclease V cleavage.3′-adapter ligation (3′ adapter, /5rApp/NNNNNNTGGAATTCTCGGGTGCCAAGG/3ddC/) followed by the 3′ adapter removing by 5′-deadenylase and RecJf digestion. After purification, SuperScript III was used to perform RT (RT primer, /ACACGACGCTCTTCCGATCT). After cDNA synthesis, 5′ adapter (5′ adapter, /5Phos/NNNNNNNNNNAGATCGGAAGAGCACACGTCTG/3ddC/) ligation were performed. After purification, qPCR was performed to evaluate the cycle numbers of each samples to avoid over-amplification. Library PCR amplification was performed using the NEB primers. The products were purified by NEBNext Sample Purification Beads or low melting point agarose gel and used for sequencing.

treatment_protocol: Total RNA was isolated from cell lines or mouse tissues with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25(NEB) and gDNA was removed by TURBO DNase (Invitrogen). Purified polyadenylated RNA was fragmented using RNA fragmentation reagents (Ambion) at 70 °C for 10 min. Fragmented RNA was incubated with freshly prepared 50 mM NaIO4 at 25°C for 30 min in the dark.The RNA cleave assays were performed using Endonuclease V (NEB) with standard reaction buffer (10mM Tris-HCl pH 7.5, 0.5mM MnCl2, 50mM KCl, 1mM dithiothreitol and 5% glycerol)  and then perform next-generation sequencing (NGS).

tag: cell line

value: eEndoV

tag: tissue type

value: human cell line


title: MF29_flg22_rep1 (MAE022)


title: S1_2 (bicolor leaf development)


title: MF29_Mock_rep3 (MAE021)


title: S1_1 (bicolor leaf development)


title: HEK293T_rep2_eEndoV


title: HEK293T_rep1_eEndoV


title: S2_3 (bicolor leaf development)


title: Yap KO_atrophy_rep1

city: Cleveland

first: Thaddeus

last: Stappenbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Lerner Research Institute

data_processing:
Quality control, sample demultiplexing, barcode processing, alignment, and UMI counting were performed with Cell Ranger Single Cell Software Suite (v4.0.0).
Filtered gene-barcode matrices generated by Cell Ranger were read into the Seurat package (v3.2.2) on RStudio (v1.3.1056) for subsequent analysis. Low quality cells with high (>9,000) and low (<500) unique gene counts and high mitochondrial counts (>20%) were first filtered out. The resulting data was log-normalized with a scale factor of 10,000 (NormalizeData function). Highly variable genes were identified (FindVariableFeatures function), and paired samples were integrated (FindIntegrationAnchors and IntegrateData functions). Principal component analysis (PCA) scores were computed on scaled data based on the top 2,000 variable genes (ScaleData and RunPCA functions). UMAP dimensionality reduction and clustering (resolution 0.2) were performed using the first 15 PCs to visualize cell states in two dimensions (RunUMAP, FindNeighbors, and FindClusters function). When integrating multiple samples, replicates (1 and 2) were compared to assess batch-to-batch variation, homeo replicate 1 and atrophy replicate 1 were compared to assess the effect of villus atrophy, and Yap WT replicate 1 and Yap KO replicate 2 were compared to assess the effect of Yap deletion.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes, and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Intestinal epithelium, villus atrophy

growth_protocol: Mice were housed under specific-pathogen-free conditions with free access to autoclaved food and water and were maintained on a 12h light/dark cycle.

extract_protocol:
Intestinal tissues were incubated in 30mM EDTA, first on ice for 20min with 1.5mM DTT and second at 37C for 10min without DTT, and then shaken to lift the epithelium. Epithelial cells were dissociated in an enzymatic cocktail containing 1mg/mL Collagenase/Dispase (Roche) and 0.2mg/mL DNase I (Roche) at 37C for 10min with intermittent shaking. The cell suspension was additionally subjected to vigorous pipetting and filtered through 70 and 40um strainers. Cells were washed in 10% FBS/PBS solution and resuspended in FACS buffer containing 2% BSA, 2mM EDTA, and 25mM HEPES in PBS. ROCK inhibitor (R&D Systems) was added to every solution throughout the experiment. After excluding debris and gating for singlets, live (SYTOX-Red negative) epithelial cells were sorted and resuspended in 10% FBS/DMEM-F12 solution for single-cell capture and sequencing.
Single cell suspensions went through GEM generation and barcoding, followed by GEM RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits (v3 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v3 (PN-1000075), Chromium Single Cell B Chip Kit (PN-1000153), Dual Index Kit TT Set A (PN-1000215) and Chromium i7 Multiplex Kit, 96 rxns (PN-120262) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28x10x10x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

treatment_protocol: Mice were given one intraperitoneal injection of 20mg/kg poly(I:C) HMW (InvivoGen) to induce villus atrophy in the proximal small intestine. An equivalent volume of saline (0.9% NaCl solution) was injected in control mice. Duodenal tissues were harvested 24h post-injection.

value: Vil1-Cre; Yap-flox/flox

value: 8 weeks

tag: cell type

value: Intestinal epithelium

tag: region

value: injured & distal uninjured duodenum

value: 24h after poly(I:C) injection


title: Yap KO_atrophy_rep2


title: HEK293T_rep3_control

value: control


title: HEK293T_rep2_control


title: MF29_Mock_rep2 (MAE020)

tag: ecotype


title: MF29_Mock_rep1 (MAE019)

tag: bacteria presence


title: Yap WT_atrophy_rep2

value: Yap-flox/flox

tag: treatment


title: HEK293T_rep1_control


title: S3_S_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default).
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

value: leaf margin

value: leaves have white center and green margin


title: S3_S_1


title: MF27_Mock_rep3 (MAE015)

value: Mock

tag: time


title: S3_C_3

value: leaf center


title: S3_S_3


title: MCF-7_rep2_control

source_name: MCF-7 cell line


title: MF27_flg22_rep1 (MAE016)

tag: experiment


title: S3_C_2


title: MCF-7_rep1_control


title: Wildtype_atrophy_rep1

tag: strain

value: JAX wild-type

value: injured duodenum


title: Wildtype_atrophy_rep2

tag: age


title: MF27_Mock_rep2 (MAE014)


title: S3_C_1


title: MF27_Mock_rep1 (MAE013)


title: MCF-7_rep1_treated

value: treated


title: MF8_flg22_rep3 (MAE012)


title: S2_3

value: leaves without veins

value: leaves begin to develop white center and have green margin


title: S2_2


title: MF8_flg22_rep2 (MAE011)


title: Wildtype_homeo_rep1

source_name: Intestinal epithelium, homeostasis

value: uninjured duodenum

value: 24h after saline injection


title: Knockout and day2, replicates3

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
After the removal of adapter and trimming of low quality bases, the reads were used for expression quantification using Salmon (v0.9.1). Expression values were quantified by counts in gene level.
Genome_build: mm10
Supplementary_files_format_and_content: Salmon output files

source_name: bone marrow

growth_protocol: Bone-marrow derived dendritic cells were generated in vitro from mouse bone marrow precursors. After washing cells were plated in 24-well tissue culture plate (0.5 x 106 /ml per well) in DMEM supplemented with 1% penicillin/streptomycin (Lonza #CC-4136), 10% FCS and 1% MEM non-essential amino acids solution (ThermoFisher) under lineage specific cytokine condition  (20 ng/ml GM-CSF)

extract_protocol:
Total RNA was isolated using either RNeasy Micro Kit (Qiagen) or miRVana isolation kit (Ambion). RNA quality was checked at Bioanalyser before library preparation.
Stranded RNA libraries were prepared with 100ng total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche)
RNA sequencing was performed on Illumina NovaSeq 6000 system (Illumina).

treatment_protocol: Cells for total RNA sequencing were collected after extraction from mouse BM and 48h after addition of GM-SCF and frozen in lysis buffer until RNA extraction.

value: KO

value: GM-CSF stimulation

value: bone marrow


title: Yap WT_atrophy_rep1

value: 8 weeks

value: Intestinal epithelium

value: injured & distal uninjured duodenum

value: 24h after poly(I:C) injection


title: K562_rep2_control

source_name: K562 cell line

value: control

value: human cell line


title: K562_rep1_control


title: S2_1


title: Knockout and day0, replicates3


title: K562_rep2_treated


title: S1_3

value: leaves are entirely green


title: Knockout and day2, replicates2


title: MF8_Mock_rep3 (MAE009)

value: Mock


title: MCF-7_rep2_treated


title: Wildtype_homeo_rep2

value: JAX wild-type


title: Knockout and day0, replicates2


title: K562_rep1_treated

value: treated


title: S1_2

value: leaves without veins


title: Knockout and day2, replicates1


title: MF8_Mock_rep2 (MAE008)


title: MF8_Mock_rep1 (MAE007)


title: HepG2_rep2_control

source_name: HepG2 cell line


title: Knockout and day0, replicates1


title: HepG2_rep1_control


title: S1_1


title: Wild-type and day2, replicates3

value: WT


title: DLD-1-356-3

city: Jinan

first: Du

last: Tiantian

state: Shandong

address: The Second Hospital of Shandong University, 247 Beiyuan Road, Jinan 250033, Shandong, China

description: LINC02476 knocked down  group

data_processing:
Raw reads sequence data (.fastq files) was acquired and filtered.
HISAT2 was used to perform reads alignment.
StringTie was used to perform transcript complication and expression estimation.
Ballgown and R were used to analyze differential gene expression and visulation.
DEseq2 was used to produce plots and differential expression tables.
Goseq  used to process GO analysis.
KOBAS（3.0）and KEGG database were used to process KEGG analysis.
Genome_build: Homo_sapiens.GRCh38.96.chr.gtf.gz
Supplementary_files_format_and_content: FPKM

source_name: Human colon adenocarcinoma cells

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit   (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly,   The poly-A containing mRNA molecules were purified using poly-T oligo-attached   magnetic beads.     Following purification, the mRNA is fragmented into small pieces   using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are   copied into first strand cDNA using reverse transcriptase and random primers. This is   followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.   These cDNA fragments then go through an end repair process, the addition of a single   ‘A’ base, and then ligation of the adapters. The products are then purified and enriched   with PCR to create the final cDNA library. Purified libraries were quantified by Qubit®   2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer   (Agilent Technologies, USA) to confirm the insert size and calculate the   mole concentration.

value: colon

value: with DMEM medium cultured in 37 C, 5%CO2.

