title: shHOXB13-Ethl-1

treatment_protocol: LNCaP cells were infected with control shRNA (pGIPZ) or shRNA targeting HOXB13 (shHOXB13) for 4 days followed by hormone starvation for 3 days. Cells were harvested for RNA-seq analysis in replicate experiments.

value: LNCaP

value: shHOXB13 Ethl


title: T29_3

status: Public on Apr 01 2022

type: SRA

city: Zhengzhou

first: Liushuai

last: Hua

state: Henan

address: No.22 Huayuan Road

department: Institute of Animal Husbandry and Veterinary Science

country: China

institute: Henan Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
Quality control. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Transcriptome assembly. The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Quantification of gene expression levels. Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample, 1) clean data were mapped back onto the assembled transcriptome, 2) the readcount for each gene was obtained from the mapping results, 3) The readcount for each gene was normalized to FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced), 4) the expression levels of each gene were estimated by PFKM
Differential expression analysis. Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Supplementary_files_format_and_content: Differentially_expressed_genes, FPKM

molecule: total RNA

organism: Mauremys reevesii

source_name: adrenal-kidney-gonad complexes

growth_protocol: Four hundred and fifty freshly laid Chinese pond turtle eggs were obtained from LVCA Company (Guangzhou Guangdong, China).

extract_protocol:
Eggs were incubated until they reached Greenbaum’s embryonic stage 16, at which point the embryonic gonads become responsive to ambient temperature. The AKG complexes, with three replicates at each incubation temperature, were collected using a stereoscopic microscope, and stored in liquid nitrogen for subsequent RNA extraction
Total RNA was isolated from the frozen AKG complexes samples using Trizol reagent (TaKaRa, Dalian, China). The quantity and quality of the RNA were determined using a NanoPhotometer spectrometer (Implen Inc., Westlake Village, CA, USA). Then the RNAs were used to constructing Illumina-indexed transcriptome analysis libraries.

treatment_protocol: The eggs were randomly allocated into plastic containers filled with moist vermiculite. Then the containers were put into one of three incubators, in which the temperatures were set at 26, 29 and 32°C, respectively.

tag: incubatioin temperature

tag: Stage

value: Greenbaum’s embryonic stage 16


title: MD24_1

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description: RNA-Seq for MM1S treated with DMSO (98 nM) - 24Hr

data_processing:
The RNA-Seq data was first preprocessed with BBDuk for single end samples
All RNA-seq datasets were aligned with HISAT2 and quantified via Cuffquant 2.2 with the hg19 ERCC annotation
Cuffnorm was utilized to normalize data
Top 3 replicates (based on correlation) were used
Inactive genes (no samples with FPKM > 10) were filtered out prior to additional analysis
Genome_build: hg19 ERCC
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: MM1S MM Cell Line

growth_protocol: Cells were grown in 12 well plates in 1 mL of RPMI media with 10% FBS

extract_protocol:
Samples (~2.5x10^5 cells) were lysed with trizol and RNA was extracted via the Zymo Directzol RNA extraction kit
RNA-Seq libraries were prepared for sequencing using standard Quantseq 3' library prep protocols

treatment_protocol: Treatment with DMSO or YKL for 6 or 24 Hr

tag: cell line

tag: cell type

value: multiple myeloma

tag: treatment

value: DMSO (98 nM)

tag: treatment time


title: PC3-pGIPZ-2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM/FPKM values were calculated by perl script
Genome_build: hg38
Supplementary_files_format_and_content: txt file of RPKM/FPKM values for each Sample

source_name: prostate tumor

growth_protocol: LNCaP and PC3 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit, according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603).using the Illumina provided protocol.
RNA-Seq samples were sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: LNCaP or PC3 cells were infected with control shRNA (pGIPZ) or shRNA targeting HOXB13 (shHOXB13) lentiviruses for 7 days. LNCaP cells with HOXB13 knockdown were rescued by HOXB13-WT or G84E .  LNCaP cells were co-infected with shRNA virus targeting HDAC1 (shHDAC1) and HDAC3 (shHDAC3) with or without concomittant HOXB13 overexpression for 7 days.