value: epithelial

tag: disease

value: Dukes' type C, colorectal adenocarcinoma


title: MF2_flg22_rep3 (MAE006)


title: MF8_flg22_rep1 (MAE010)


title: MF2_flg22_rep2 (MAE005)


title: Wild-type and day0, replicates3

tag: genotype

value: bone marrow


title: DLD-1-356-1

institute: The Second Hospital of Shandong University

description: LINC02474 knocked down  group


title: MF2_flg22_rep1 (MAE004)


title: HepG2_rep1_treated


title: HepG2_rep2_treated


title: Wild-type and day0, replicates2


title: Hela_rep1_control

source_name: Hela cell line

value: Hela


title: DLD-1-NC2

description: control group


title: Wild-type and day2, replicates1

value: GM-CSF stimulation


title: Wild-type and day0, replicates1


title: DLD-1-NC1

description: control group


title: Hela_rep1_treated


title: MF2_Mock_rep1 (MAE001)


title: Hela_rep2_treated


title: MF2_Mock_rep2 (MAE002)


title: DLD-1-356-2

description: LINC02475 knocked down  group


title: Wild-type and day2, replicates2


title: Hela_rep2_control


title: inflorescence meristems, GFP_MYB3R1_ChIP-seq_rep2

status: Public on Mar 26 2021

city: Cambridge

first: Weibing

state: Select...

address: 47 Bateman Street, Cambridge

country: United Kingdom

institute: Sainsbury Laboratory  University of Cambridge

library_source: genomic

data_processing:
The raw reads obtained from the sequencing facilities were analyzed in house. We first assessed the quality of reads using FastQC  (www.bioinformatics.babraham.ac.uk/projects/fastqc/).   Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 reference genome using Bowtie2 (Langmead et al., 2009). Potential optical duplicates were removed using Picard, as described earlier. The read counts mapped to each bp in each sample was normalized by the sample’s genome-wide mappable reads coverage per bp, and used in the subsequent statistical analyses.Peak calling was performed using MACS (Zhang et al., 2008).
Genome_build: TAIR10
Supplementary_files_format_and_content: narrowPeak

molecule: genomic DNA

source_name: Col0 pMYB3R1::inflorescence meristems, GFP-MYB3R1 inflorescence meristems

growth_protocol: Arabidopsis plants were grown in a growth chamber under the following conditions: long-day photoperiod (16-h light/8-h dark), light intensity 170 μmoles m-2 s-1, day/night temperature 21°C/17 °C. Shortly after bolting (with stem length ~1 cm), the shoot apices were cut and the SAMs were dissected by removing fully open flowers.

extract_protocol:
ChIP was performed as described (Gendrel et al., 2002) with minor modifications. In brief, chromatin was extracted from approximately 1 to 2 g of crosslinked materials. Chromatin was fragmented by sonication using a bioruptor (Diagenode) in lysis buffer (10 mM Tris-HCl [pH 8], 150 mM NaCl, 1 mM EDTA [pH 8], 0.1% deoxycholate, and 1X protease inhibitor cocktail). All ChIPs were performed in a buffer containing 20mM Tris-HCl (pH8), 150mM NaCl, 2mM EDTA, 1% triton X-100 and 1X protease inhibitor cocktail. ChIP were performed using Anti-inflorescence meristems, GFP antibody - ChIP Grade (Abcam, ab290) coupled to a 1/1 mix of protein-A and protein-G Dynabeads (life technologies, 10001D and 10003D). All ChIPs were performed in a buffer containing 10 mM Tris-HCl [pH 8.0], 5 mM EDTA [pH 8.0], 150 mM NaCl, 1% Triton X-100, and 1× protease inhibitor cocktail. The elution was done with elution buffer (1% SDS, 0.1M NaHCO3).
The efficiency of ChIP materials was assessed by qPCR in prior to in-house library preparation, using the TruSeq ChIP sample preparation kit (Illumina, IP-202-1012) following the manufacturer’s instructions.  Library preparation was performed by Novogene using another method for some of the samples. The libraries were sequenced on Illumina sequencer by Novogene using paired-end 150bp length reads, and on NextSeq500 at the Sainsbury Laboratory Cambridge University using single-end 75 bp length reads .

value: inflorescence meristems

tag: replicate

tag: chip antibody

value: Anti-inflorescence meristems, GFP antibody - ChIP Grade (ab290)


title: DLD-1-NC3

description: control group

tag: tissue


title: inflorescence meristems, GFP_MYB3R4_ChIP-seq_rep1

source_name: Col0 pMYB3R4::inflorescence meristems, GFP-MYB3R4 inflorescence meristems


title: inflorescence meristems, GFP_MYB3R1_input_rep1

value: Col0 pMYB3R1::inflorescence meristems, GFP-MYB3R1


title: inflorescence meristems, GFP_MYB3R4_ChIP-seq_rep2

value: Col0 pMYB3R4::inflorescence meristems, GFP-MYB3R4


title: MF2_Mock_rep3 (MAE003)


title: inflorescence meristems, GFP_MYB3R1_ChIP-seq_rep1


title: mutant_D8_EB_Suz12_rep2

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
library strategy: Cut-n-run-seq
Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3

source_name: embryoid bodies

growth_protocol: All Embryonic Stem cells were cultured in DMEM supplemented with Pen/strep, glutamax, LIF and 20%FBS. The were suported on a feeder layer of PMEF-N from SIgma. Embryoid bodies were differentiated via hanging drops in IMDM supplemented with Pen/strep, glutamx and 20% FBS.

extract_protocol:
RNA was extracted uning the nucleospin kit from Marchery-Nagel. cDNA was made using the Superscript Vilo kit
DNA was extracted as part of the  Cut and Run assay orginally published by the Henikoff laboratory
Modified Illumina method detailed in Bowman et al 2013 BMC Genomics

treatment_protocol:
Cells treated with GSK343 had 4uM of the drug added to the media for three days prior to the start of differentiation trough the end of the experiment. DMSO treated cells had a equivalent volume addeed to the culture media for the same amout of time.
Replated cells were first differentiated as embyoid bodies and then placed into ES media for 5 days prior to collection.

tag: condition

value: mutant

value: 8 days

tag: antibody


title: inflorescence meristems, GFP_MYB3R1_input_rep2


title: inflorescence meristems, GFP_MYB3R4_input_rep1


title: mutant_ESC_Suz12_rep2

source_name: embryonic stem cells

tag: cell line

value: 0 days


title: mutant_D8_EB_Suz12_rep1


title: mutant_ESC_Suz12_rep1


title: mutant_D4_EB_Suz12_rep1

value: 4 days


title: WT_D8_EB_Suz12_rep2

value: wild type


title: WT_ESC_Suz12_rep2


title: WT_D8_EB_IgG

description: CJ7 cells

data_processing:
Reads were aligned to the mm10 genome using bowtie 2 v2.3.4.3
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3

value: CJ7 cells

tag: differentiation status

value: embryoid bodies

value: IgG


title: WT_D4_EB_Suz12_rep2


title: mutant_D4_EB_Suz12_rep2


title: WT_D4_EB_IgG

description: CJ7 cells


title: WT_D8_EB_Ezh2

description:
CJ7 cells
WT_Ezh2_ESC_D4EB_D8EB_merged_peaks.bed


title: WT_ESC_IgG

description: CJ7 cells

value: embryonic stem cells


title: WT_D4_EB_Ezh2


title: Shox2-/-_J2Diff7

city: Heidelberg

first: Sandra

last: Hoffmann

address: Im Neuneheimer Feld 366

department: Human Molecular Genetics

country: Germany

institute: University of Heidelberg

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned by 'bwa mem' to the Ensmbl Mus musculus transcriptom mm10
Counting the reads to each gene was doen vioa HTSeq-count python script (0.6.0)
Data was preprossed and analyzed in R eb´nviroment (3.3.2/3.4) loading DESeq2 (1.14.0) (see Love MI et.al. ,Genome Biol 2014) and packages (see Tarazona et.al., Nucleic Acids Res 2015)
Normalization, estimation of dispersions and testing for differentially expressed genes based on a test assuming negative bionomial data distribution was computed via DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 data for each gene and sample

growth_protocol: ESC clones were cultivated and expanded on mouse embryonic fibroblasts in ESC proliferation medium and were differentiated according to a standard hanging drop protocol as described earlier (Wobus et al., 2002).To enrich ESC-derived SAN-like cells, ESCs were differentiated according to a previously described protocol (Hoffmann et al., 2017). In brief, this protocol utilizes FACS to isolate SAN-like cardiomyocytes during murine ESC differentiation using the surface marker CD166 (Scavone et al., 2013)

extract_protocol:
Shox2+/+ and Shox2-/- ESC clones were FACS-sorted at stage 7+1 day and RNA was isolated from the sorted cells using TRIzol® reagent (Thermo Fisher Scientific).
500 ng of total RNA from Shox2+/+ and Shox2-/- ESC-derived CD166-positive SAN-like cells (three replicates each) was used for RNA-seq, which was conducted with the Illumina HiSeq™2000 sequencing system (Illumina).

tag: cell type

value: ESC-derived sinoatrial node-like cardiomyocytes


title: Shox2-/-_J2Diff9


title: WT_210114Diff811

source_name: WT_Sinoatrial node-like cardiomyocytes

value: Wildtype


title: Shox2-/-_J2Diff8


title: WT_H1IIDiff9


title: WT_H1IDiff9


title: WT_D4_EB_Suz12

description:
CJ7 cells
WT_Suz12_ESC_D4EB_D8EB_merged_peaks.bed


title: WT_D8_EB_Suz12


title: WT_ESC_Ezh2


title: WT_ESC_Ring1B

description:
CJ7 cells
WT_Ring1B_ESC_D4EB_D8EB_merged_peaks.bed


title: WT_D8_EB_Ring1B


title: mutant_D4_EB_H3K27me3

description:
CJ7 cells
WT_H3K27me3_ESC_D4EB_D8EB_merged_peaks.bed


title: WT_ESC_Suz12


title: WT_D4_EB_Ring1B


title: mutant_D8_EB_H3K27me3


title: WT_D4_EB_H3K27me3


title: WT_D8_EB_H3K27me3


title: WT_ESC_H3K27me3


title: GSK343_GSK343_rep3

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt

data_processing:
Reads were aligned to the mm10 genome using STAR v2.5.3
Reads in gene exons were counted using featureCounts v1.6.1
Gene annotations were obtained from ncbi refseq
EdgeR was used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3

value: starting GSK343, replated GSK343

value: 14 days


title: mutant_ESC_H3K27me3


title: GSK343_GSK343_rep2

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt


title: DMSO_GSK343_rep3

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt

value: starting DMSO, replated GSK343


title: GSK343_GSK343_rep1

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt


title: GSK343_DMSO_rep1

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt

value: starting GSK343, replated DMSO


title: GSK343_DMSO_rep3

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt


title: GSK343_DMSO_rep2

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt


title: mutant_D8_EB_rep2

description:
CJ7 cells
WT_mutant_ESC_D4EB_D8EB_RPKMs.txt


title: mutant_D8_EB_rep3


title: mutant_D8_EB_rep1


title: DMSO_DMSO_rep3

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt

value: starting DMSO, replated DMSO


title: DMSO_GSK343_rep1

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt


title: DMSO_DMSO_rep2

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt


title: mutant_D4_EB_rep2


title: mutant_D4_EB_rep3


title: DMSO_DMSO_rep1

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt


title: mutant_D4_EB_rep1


title: mutant_ESC_rep2


title: mutant_ESC_rep1


title: WT_D8_EB_rep3


title: WT_D4_EB_rep1


title: WT_D8_EB_rep2


title: GSK343_ESC_rep2

description:
CJ7 cells
DMSO_GSK_RPKMs.txt

value: GSK343 treatment


title: GSK343_ESC_rep1

description:
CJ7 cells
DMSO_GSK_RPKMs.txt


title: WT_ESC_rep1


title: WT_D8_EB_rep1


title: WT_D4_EB_rep2


title: WT_D4_EB_rep3


title: GSK343_D8_EB_rep2

description:
CJ7 cells
DMSO_GSK_RPKMs.txt


title: WT_ESC_rep3


title: GSK343_D4_EB_rep1

description:
CJ7 cells
DMSO_GSK_RPKMs.txt


title: mutant_ESC_rep3

value: mutant


title: WT_ESC_rep2


title: GSK343_D4_EB_rep2

description:
CJ7 cells
DMSO_GSK_RPKMs.txt


title: DMSO_D8_EB_rep1

description:
CJ7 cells
DMSO_GSK_RPKMs.txt

value: DMSO treatment

value: 8 days


title: DMSO_D4_EB_rep1

description:
CJ7 cells
DMSO_GSK_RPKMs.txt

value: 4 days


title: DMSO_D8_EB_rep2

description:
CJ7 cells
DMSO_GSK_RPKMs.txt


title: DMSO_D4_EB_rep2

description:
CJ7 cells
DMSO_GSK_RPKMs.txt


title: DMSO_ESC_rep1

description:
CJ7 cells
DMSO_GSK_RPKMs.txt

value: 0 days


title: PA_PA5499_cycle3_Rep1

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt

data_processing:
Library strategy: HT-SELEX
Illumina Casava v1.7 software used for basecalling.
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas aeruginosa PAO1 (GCF_000006765.1, ASM676v1)
Supplementary_files_format_and_content: 0_PA_all_PWM_results.txt: Tab-delimited text file includes position weight matrix (PWM) results for each transcription factor (TF).
Supplementary_files_format_and_content: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt: Tab-delimited text file includes all TFs' genome wide target scan results based on the output of FIMO software.

organism: Pseudomonas aeruginosa PAO1

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary Table3 and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul Promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary Table3, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer.

treatment_protocol: 0.5 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce each TF expression at 16 °C for 16 h.

value: wild type

tag: growth phase

value: exponential phase

tag: transcription factor


title: PA_PA5483_cycle3_Rep1


title: PA_PA5511_cycle1_Rep1


title: PA_PA5483_cycle4_Rep1


title: PA_PA5499_cycle2_Rep1


title: PA_PA5499_cycle4_Rep1


title: PA_PA5511_cycle3_Rep1


title: PA_PA5499_cycle1_Rep1


title: PA_PA5511_cycle2_Rep1


title: PA_PA5499_cycle0_Rep1

source_name: no protein

value: no protein


title: PA_PA5483_cycle0_Rep1


title: PA_PA5511_cycle0_Rep1


title: PA_PA5403_cycle4_Rep1


title: PA_PA5483_cycle1_Rep1


title: PA_PA5403_cycle3_Rep1


title: PA_PA5483_cycle2_Rep1


title: PA_PA5403_cycle2_Rep1


title: PA_PA5403_cycle1_Rep1


title: PA_PA5360_cycle0_Rep1


title: PA_PA5360_cycle2_Rep1


title: PA_PA5360_cycle3_Rep1


title: PA_PA5403_cycle0_Rep1


title: PA_PA5293_cycle2_Rep1


title: PA_PA5360_cycle1_Rep1


title: PA_PA5293_cycle1_Rep1


title: PA_PA5293_cycle3_Rep1


title: PA_PA5293_cycle0_Rep1


title: SAMPLE 3: normal cervical sample 3

type: genomic

city: jiang su

last: Qu

state: su zhou

address: Industrial park

institute: suzhou university

description: normal cervical sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting  Infinium MethylationEPIC  Infinium MethylationEPIC

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: genomic DNA from FFPE 3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE samples using QIAGEN QIAamp DNA Mini Kit according to standard instructions

treatment_protocol: tissues were formalin-fixed , paraffin-embedded and sectioned by following the company instructions

tag: gender

value: Female

tag: sample type

value: FFPE

tag: hpv type

value: negative

tag: disease state

value: normal


title: SAMPLE 1: normal cervical sample 1

description: normal cervical sample

source_name: genomic DNA from FFPE 1


title: PA_PA5261_cycle1_Rep1


title: PA_PA5261_cycle4_Rep1


title: PA_PA5511_cycle4_Rep1


title: PA_PA5261_cycle3_Rep1


title: PA_PA5261_cycle0_Rep1


title: DMSO_ESC_rep2

description:
CJ7 cells
DMSO_GSK_RPKMs.txt

value: CJ7 cells

value: embryonic stem cells

tag: age


title: PA_PA5200_cycle0_Rep1


title: PA_PA5261_cycle2_Rep1


title: PA_PA5189_cycle0_Rep1


title: PA_PA5200_cycle4_Rep1


title: PA_PA5200_cycle2_Rep1


title: PA_PA5360_cycle4_Rep1


title: PA_PA5200_cycle3_Rep1


title: SAMPLE 6: cervical cancer 3

description: cervical cancer sample

source_name: genomic DNA from FFPE 9

value: cervical cancer


title: SAMPLE 7: cervical cancer 4

description: cervical cancer sample

source_name: genomic DNA from FFPE 10


title: SAMPLE 4: cervical cancer 1

description: cervical cancer sample

source_name: genomic DNA from FFPE 7


title: SAMPLE 2: normal cervical sample 2

description: normal cervical sample

source_name: genomic DNA from FFPE 2


title: PA_PA5200_cycle1_Rep1


title: PA_PA5125_cycle3_Rep1


title: PA_PA5189_cycle1_Rep1


title: PA_PA5189_cycle4_Rep1


title: PA_PA5189_cycle2_Rep1


title: SAMPLE 9: cervical cancer 6

description: cervical cancer sample

source_name: genomic DNA from FFPE 12


title: GSK343_D8_EB_rep1

description:
CJ7 cells
DMSO_GSK_RPKMs.txt

value: embryoid bodies


title: PA_PA5059_cycle4_Rep1


title: PA_PA5125_cycle4_Rep1


title: DMSO_GSK343_rep2

description:
CJ7 cells
replating_DMSO_GSK_RPKMs.txt

value: starting DMSO, replated GSK343

value: 14 days


title: SAMPLE 8: cervical cancer 5

description: cervical cancer sample

source_name: genomic DNA from FFPE 11


title: PA_PA5125_cycle2_Rep1


title: PA_PA5125_cycle1_Rep1


title: PA_PA5189_cycle3_Rep1


title: PA_PA5125_cycle0_Rep1


title: PA_PA5059_cycle1_Rep1


title: PA_PA5059_cycle0_Rep1


title: PA_PA5059_cycle2_Rep1


title: SAMPLE 5: cervical cancer 2

description: cervical cancer sample

source_name: genomic DNA from FFPE 8


title: PA_PA4989_cycle4_Rep1


title: PA_PA4989_cycle2_Rep1


title: PA_PA4989_cycle3_Rep1


title: PA_PA4989_cycle1_Rep1


title: PA_PA4987_cycle4_Rep1


title: PA_PA4987_cycle3_Rep1


title: PA_PA5059_cycle3_Rep1


title: PA_PA4984_cycle2_Rep1


title: PA_PA4987_cycle0_Rep1


title: PA_PA4984_cycle1_Rep1


title: PA_PA4984_cycle4_Rep1


title: PA_PA4984_cycle3_Rep1


title: PA_PA4987_cycle1_Rep1


title: PA_PA4984_cycle0_Rep1


title: PA_PA4983_cycle4_Rep1


title: PA_PA4983_cycle0_Rep1


title: PA_PA4983_cycle3_Rep1


title: PA_PA4983_cycle1_Rep1


title: PA_PA4983_cycle2_Rep1


title: PA_PA4906_cycle3_Rep1


title: PA_PA4906_cycle4_Rep1


title: PA_PA4989_cycle0_Rep1


title: PA_PA4902_cycle3_Rep1


title: PA_PA4902_cycle4_Rep1


title: PA_PA4906_cycle2_Rep1


title: PA_PA4987_cycle2_Rep1


title: PA_PA4787_cycle4_Rep1


title: PA_PA4787_cycle3_Rep1


title: PA_PA4902_cycle0_Rep1


title: PA_PA4902_cycle2_Rep1


title: PA_PA5293_cycle4_Rep1


title: PA_PA4769_cycle4_Rep1


title: PA_PA4776_cycle0_Rep1


title: PA_PA4776_cycle3_Rep1


title: PA_PA4787_cycle0_Rep1


title: PA_PA4776_cycle1_Rep1


title: PA_PA4776_cycle4_Rep1


title: PA_PA4769_cycle3_Rep1


title: PA_PA4776_cycle2_Rep1


title: PA_PA4906_cycle1_Rep1


title: PA_PA4906_cycle0_Rep1


title: PA_PA4769_cycle1_Rep1


title: PA_PA4726_cycle1_Rep1


title: PA_PA4769_cycle0_Rep1


title: PA_PA4726_cycle4_Rep1


title: PA_PA4902_cycle1_Rep1


title: PA_PA4726_cycle0_Rep1


title: PA_PA4726_cycle3_Rep1


title: PA_PA4787_cycle2_Rep1


title: PA_PA4659_cycle2_Rep1


title: PA_PA4726_cycle2_Rep1


title: PA_PA4659_cycle3_Rep1


title: PA_PA4659_cycle1_Rep1


title: PA_PA4769_cycle2_Rep1


title: PA_PA4659_cycle0_Rep1


title: PA_PA4659_cycle4_Rep1


title: PA_PA4600_cycle4_Rep1


title: PA_PA4787_cycle1_Rep1


title: PA_PA4600_cycle3_Rep1


title: PA_PA4600_cycle2_Rep1


title: PA_PA4581_cycle4_Rep1


title: PA_PA4600_cycle0_Rep1


title: PA_PA4581_cycle3_Rep1


title: PA_PA4581_cycle1_Rep1


title: PA_PA4581_cycle0_Rep1


title: PA_PA4581_cycle2_Rep1


title: PA_PA4547_cycle4_Rep1


title: PA_PA4547_cycle3_Rep1


title: PA_PA4547_cycle2_Rep1


title: PA_PA4547_cycle1_Rep1


title: PA_PA4547_cycle0_Rep1


title: PA_PA4508_cycle3_Rep1


title: PA_PA4508_cycle2_Rep1


title: PA_PA4508_cycle1_Rep1


title: PA_PA4600_cycle1_Rep1


title: PA_PA4499_cycle3_Rep1


title: PA_PA4499_cycle2_Rep1


title: PA_PA4499_cycle1_Rep1


title: PA_PA4499_cycle4_Rep1


title: PA_PA4462_cycle4_Rep1


title: PA_PA4462_cycle3_Rep1


title: PA_PA4499_cycle0_Rep1


title: PA_PA4508_cycle0_Rep1


title: PA_PA4462_cycle1_Rep1


title: PA_PA4462_cycle0_Rep1


title: PA_PA4436_cycle4_Rep1


title: PA_PA4436_cycle0_Rep1


title: PA_PA4436_cycle2_Rep1


title: PA_PA4315_cycle4_Rep1


title: PA_PA4315_cycle3_Rep1


title: PA_PA4315_cycle1_Rep1


title: PA_PA4508_cycle4_Rep1


title: PA_PA4288_cycle2_Rep1


title: PA_PA4315_cycle0_Rep1


title: PA_PA4288_cycle3_Rep1


title: PA_PA4315_cycle2_Rep1


title: PA_PA4288_cycle1_Rep1


title: PA_PA4462_cycle2_Rep1


title: PA_PA4288_cycle0_Rep1


title: PA_PA4436_cycle3_Rep1


title: PA_PA4203_cycle1_Rep1


title: PA_PA4203_cycle3_Rep1


title: PA_PA4227_cycle0_Rep1


title: PA_PA4227_cycle3_Rep1


title: PA_PA4227_cycle1_Rep1


title: PA_PA4203_cycle2_Rep1


title: PA_PA4203_cycle4_Rep1


title: PA_PA4436_cycle1_Rep1


title: PA_PA4184_cycle4_Rep1


title: PA_PA4184_cycle3_Rep1


title: PA_PA4203_cycle0_Rep1


title: PA_PA4227_cycle2_Rep1


title: PA_PA4184_cycle1_Rep1


title: PA_PA4288_cycle4_Rep1


title: PA_PA4135_cycle2_Rep1


title: PA_PA4135_cycle4_Rep1


title: PA_PA4135_cycle3_Rep1


title: PA_PA4184_cycle0_Rep1


title: PA_PA4135_cycle1_Rep1


title: PA_PA4120_cycle2_Rep1


title: PA_PA4120_cycle3_Rep1


title: PA_PA4120_cycle4_Rep1


title: PA_PA4120_cycle0_Rep1


title: PA_PA4227_cycle4_Rep1


title: PA_PA4101_cycle3_Rep1


title: PA_PA4101_cycle4_Rep1


title: PA_PA4101_cycle2_Rep1


title: PA_PA4184_cycle2_Rep1


title: PA_PA4135_cycle0_Rep1


title: PA_PA4101_cycle0_Rep1


title: PA_PA4101_cycle1_Rep1


title: PA_PA4032_cycle3_Rep1


title: PA_PA4032_cycle2_Rep1


title: PA_PA4032_cycle4_Rep1


title: PA_PA4032_cycle1_Rep1


title: PA_PA4021_cycle3_Rep1


title: PA_PA4021_cycle2_Rep1


title: PA_PA4032_cycle0_Rep1


title: PA_PA3995_cycle1_Rep1


title: PA_PA4021_cycle1_Rep1


title: PA_PA3995_cycle2_Rep1


title: PA_PA3895_cycle4_Rep1


title: PA_PA3995_cycle4_Rep1


title: PA_PA3995_cycle3_Rep1


title: PA_PA4021_cycle0_Rep1


title: PA_PA4021_cycle4_Rep1


title: PA_PA4120_cycle1_Rep1


title: PA_PA3895_cycle2_Rep1


title: PA_PA3895_cycle0_Rep1


title: PA_PA3879_cycle4_Rep1


title: PA_PA3895_cycle3_Rep1


title: PA_PA3879_cycle3_Rep1


title: PA_PA3879_cycle2_Rep1


title: PA_PA3879_cycle0_Rep1


title: PA_PA3864_cycle4_Rep1


title: PA_PA3864_cycle3_Rep1


title: PA_PA3995_cycle0_Rep1


title: PA_PA3864_cycle1_Rep1


title: PA_PA3864_cycle0_Rep1


title: PA_PA3782_cycle3_Rep1


title: PA_PA3782_cycle2_Rep1


title: PA_PA3782_cycle1_Rep1


title: PA_PA3778_cycle4_Rep1


title: PA_PA3782_cycle4_Rep1


title: PA_PA3778_cycle3_Rep1


title: PA_PA3771_cycle4_Rep1


title: PA_PA3895_cycle1_Rep1


title: PA_PA3771_cycle2_Rep1


title: PA_PA3771_cycle1_Rep1


title: PA_PA3771_cycle3_Rep1


title: PA_PA3778_cycle1_Rep1


title: PA_PA3771_cycle0_Rep1


title: PA_PA3778_cycle2_Rep1


title: PA_PA3757_cycle4_Rep1


title: PA_PA3757_cycle3_Rep1


title: PA_PA3757_cycle2_Rep1


title: PA_PA3757_cycle1_Rep1


title: PA_PA3757_cycle0_Rep1


title: PA_PA3864_cycle2_Rep1


title: PA_PA3630_cycle1_Rep1


title: PA_PA3630_cycle3_Rep1


title: PA_PA3630_cycle2_Rep1


title: PA_PA3879_cycle1_Rep1


title: PA_PA3782_cycle0_Rep1


title: PA_PA3594_cycle2_Rep1


title: PA_PA3778_cycle0_Rep1


title: PA_PA3594_cycle4_Rep1


title: PA_PA3594_cycle1_Rep1


title: PA_PA3630_cycle0_Rep1


title: PA_PA3594_cycle3_Rep1


title: PA_PA3594_cycle0_Rep1


title: PA_PA3398_cycle2_Rep1


title: PA_PA3398_cycle3_Rep1


title: PA_PA3398_cycle1_Rep1


title: PA_PA3458_cycle3_Rep1


title: PA_PA3458_cycle2_Rep1


title: PA_PA3385_cycle4_Rep1


title: PA_PA3458_cycle1_Rep1


title: PA_PA3398_cycle4_Rep1


title: PA_PA3458_cycle0_Rep1


title: PA_PA3385_cycle3_Rep1


title: PA_PA3398_cycle0_Rep1


title: PA_PA3385_cycle2_Rep1


title: PA_PA3385_cycle1_Rep1


title: PA_PA3381_cycle4_Rep1


title: PA_PA3630_cycle4_Rep1


title: PA_PA3385_cycle0_Rep1


title: PA_PA3381_cycle3_Rep1


title: PA_PA3381_cycle1_Rep1


title: PA_PA3381_cycle2_Rep1


title: PA_PA3381_cycle0_Rep1


title: PA_PA3458_cycle4_Rep1


title: PA_PA3341_cycle4_Rep1


title: PA_PA3249_cycle3_Rep1


title: PA_PA3249_cycle4_Rep1


title: PA_PA3341_cycle3_Rep1


title: PA_PA3341_cycle1_Rep1


title: PA_PA3341_cycle2_Rep1


title: PA_PA3249_cycle1_Rep1


title: PA_PA3249_cycle0_Rep1


title: PA_PA3204_cycle2_Rep1


title: PA_PA3225_cycle2_Rep1


title: PA_PA3204_cycle0_Rep1


title: PA_PA3204_cycle3_Rep1


title: PA_PA3192_cycle2_Rep1


title: PA_PA3192_cycle3_Rep1


title: PA_PA3192_cycle1_Rep1


title: PA_PA3249_cycle2_Rep1


title: PA_PA3204_cycle1_Rep1


title: PA_PA3192_cycle0_Rep1


title: PA_PA3184_cycle4_Rep1


title: PA_PA3225_cycle0_Rep1


title: PA_PA3184_cycle3_Rep1


title: PA_PA3225_cycle4_Rep1


title: PA_PA3192_cycle4_Rep1


title: PA_PA3184_cycle2_Rep1


title: PA_PA3184_cycle1_Rep1


title: PA_PA3135_cycle4_Rep1


title: PA_PA3225_cycle3_Rep1


title: PA_PA3341_cycle0_Rep1


title: PA_PA3135_cycle2_Rep1


title: PA_PA3135_cycle0_Rep1


title: PA_PA3133_cycle4_Rep1


title: PA_PA3135_cycle1_Rep1


title: PA_PA3225_cycle1_Rep1


title: PA_PA3135_cycle3_Rep1


title: PA_PA3184_cycle0_Rep1


title: PA_PA3133_cycle3_Rep1


title: PA_PA3133_cycle2_Rep1


title: PA_PA3077_cycle3_Rep1


title: PA_PA3133_cycle1_Rep1


title: PA_PA3077_cycle4_Rep1


title: PA_PA3133_cycle0_Rep1


title: PA_PA3077_cycle2_Rep1


title: PA_PA3204_cycle4_Rep1


title: PA_PA3077_cycle1_Rep1


title: PA_PA3077_cycle0_Rep1


title: PA_PA3067_cycle4_Rep1


title: PA_PA3067_cycle3_Rep1


title: PA_PA3067_cycle2_Rep1


title: PA_PA3067_cycle1_Rep1


title: PA_PA3067_cycle0_Rep1


title: PA_PA3034_cycle0_Rep1


title: PA_PA3034_cycle4_Rep1


title: PA_PA3034_cycle3_Rep1


title: PA_PA3034_cycle2_Rep1


title: PA_PA3034_cycle1_Rep1


title: PA_PA3006_cycle1_Rep1


title: PA_PA3006_cycle4_Rep1


title: PA_PA3006_cycle3_Rep1


title: PA_PA2921_cycle4_Rep1


title: PA_PA3006_cycle0_Rep1


title: PA_PA3006_cycle2_Rep1


title: PA_PA2921_cycle3_Rep1


title: PA_PA2921_cycle1_Rep1


title: PA_PA2921_cycle2_Rep1


title: PA_PA2921_cycle0_Rep1


title: PA_PA2897_cycle3_Rep1


title: PA_PA2897_cycle0_Rep1


title: PA_PA2897_cycle1_Rep1


title: PA_PA2879_cycle3_Rep1


title: PA_PA2879_cycle4_Rep1


title: PA_PA2897_cycle2_Rep1


title: PA_PA2897_cycle4_Rep1


title: PA_PA2879_cycle2_Rep1


title: PA_PA2877_cycle4_Rep1


title: PA_PA2877_cycle3_Rep1


title: PA_PA2877_cycle1_Rep1


title: PA_PA2877_cycle2_Rep1


title: PA_PA2846_cycle3_Rep1


title: PA_PA2846_cycle4_Rep1


title: PA_PA2846_cycle1_Rep1


title: PA_PA2846_cycle0_Rep1


title: PA_PA2846_cycle2_Rep1


title: PA_PA2838_cycle3_Rep1


title: PA_PA2838_cycle4_Rep1


title: PA_PA2838_cycle2_Rep1


title: PA_PA2879_cycle1_Rep1


title: PA_PA2879_cycle0_Rep1


title: PA_PA2838_cycle0_Rep1


title: PA_PA2809_cycle4_Rep1


title: PA_PA2809_cycle3_Rep1


title: PA_PA2809_cycle0_Rep1


title: PA_PA2809_cycle1_Rep1


title: PA_PA2809_cycle2_Rep1


title: PA_PA2802_cycle4_Rep1


title: PA_PA2877_cycle0_Rep1


title: PA_PA2802_cycle2_Rep1


title: PA_PA2802_cycle1_Rep1


title: PA_PA2802_cycle3_Rep1


title: PA_PA2802_cycle0_Rep1


title: PA_PA2758_cycle3_Rep1


title: PA_PA2758_cycle4_Rep1


title: PA_PA2758_cycle2_Rep1


title: PA_PA2758_cycle0_Rep1


title: PA_PA2758_cycle1_Rep1


title: PA_PA2681_cycle4_Rep1


title: PA_PA2681_cycle1_Rep1


title: PA_PA2681_cycle2_Rep1


title: PA_PA2838_cycle1_Rep1


title: PA_PA2681_cycle0_Rep1


title: PA_PA2657_cycle2_Rep1


title: PA_PA2657_cycle3_Rep1


title: PA_PA2657_cycle0_Rep1


title: PA_PA2586_cycle3_Rep1


title: PA_PA2586_cycle4_Rep1


title: PA_PA2588_cycle0_Rep1


title: PA_PA2588_cycle1_Rep1


title: PA_PA2534_cycle4_Rep1


title: PA_PA2586_cycle0_Rep1


title: PA_PA2534_cycle2_Rep1


title: PA_PA2681_cycle3_Rep1


title: PA_PA2534_cycle3_Rep1


title: PA_PA2588_cycle4_Rep1


title: PA_PA2586_cycle2_Rep1


title: PA_PA2534_cycle1_Rep1


title: PA_PA2519_cycle4_Rep1


title: PA_PA2519_cycle3_Rep1


title: PA_PA2519_cycle0_Rep1


title: PA_PA2657_cycle1_Rep1


title: PA_PA2510_cycle3_Rep1


title: PA_PA2510_cycle2_Rep1


title: PA_PA2510_cycle4_Rep1


title: PA_PA2497_cycle3_Rep1


title: PA_PA2497_cycle4_Rep1


title: PA_PA2510_cycle0_Rep1


title: PA_PA2497_cycle2_Rep1


title: PA_PA2657_cycle4_Rep1


title: PA_PA2497_cycle0_Rep1


title: PA_PA2519_cycle2_Rep1


title: PA_PA2534_cycle0_Rep1


title: PA_PA2497_cycle1_Rep1


title: PA_PA2492_cycle4_Rep1


title: PA_PA2489_cycle3_Rep1


title: PA_PA2492_cycle0_Rep1


title: PA_PA2492_cycle1_Rep1


title: PA_PA2588_cycle3_Rep1


title: PA_PA2479_cycle3_Rep1


title: PA_PA2489_cycle0_Rep1


title: PA_PA2492_cycle2_Rep1


title: PA_PA2479_cycle4_Rep1


title: PA_PA2489_cycle2_Rep1


title: PA_PA2510_cycle1_Rep1


title: PA_PA2489_cycle4_Rep1


title: PA_PA2479_cycle1_Rep1


title: PA_PA2469_cycle4_Rep1


title: PA_PA2479_cycle2_Rep1


title: PA_PA2479_cycle0_Rep1


title: PA_PA2383_cycle4_Rep1


title: PA_PA2489_cycle1_Rep1


title: PA_PA2469_cycle3_Rep1


title: PA_PA2469_cycle2_Rep1


title: PA_PA2469_cycle1_Rep1


title: PA_PA2383_cycle2_Rep1


title: PA_PA2383_cycle1_Rep1


title: PA_PA2383_cycle3_Rep1


title: PA_PA2469_cycle0_Rep1


title: PA_PA2383_cycle0_Rep1


title: PA_PA2376_cycle3_Rep1


title: PA_PA2376_cycle2_Rep1


title: PA_PA2376_cycle1_Rep1


title: PA_PA2359_cycle0_Rep1


title: PA_PA2376_cycle0_Rep1


title: PA_PA2376_cycle4_Rep1


title: PA_PA2354_cycle0_Rep1


title: PA_PA2337_cycle4_Rep1


title: PA_PA2354_cycle4_Rep1


title: PA_PA2359_cycle2_Rep1


title: PA_PA2354_cycle3_Rep1


title: PA_PA2354_cycle1_Rep1


title: PA_PA2337_cycle3_Rep1


title: PA_PA2337_cycle2_Rep1


title: PA_PA2337_cycle1_Rep1


title: PA_PA2337_cycle0_Rep1


title: PA_PA2334_cycle4_Rep1


title: PA_PA2334_cycle1_Rep1


title: PA_PA2334_cycle0_Rep1


title: PA_PA2334_cycle3_Rep1


title: PA_PA2332_cycle4_Rep1


title: PA_PA2332_cycle3_Rep1


title: PA_PA2332_cycle2_Rep1


title: PA_PA2334_cycle2_Rep1


title: PA_PA2359_cycle3_Rep1


title: PA_PA2332_cycle0_Rep1


title: PA_PA2354_cycle2_Rep1


title: PA_PA2332_cycle1_Rep1


title: PA_PA2316_cycle4_Rep1


title: PA_PA2316_cycle3_Rep1


title: PA_PA2359_cycle1_Rep1


title: PA_PA2267_cycle4_Rep1


title: PA_PA2267_cycle0_Rep1


title: PA_PA2316_cycle2_Rep1


title: PA_PA2259_cycle4_Rep1


title: PA_PA2259_cycle1_Rep1


title: PA_PA2316_cycle1_Rep1


title: PA_PA2316_cycle0_Rep1


title: PA_PA2220_cycle4_Rep1


title: PA_PA2359_cycle4_Rep1


title: PA_PA2258_cycle0_Rep1


title: PA_PA2267_cycle3_Rep1


title: PA_PA2259_cycle0_Rep1


title: PA_PA2267_cycle2_Rep1


title: PA_PA2206_cycle2_Rep1


title: PA_PA2220_cycle0_Rep1


title: PA_PA2258_cycle3_Rep1


title: PA_PA2258_cycle4_Rep1


title: PA_PA2258_cycle2_Rep1


title: PA_PA2259_cycle2_Rep1


title: PA_PA2267_cycle1_Rep1


title: PA_PA2206_cycle1_Rep1


title: PA_PA2121_cycle4_Rep1


title: PA_PA2220_cycle3_Rep1


title: PA_PA2588_cycle2_Rep1


title: PA_PA2258_cycle1_Rep1


title: PA_PA2121_cycle1_Rep1


title: PA_PA2220_cycle1_Rep1


title: PA_PA2206_cycle4_Rep1


title: PA_PA2220_cycle2_Rep1


title: PA_PA2206_cycle3_Rep1


title: PA_PA2586_cycle1_Rep1


title: PA_PA2118_cycle3_Rep1


title: PA_PA2118_cycle1_Rep1


title: PA_PA2118_cycle0_Rep1


title: PA_PA2206_cycle0_Rep1


title: PA_PA2121_cycle3_Rep1


title: PA_PA2100_cycle1_Rep1


title: PA_PA2100_cycle0_Rep1


title: PA_PA2121_cycle2_Rep1


title: PA_PA2028_cycle1_Rep1


title: PA_PA2028_cycle4_Rep1


title: PA_PA2121_cycle0_Rep1


title: PA_PA2118_cycle4_Rep1


title: PA_PA2118_cycle2_Rep1


title: PA_PA2100_cycle4_Rep1


title: PA_PA2100_cycle3_Rep1


title: PA_PA2005_cycle0_Rep1


title: PA_PA1980_cycle3_Rep1


title: PA_PA1980_cycle1_Rep1


title: PA_PA2028_cycle3_Rep1


title: PA_PA2259_cycle3_Rep1


title: PA_PA2100_cycle2_Rep1


title: PA_PA2028_cycle2_Rep1


title: PA_PA1945_cycle4_Rep1


title: PA_PA2005_cycle2_Rep1


title: PA_PA2005_cycle3_Rep1


title: PA_PA1945_cycle1_Rep1


title: PA_PA1884_cycle4_Rep1


title: PA_PA2005_cycle1_Rep1


title: PA_PA1980_cycle4_Rep1


title: PA_PA2005_cycle4_Rep1


title: PA_PA1980_cycle2_Rep1


title: PA_PA1884_cycle1_Rep1


title: PA_PA1980_cycle0_Rep1


title: PA_PA1884_cycle0_Rep1


title: PA_PA1945_cycle3_Rep1


title: PA_PA1945_cycle0_Rep1


title: PA_PA1826_cycle3_Rep1


title: PA_PA1826_cycle4_Rep1


title: PA_PA1826_cycle1_Rep1


title: PA_PA1884_cycle2_Rep1


title: PA_PA1799_cycle4_Rep1


title: PA_PA1799_cycle3_Rep1


title: PA_PA2492_cycle3_Rep1


title: PA_PA1864_cycle4_Rep1


title: PA_PA1864_cycle3_Rep1


title: PA_PA1760_cycle4_Rep1


title: PA_PA1884_cycle3_Rep1


title: PA_PA2028_cycle0_Rep1


title: PA_PA1864_cycle2_Rep1


title: PA_PA1864_cycle1_Rep1


title: PA_PA1760_cycle3_Rep1


title: PA_PA2519_cycle1_Rep1


title: PA_PA1760_cycle0_Rep1


title: PA_PA1864_cycle0_Rep1


title: PA_PA1754_cycle2_Rep1


title: PA_PA1754_cycle0_Rep1


title: PA_PA1826_cycle0_Rep1


title: PA_PA1826_cycle2_Rep1


title: PA_PA1738_cycle1_Rep1


title: PA_PA1945_cycle2_Rep1


title: PA_PA1799_cycle2_Rep1


title: PA_PA1799_cycle1_Rep1


title: PA_PA1799_cycle0_Rep1


title: PA_PA1760_cycle1_Rep1


title: PA_PA1760_cycle2_Rep1


title: PA_PA1754_cycle4_Rep1


title: PA_PA1713_cycle3_Rep1


title: PA_PA1704_cycle3_Rep1


title: PA_PA1704_cycle4_Rep1


title: PA_PA1738_cycle4_Rep1


title: PA_PA1754_cycle1_Rep1


title: PA_PA1704_cycle1_Rep1


title: PA_PA1637_cycle4_Rep1


title: PA_PA1738_cycle2_Rep1


title: PA_PA1637_cycle2_Rep1


title: PA_PA1754_cycle3_Rep1


title: PA_PA1637_cycle1_Rep1


title: PA_PA1713_cycle1_Rep1


title: PA_PA1713_cycle2_Rep1


title: PA_PA1704_cycle2_Rep1


title: PA_PA1738_cycle3_Rep1


title: PA_PA1637_cycle3_Rep1


title: PA_PA1630_cycle4_Rep1


title: PA_PA1630_cycle2_Rep1


title: PA_PA1630_cycle3_Rep1


title: PA_PA1637_cycle0_Rep1


title: PA_PA1630_cycle1_Rep1


title: PA_PA1713_cycle0_Rep1


title: PA_PA1627_cycle4_Rep1


title: PA_PA1627_cycle0_Rep1


title: PA_PA1704_cycle0_Rep1


title: PA_PA1627_cycle2_Rep1


title: PA_PA1603_cycle1_Rep1


title: PA_PA1603_cycle3_Rep1


title: PA_PA1603_cycle0_Rep1


title: PA_PA1599_cycle4_Rep1


title: PA_PA1713_cycle4_Rep1


title: PA_PA1603_cycle2_Rep1


title: PA_PA1603_cycle4_Rep1


title: PA_PA1599_cycle2_Rep1


title: PA_PA1599_cycle0_Rep1


title: PA_PA1570_cycle3_Rep1


title: PA_PA1599_cycle1_Rep1


title: PA_PA1570_cycle1_Rep1


title: PA_PA1570_cycle4_Rep1


title: PA_PA1599_cycle3_Rep1


title: PA_PA1570_cycle0_Rep1


title: PA_PA1526_cycle3_Rep1


title: PA_PA1526_cycle2_Rep1


title: PA_PA1627_cycle1_Rep1


title: PA_PA1627_cycle3_Rep1


title: PA_PA1526_cycle0_Rep1


title: PA_PA1526_cycle4_Rep1


title: PA_PA1526_cycle1_Rep1


title: PA_PA1520_cycle4_Rep1


title: PA_PA1520_cycle3_Rep1


title: PA_PA1490_cycle4_Rep1


title: PA_PA1520_cycle0_Rep1


title: PA_PA1520_cycle1_Rep1


title: PA_PA1520_cycle2_Rep1


title: PA_PA1490_cycle3_Rep1


title: PA_PA1490_cycle0_Rep1


title: PA_PA1490_cycle1_Rep1


title: PA_PA1630_cycle0_Rep1


title: PA_PA1437_cycle4_Rep1


title: PA_PA1437_cycle3_Rep1


title: PA_PA1490_cycle2_Rep1


title: PA_PA1437_cycle1_Rep1


title: PA_PA1437_cycle2_Rep1


title: PA_PA1437_cycle0_Rep1


title: PA_PA1570_cycle2_Rep1


title: PA_PA1431_cycle4_Rep1


title: PA_PA1431_cycle2_Rep1


title: PA_PA1431_cycle3_Rep1


title: PA_PA1431_cycle1_Rep1


title: PA_PA1431_cycle0_Rep1


title: PA_PA1430_cycle4_Rep1


title: PA_PA1430_cycle2_Rep1


title: PA_PA1430_cycle1_Rep1


title: PA_PA1430_cycle0_Rep1


title: PA_PA1430_cycle3_Rep1


title: PA_PA1413_cycle2_Rep1


title: PA_PA1413_cycle3_Rep1


title: PA_PA1413_cycle4_Rep1


title: PA_PA1399_cycle4_Rep1


title: PA_PA1399_cycle3_Rep1


title: PA_PA1397_cycle4_Rep1


title: PA_PA1399_cycle0_Rep1


title: PA_PA1397_cycle0_Rep1


title: PA_PA1413_cycle1_Rep1


title: PA_PA1399_cycle1_Rep1


title: PA_PA1397_cycle2_Rep1


title: PA_PA1397_cycle1_Rep1


title: PA_PA1399_cycle2_Rep1


title: PA_PA1359_cycle4_Rep1


title: PA_PA1359_cycle3_Rep1


title: PA_PA1359_cycle0_Rep1


title: PA_PA1397_cycle3_Rep1


title: PA_PA1359_cycle1_Rep1


title: PA_PA1328_cycle4_Rep1


title: PA_PA1328_cycle3_Rep1


title: PA_PA1328_cycle2_Rep1


title: PA_PA1328_cycle1_Rep1


title: PA_PA1328_cycle0_Rep1


title: PA_PA1315_cycle4_Rep1


title: PA_PA1315_cycle3_Rep1


title: PA_PA1315_cycle0_Rep1


title: PA_PA1315_cycle1_Rep1


title: PA_PA1315_cycle2_Rep1


title: PA_PA1413_cycle0_Rep1


title: PA_PA1290_cycle3_Rep1


title: PA_PA1290_cycle4_Rep1


title: PA_PA1290_cycle1_Rep1


title: PA_PA1290_cycle0_Rep1


title: PA_PA1269_cycle3_Rep1


title: PA_PA1269_cycle1_Rep1


title: PA_PA1359_cycle2_Rep1


title: PA_PA1264_cycle3_Rep1


title: PA_PA1264_cycle0_Rep1


title: PA_PA1241_cycle3_Rep1


title: PA_PA1241_cycle4_Rep1


title: PA_PA1241_cycle2_Rep1


title: PA_PA1241_cycle1_Rep1


title: PA_PA1241_cycle0_Rep1


title: PA_PA1235_cycle3_Rep1


title: PA_PA1235_cycle1_Rep1


title: PA_PA1235_cycle4_Rep1


title: PA_PA1264_cycle2_Rep1


title: PA_PA1235_cycle2_Rep1


title: PA_PA1226_cycle2_Rep1


title: PA_PA1226_cycle1_Rep1


title: PA_PA1235_cycle0_Rep1


title: PA_PA1226_cycle4_Rep1


title: PA_PA1226_cycle0_Rep1


title: PA_PA1290_cycle2_Rep1


title: PA_PA1269_cycle4_Rep1


title: PA_PA1269_cycle2_Rep1


title: PA_PA1269_cycle0_Rep1


title: PA_PA1223_cycle4_Rep1


title: PA_PA1264_cycle4_Rep1


title: PA_PA1738_cycle0_Rep1


title: PA_PA1223_cycle3_Rep1


title: PA_PA1223_cycle2_Rep1


title: PA_PA1264_cycle1_Rep1


title: PA_PA1223_cycle0_Rep1


title: PA_PA1223_cycle1_Rep1


title: PA_PA1201_cycle4_Rep1


title: PA_PA1226_cycle3_Rep1


title: PA_PA1145_cycle4_Rep1


title: PA_PA1142_cycle4_Rep1


title: PA_PA1201_cycle3_Rep1


title: PA_PA1196_cycle0_Rep1


title: PA_PA1201_cycle0_Rep1


title: PA_PA1201_cycle1_Rep1


title: PA_PA1196_cycle4_Rep1


title: PA_PA1201_cycle2_Rep1


title: PA_PA1196_cycle1_Rep1


title: PA_PA1145_cycle2_Rep1


title: PA_PA1145_cycle0_Rep1


title: PA_PA1142_cycle0_Rep1


title: PA_PA1145_cycle1_Rep1


title: PA_PA1196_cycle3_Rep1


title: PA_PA1142_cycle2_Rep1


title: PA_PA1145_cycle3_Rep1


title: PA_PA1196_cycle2_Rep1


title: PA_PA1142_cycle1_Rep1


title: PA_PA1141_cycle3_Rep1


title: PA_PA1141_cycle2_Rep1


title: PA_PA1141_cycle1_Rep1


title: PA_PA1141_cycle4_Rep1


title: PA_PA1142_cycle3_Rep1


title: PA_PA1141_cycle0_Rep1


title: PA_PA1128_cycle4_Rep1


title: PA_PA1128_cycle0_Rep1


title: PA_PA1128_cycle1_Rep1


title: PA_PA1128_cycle3_Rep1


title: PA_PA1099_cycle2_Rep1


title: PA_PA1099_cycle3_Rep1


title: PA_PA1128_cycle2_Rep1


title: PA_PA1099_cycle4_Rep1


title: PA_PA1099_cycle0_Rep1


title: 60CF14

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

country: France

institute: INRAE

data_processing:
The cDNA sequence database for Bos taurus was obtained from Ensembl genome browser (release-98101; Bos_taurus.ARS-UCD1.2.cdna.all.fa) and used to build a reference index for the bovine transcriptome.
RNA-Seq reads were pseudo-aligned to the reference index with Salmon (Release 1.1.0).
Gene-level counts were prepared for differential expression analysis with tximport (release 1.14.2) as part of the Bioconductor package.
Differential expression was measured using DESeq2 (release 1.26.0) with default parameters as part of the Bioconductor package.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: GSCN*.quant.sf is the quantification file output of Salmon (quasi-mapping and transcript quantification tool for RNA-seq data). This is a plain text, tab-separated file. The columns have the following interpretation:
Supplementary_files_format_and_content: Name: the name of the target transcript.
Supplementary_files_format_and_content: Length: the length of the target transcript in nucleotides.
Supplementary_files_format_and_content: EffectiveLength: the computed effective length of the target transcript.
Supplementary_files_format_and_content: TPM: salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
Supplementary_files_format_and_content: NumReads: Salmon's estimate of the number of reads mapping to each transcript that was quantified. It is an estimate insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

molecule: polyA RNA

organism: Bos taurus

source_name: endometrium

extract_protocol:
Total RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems, Life Technologies), according to the manufacturer’s instructions
Full length cDNA were generated from 300 pg of total RNA  using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: The three endometrial cell types (luminal epithelium, glandular epithelium and stroma cells) were collected by laser microdissection from endometrial biopsies performed at 80 days postpartum

value: endometrium

tag: breed

value: Swedish Red breed

value: stromal cells

tag: Stage

value: day-15 of oestrous cycle

tag: energy balance

value: SevereEnergyBalance


title: 18CF14


title: 60CE14

value: glandular cells


title: 36LL14

value: luminal cells

value: ModerateEnergyBalance


title: 18CE14


title: 36LE14


title: Mild coronary stenosis-3

type: RNA

city: Harbin

first: Wen

address: No.23 youzheng road,nangang district

institute: The First Affiliated Hospital of Harbin Medical University

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.4 system,whole blood, Mild coronary stenosis-3

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA version 2.0 (8x15K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: whole blood, Mild coronary stenosis-3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA  according to the manufacturer's instructions,  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: This study extracted total RNA using TRI Reagent BD (Molecular Research Center, OH, USA).Total RNA from each sample was quantified using the NanoDrop ND-1000. All samples' preparation and microarray hybridization were conducted based on the Arraystar's standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched circular RNAs were then amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar, MD, USA).

treatment_protocol: Whole blood samples (1 mL per patient) were drawn from the study donors via direct venous puncture into 2.0 mL siliconized vacuum tubes containing K2 ethylene diamine tetraacetic acid (EDTA) for Microarray analysis and RT-qPCR. After blood collection, the blood samples were immediately placed into a liquid nitrogen tank and quickly transferred to an ultra-low temperature freezer at -80℃ for storage until use

value: whole blood

value: male


title: 52CE14


title: Mild coronary stenosis-4

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.4 system,whole blood, Mild coronary stenosis-4

source_name: whole blood, Mild coronary stenosis-4


title: 26LL14


title: 52CF14


title: Mild coronary stenosis-2

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.4 system,whole blood, Mild coronary stenosis-2

source_name: whole blood, Mild coronary stenosis-2


title: AMI-3

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.0 system,whole blood, AMI-3

source_name: whole blood, AMI-3


title: AMI-4

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.0 system,whole blood, AMI-4

source_name: whole blood, AMI-4


title: Mild coronary stenosis-1

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.4 system,whole blood, Mild coronary stenosis-1

source_name: whole blood, Mild coronary stenosis-1


title: PA_PA1097_cycle4_Rep1

tag: genotype

value: wild type

value: exponential phase


title: 36LF14

tag: tissue


title: PA_PA1099_cycle1_Rep1


title: PA_PA1097_cycle3_Rep1


title: PA_PA1097_cycle2_Rep1


title: AMI-1

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.0 system,whole blood, AMI-1

source_name: whole blood, AMI-1


title: AMI-2

description: CircRNA expression after the Arraystar Human Circular RNA Microarray Version 2.0 system,whole blood, AMI-2

source_name: whole blood, AMI-2


title: 26LE14


title: PA_PA1097_cycle1_Rep1


title: PA_PA1097_cycle0_Rep1

source_name: no protein

value: no protein


title: 32LE14


title: 32LF14


title: 32LL14


title: 23LL14


title: PA_PA0929_cycle3_Rep1


title: PA_PA0929_cycle0_Rep1


title: PA_PA0906_cycle4_Rep1


title: PA_PA0929_cycle1_Rep1


title: PA_PA0906_cycle3_Rep1


title: 23LF14


title: 33CF14


title: 55CF14


title: 33CL14


title: 23LE14


title: 55CL14


title: PA_PA0906_cycle2_Rep1


title: 55CE14


title: PA_PA0906_cycle1_Rep1


title: 33CE14


title: 26LF14


title: PA_PA0906_cycle0_Rep1


title: PA_PA0864_cycle4_Rep1


title: PA_PA0864_cycle2_Rep1


title: PA_PA0929_cycle4_Rep1


title: PA_PA0929_cycle2_Rep1


title: PA_PA0864_cycle3_Rep1


title: PA_PA0864_cycle1_Rep1


title: PA_PA0839_cycle3_Rep1


title: PA_PA0839_cycle0_Rep1


title: PA_PA0839_cycle1_Rep1


title: PA_PA0828_cycle4_Rep1


title: PA_PA0839_cycle2_Rep1


title: PA_PA0828_cycle3_Rep1


title: PA_PA0864_cycle0_Rep1


title: PA_PA0839_cycle4_Rep1


title: Blood sample patient14 day 4

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 4

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the human Clariom D GeneChip according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 system.

data_processing: The microarray data were summarized applying the SST-RMA (signal space transformation - robust multi-array average) gene level method as implemented in the Transcriptome Analysis Console (TAC) 4.0 software (ThermoFisher Scientific).

label: Biotin

source_name: Blood sample day 4

label_protocol: Biotinylated cRNA was prepared according to the protocol for the human Clariom D assay (ThermoFisher Scientific).

extract_protocol: PBMCs were isolated from blood samples taken from psoriatic patients and then total RNA from the PBMCs was isolated using the SV Total RNA Isolation System according to the manufacturer's instructions.

tag: patient diagnosis

value: psoriasis

value: blood

value: Female

tag: day


title: Blood sample patient13 day 84

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 84

source_name: Blood sample day 84

value: Male


title: Blood sample patient14 day 14

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 14

source_name: Blood sample day 14


title: Blood sample patient14 day 0

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 0

source_name: Blood sample day 0


title: Blood sample patient14 day 42

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 42

source_name: Blood sample day 42


title: PA_PA0828_cycle1_Rep1


title: Blood sample patient14 day 84


title: Blood sample patient13 day 0


title: Blood sample patient13 day 4


title: Blood sample patient12 day 42


title: Blood sample patient13 day 42


title: HEK293-PC rep 2

city: Bangkok

first: Warayupa

last: Thompat

address: Praram 4

country: Thailand

institute: Chulalongkorn University

description:
expression profiling of HEK293 after teated by plasmid control, rep 2
SG12494263_257236317151_S001_GE1_1100_Jul11_1_4

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays (Agilent®).

scan_protocol: The slides were incubated for 17 h at 65°C in an Agilent hybridization oven, and then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies)

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: All cell lines were collected from Transwell culture and then RNA was harvested using Trizol reagent.

treatment_protocol: H1650, H1975 and HEK-293 cell lines were grown on 70-80% confluent and seeded the cells amount 250,000 cells/well in 6 wells plate. The cell lines were grown with DMEM medium supplemented with 10% FBS at 37oC, 5% CO2 in culture plates for 24 hour that before to transfected. Briefly, BoxA of HMGB1 (600 ng), Alu-siRNA (100 NM), plasmid control and transfected mock with only Lipofectamine reagent (lipofect) were represented internal control. The dilution was added in Opti-MEM medium (Invitrogen) and then added Lipofectamine 3000 reagent (Invitrogen) 1.0 µl, mixed the solution. The solution was incubated at room temperature for 15 minutes and then removed the media, added fresh media. The solution was added the complex into cells. The cells were harvested after transfected cells for 4 hour. RNAs from these cell lines were hybridization with Agilent platform.

tag: cell line

value: Embryonic kidney cell line HEK293

tag: transfection

value: plasmid control


title: HEK293-Mock rep 1

description:
expression profiling of HEK293 after teated by Mock, rep 1
SG12494263_257236317151_S001_GE1_1100_Jul11_2_3

value: Mock


title: PA_PA0828_cycle0_Rep1


title: HEK293-PC rep 1

description:
expression profiling of HEK293 after teated by plasmid control, rep 1
SG12494263_257236317151_S001_GE1_1100_Jul11_1_3


title: PA_PA0828_cycle2_Rep1

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt


title: HEK293-Mock rep 2

description:
expression profiling of HEK293 after teated by Mock, rep 2
SG12494263_257236317151_S001_GE1_1100_Jul11_2_4


title: HEK293-BoxA of HMGB1 rep 1

description:
expression profiling of HEK293 after teated by BoxA of HMGB1, rep 1
SG12494263_257236317151_S001_GE1_1100_Jul11_1_1

source_name: HEK293-BoxA of HMGB1

value: BoxA of HMGB1


title: HEK293-siRNA-Alu rep 1

description:
expression profiling of HEK293 after teated by siRNA-Alu, rep 1
SG12494263_257236317151_S001_GE1_1100_Jul11_2_1

value: siRNA-Alu


title: PA_PA0791_cycle4_Rep1


title: HEK293-siRNA-Alu rep 2

description:
expression profiling of HEK293 after teated by siRNA-Alu, rep 2
SG12494263_257236317151_S001_GE1_1100_Jul11_2_2


title: HEK293-BoxA of HMGB1 rep 2

description:
expression profiling of HEK293 after teated by BoxA of HMGB1, rep 2
SG12494263_257236317151_S001_GE1_1100_Jul11_1_2


title: Blood sample patient12 day 14


title: Blood sample patient12 day 84


title: Blood sample patient12 day 4


title: H1650-Mock rep 1

description:
expression profiling of H1650 after teated by Mock, rep 1
SG12494263_257236317150_S001_GE1_1100_Jul11_2_3

value: Human lung cancer cell line H1650


title: PA_PA0791_cycle3_Rep1


title: H1650-siRNA-Alu rep 2

description:
expression profiling of H1650 after teated by siRNA-Alu, rep 2
SG12494263_257236317150_S001_GE1_1100_Jul11_2_2


title: PA_PA0791_cycle2_Rep1


title: Blood sample patient12 day 0


title: PA_PA0791_cycle1_Rep1


title: H1650-siRNA-Alu rep 1

description:
expression profiling of H1650 after teated by siRNA-Alu, rep 1
SG12494263_257236317150_S001_GE1_1100_Jul11_2_1


title: PA_PA0791_cycle0_Rep1


title: H1650-PC rep 1

description:
expression profiling of H1650 after teated by plasmid control, rep 1
SG12494263_257236317150_S001_GE1_1100_Jul11_1_3


title: H1650-Mock rep 2

description:
expression profiling of H1650 after teated by Mock, rep 2
SG12494263_257236317150_S001_GE1_1100_Jul11_2_4


title: H1650-PC rep 2

description:
expression profiling of H1650 after teated by plasmid control, rep 2
SG12494263_257236317150_S001_GE1_1100_Jul11_1_4


title: Blood sample patient13 day 14

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 14


title: Blood sample patient11 day 84

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 84


title: H1650-BoxA of HMGB1 rep 1

description:
expression profiling of H1650 after teated by BoxA of HMGB1, rep 1
SG12494263_257236317150_S001_GE1_1100_Jul11_1_1

source_name: H1650-BoxA of HMGB1


title: h1 h2a.w-2 bisulfite-seq rep 2

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with parameters -q 25 -a AGATCGGAAGAG, and all other params default.
ChIP-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Pileup tracks of each ChIP-seq sample over its matched H3 sample (log2) were generated using the deeptools v.3.3.0 function bamCompare, while coverage tracks of input samples were generated using deeptools function bamCoverage; both functions used parameters --normalizeUsing CPM, --binSize 10.
ATAC-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only properly paired reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Sample tracks were obtained using Genrich (https://github.com/jsh58/Genrich) with parameters -p 0.01, -a 200, -l 100, -g 100. ChrM, ChrC, and several high-copy number rRNA regions were excluded from the analysis (provided as a supplementary file in the paper).
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.0c (parameters: --alignIntronMin 70 --alignIntronMax 5000 --alignMatesGapMax 100000 -outFilterMismatchNoverReadLmax 0.05, all others default). Only pairs with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite.  Read counts for each gene and TE were obtained using htseq-count (parameters: --nonunique none -m intersection-strict) using the araport11 annotations (PMID: 27862469). Differential expression analysis was performed using DESeq2 (PMID: 25516281), and genes were considered differentially expressed with an adjusted p-value < 0.05 and abs[log2(fold change)] > 1.
BS-seq datasets: reads were trimmed, mapped to the TAIR10 genome, and methylation called using methylpy (version 1.4.3). Only uniquely mapping reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig tracks for all ChIP-seq samples (except for input samples) are provided, containing normalized sequencing depth of the IP sample vs. its matched input control. For input DNA samples, bigWig tracks contain coverage normalized by total library depth (CPM) instead. For ATAC-seq, normalized coverage tracks created by Genrich are provided. For RNA-seq, the output of DESeq2 analysis is provided, including overall per-gene/TE expression estimates (baseMean), log2(WT / mutant) (mutant = h2a.w-1 or h2a.w-2), and the adjusted p-value. Note that positive log2(FC) numbers indicate that mutant > WT, negative numbers indicate mutant < WT. For BS-seq, 'CGmap' text files containing all methylation data are provided, along with separate bigWig tracks of methylation levels for CG, CHG and CHH methylation. Only positions with 8+ coverage were used to generate the bigWig files.

source_name: seedlings

growth_protocol: Plants were grown in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol:
DNA was extracted from 10-day-old seedlings using the Wizard Genomic DNA Purification kit (Promega).
Methylated adapters were ligated prior to bisulfite treatment using the ZYMO EZ DNA methylation Gold kit. Libraries were prepared using the Nugen ultralow methyl-seq kit, and sequenced on NovaSeq 6000. WT reps 3 and 4 were processed alongsize h1 and h1 h2aw2 reps 1 and 2.

treatment_protocol: no treatment

tag: ecotype background

tag: developmental stage

value: 10-day-old seedlings


title: h1 bisulfite-seq rep 2


title: PA_PA0784_cycle4_Rep1

tag: growth phase

tag: transcription factor


title: H1975-siRNA-Alu rep 2

description:
expression profiling of H1975 after teated by siRNA-Alu, rep 2
SG12494263_257236317149_S001_GE1_1100_Jul11_2_2

value: Human lung cancer cell line H1975


title: H1975-PC rep 1

description:
expression profiling of H1975 after teated by plasmid control, rep 1
SG12494263_257236317149_S001_GE1_1100_Jul11_1_3


title: H1650-BoxA of HMGB1 rep 2

description:
expression profiling of H1650 after teated by BoxA of HMGB1, rep 2
SG12494263_257236317150_S001_GE1_1100_Jul11_1_2


title: PA_PA0784_cycle2_Rep1

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt


title: Blood sample patient11 day 14

tag: gender


title: H1975-Mock rep 2

description:
expression profiling of H1975 after teated by Mock, rep 2
SG12494263_257236317149_S001_GE1_1100_Jul11_2_4


title: PA_PA0784_cycle3_Rep1


title: PA_PA0784_cycle1_Rep1


title: Blood sample patient11 day 0

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 0


title: H1975-Mock rep 1

description:
expression profiling of H1975 after teated by Mock, rep 1
SG12494263_257236317149_S001_GE1_1100_Jul11_2_3


title: Blood sample patient11 day 42

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 42


title: Blood sample patient10 day 84


title: H1975-PC rep 2

description:
expression profiling of H1975 after teated by plasmid control, rep 2
SG12494263_257236317149_S001_GE1_1100_Jul11_1_4


title: Blood sample patient11 day 4

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 4


title: H1975-siRNA-Alu rep 1

description:
expression profiling of H1975 after teated by siRNA-Alu, rep 1
SG12494263_257236317149_S001_GE1_1100_Jul11_2_1


title: Hypoxia, P30, #5

city: Washington

first: Nikki

middle: Gillum

last: Posnack

state: Please select a region, state or province.

address: 111 Michigan Ave, NW

institute: Childrens National Hospital

description: gene expression

hyb_protocol: hybridized to affymetrix genchip mouse clariom s array for 16 hours at 48C

scan_protocol: affymetrix HCS3000 7G scanner

data_processing: quality control evaluated via affymetrix expression console software; data analyzed in Transcriptoe Analysis Console (applied biosciences), 1.5 Fold change relative to Normoxia p8, p<0.05,  0.1 FDR cutoff

label: biotin

source_name: Hypoxia, p30

label_protocol: biotin-labelled using WT Plus reagent kit

extract_protocol: Total RNA extracted with Qiagen Rneasy (fibrous) kit

treatment_protocol: Normoxia or hypoxia (11%)

value: Heart

tag: oxygen status

value: hypoxia


title: H1975-BoxA of HMGB1 rep 1

description:
expression profiling of H1975 after teated by BoxA of HMGB1, rep 1
SG12494263_257236317149_S001_GE1_1100_Jul11_1_1

source_name: H1975-BoxA of HMGB1


title: h1 bisulfite-seq rep 1


title: PA_PA0784_cycle0_Rep1


title: h1 h2a.w-2 bisulfite-seq rep 1


title: Hypoxia, P30, #2

description: gene expression


title: Hypoxia, P30, #3

description: gene expression


title: PA_PA0739_cycle4_Rep1

value: wild type


title: Hypoxia, P30, #1

description: gene expression


title: wild-type bisulfite-seq rep 3

value: wild-type


title: Blood sample patient10 day 14


title: Blood sample patient10 day 42


title: H1975-BoxA of HMGB1 rep 2

description:
expression profiling of H1975 after teated by BoxA of HMGB1, rep 2
SG12494263_257236317149_S001_GE1_1100_Jul11_1_2


title: Normoxia, P30, #5

description: gene expression

source_name: Normoxia, p30

value: normoxia


title: Normoxia, P30, #4

description: gene expression


title: Blood sample patient10 day 4

value: psoriasis


title: PA_PA0739_cycle2_Rep1

value: exponential phase


title: PA_PA0739_cycle3_Rep1


title: Adult rep1

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

institute: King’s College London

data_processing:
Raw sequencing reads were trimmed using the Trimmomatic v0.39 with the default settings.
Reads were mapped to the mm10 reference genome using STAR (Galaxy Version 2.7.5b).
Aligned reads were counted over genes (GRCm38 annotations downloaded from Ensembl version 96) using the “--quantMode GeneCounts” option of STAR.
Gene counts were normalised using the DESeq2 R/Bioconductor package (v1.30.0).
Genome_build: mm10
Supplementary_files_format_and_content: Table with gene counts generated by STAR

source_name: Anterior pituitary

extract_protocol:
Samples were collected in TRIzol (Thermo Fisher) and kept at -80 °C until further processed. RNA was prepared following the manufacturer’s protocol with the following modifications: The aqueous solution was precipitated overnight using isopropanol and 10 μg of glycogen (Ambion) to increase the recovery of RNA. Samples were centrifugated at 12,000 g for 45 min, washed twice with 70% EtOH and RNA was dissolved in RNAse-free water (Qiagen). Samples were quantified using QuBit fluorometers (Thermo Fisher) and RNA purity was measured using a Nanodrop. A Bioanalyser RNA 6000 Pico assay (Agilent) was used to check the RNA quality. RNA samples with an RNA integrity number (RIN) above 9 (9–9.5) were selected and sent to the Oxford Genomic Centre (Oxford, UK) for the RNAseq experiment. Samples were normalised to a 50 ng input.
The purification of mRNA, generation of double-stranded cDNA and library construction were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the centre’s adapters and barcode tags, before sequencing on an Illumina HiSeq 4000 as 75 bp paired end.

tag: strain

value: Anterior pituitary

value: Postnatal week 8


title: PA_PA0708_cycle4_Rep1


title: Adult rep2

tag: age


title: PA_PA0739_cycle0_Rep1

value: no protein


title: Normoxia, P30, #3

description: gene expression


title: Embryo rep6

source_name: Rathke's pouch

value: Rathke's pouch

value: Embryonic day 13.5


title: Hypoxia, P30, #4

description: gene expression


title: Embryo rep7


title: Normoxia, P30, #2

description: gene expression


title: Embryo rep5


title: Hypoxia, P8, #8

description: gene expression

source_name: Hypoxia, p8


title: Hypoxia, P8, #7

description: gene expression


title: PA_PA0739_cycle1_Rep1


title: PA_PA0708_cycle2_Rep1


title: Embryo rep4


title: Blood sample patient10 day 0

value: blood

value: Male


title: Hypoxia, P8, #5

description: gene expression


title: PA_PA0708_cycle1_Rep1


title: Embryo rep3


title: Blood sample patient9 day 84

value: Female


title: Hypoxia, P8, #6

description: gene expression


title: PA_PA0708_cycle3_Rep1


title: Embryo rep2


title: PA_PA0708_cycle0_Rep1


title: PA_PA0652_cycle4_Rep1


title: Embryo rep1


title: Blood sample patient9 day 4


title: Blood sample patient9 day 14


title: Blood sample patient9 day 42


title: Normoxia, P8, #23

description: gene expression

source_name: Normoxia, p8


title: PA_PA0652_cycle3_Rep1


title: PA_PA0652_cycle2_Rep1


title: Blood sample patient8 day 84


title: Normoxia, P8, #24

description: gene expression


title: Blood sample patient9 day 0


title: PA_PA0652_cycle1_Rep1


title: Blood sample patient8 day 42


title: Normoxia, P8, #13

description: gene expression


title: PA_PA0652_cycle0_Rep1


title: Normoxia, P8, #22

description: gene expression


title: Blood sample patient8 day 14