tag: treatment/infection

value: pGIPZ

tag: genotype

value: WT


title: PC3-pGIPZ-1


title: LZE22D1

city: Beijing

first: Chen

last: Wu

state: Beijing

address: 17 Panjiayuan Nanli

department: Department of Etiology

institute: CAMS Cancer Hospital

data_processing:
Raw sequencing data was processed using the cell-ranger pipeline (version 2.1.0, 10X Genomics) with default parameters and mapped to GRCh38 reference genome to generate matrices of gene counts by cell barcodes. Gene count matrices were analyzed with Seurat package (version 3.1.5, 100) in R (version 3.6.3, The R Foundation)
Filtering genes and cells: Cells had to express a minimum of 200 genes with a mitochondrial fraction less than 20%. Suspected doublets were annotated using DoubletFinder package (version 2.0.3) and removed. We removed ribosomal genes and retained genes that were expressed in at least 0.1% of all cells.
Identification of epithelial cell: Raw unique molecular identifier (UMI) counts were normalized using SCTransform function with default parameters. Batch effect was adjusted by implementing Harmony package (version 1.0; 101). Dimension reduction was performed using principal-component analysis (PCA) and the optimal number of principal components (PCs) selected using ElbowPlot function. The same PCs are also applied in cell cluster identification with modularity optimization using kNN graph algorithm as input. Cell clusters were visualized using UMAP algorithm 102. And with resolution of 0.3 we obtained nine distinct cell clusters. These clusters were annotated based on the expression of known markers. For epithelial cells, the marker genes included EPCAM, SFN, KRT5, and KRT14, resulting in 5,070 epithelial cells, including 215 from tissue of normal or inflammatory esophageal epithelium, 44 from LGIN, 1,456 from HGIN, and 3,355 from ICA (657, 1,540, 1,137, and 21 for stage I, II, III, and IV, respectively)
Extract count matrix: Using cell barcode to extract original cell count by  gene matrix for 5070 epithelial cells.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include UMI counts for each gene and each cell barcode
Supplementary files format and content: scTDN_UMI_matrix_epithelial_cell.txt.gz: raw counts

source_name: High-grade intraepithelial neoplasia of esophagus

extract_protocol:
Fresh tissues were rinsed with cold 10% FBS PBS, cut into small pieces on ice, and digested in RPMI-1640 medium containing 2 mg/ml collagenase IV (Gibco, Cat:17104-019) and 0.5 mg/ml hyaluronidase (Sigma Aldrich, Cat:7326-33-3 ) for 1 hour at 37 degree centigrade. The digested cell suspension was subsequently filtered through a 70-μm cell strainer (Falcon, Cat:352350) before centrifuging at 560 rcf for 6 minutes at 4°C. Cells were treated with 2ml of 1x red blood cell lysis buffer (BD Biosciences, Cat: 555899) for 5 min following centrifuging of the same parameter. The remaining cells were suspended in 50 μl of 1% FBS PBS after washing once with the same medium. Single-cell suspension was stained with 4',6-diamidino-2-phenylindole (DAPI, Solarbio, Cat:C0065) prior to fluorescence-activated cell sorting (FACS) on a BD FACSAria II flow cytometer (BD Biosciences) to remove dead cells and debris. The number and viability cells were examined using cell pellet by staining trypan blue (20μl mix of 10μl suspension and 10ul 0.4% trypan solution, Thermo Fisher Scientific, Cat: 15250061), following centrifuging at 500g for 5 minutes at 4°C immediately after FACS. We targeted for ~4,000 cells recovered from each channel.
Libraries were prepared using Chromium Single Cell 5’ Reagent Kits (V1, 10X Genomics, Pleasanton, CA, Cat# PN-1000006, PN-1000020) and sequencing was accomplished with an Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA) with 2 × 150 bp paired-end mode.

treatment_protocol: Tissue samples were placed in RPMI-1640 medium (Corning, Cat:10-040-CV) with 20% fetal bovine serum (FBS, Cell technologies, Cat:30070.03) immediately after surgical resection. Tissue was processed for single cell RNA sequencing (scRNA-seq) with a portion being cryo-sectioned and hematoxylin-eosin (H&E) stained to confirm the histological staging.

tag: patient

tag: tissue

value: esophagus

value: epithelial cell


title: HY24_2

description: RNA-Seq for H929 treated with YKL-5-124 (83 nM) - 24Hr

source_name: H929 MM Cell Line


title: T26_1


title: shHOXB13-Ethl-2


title: LZE20D2


title: shHDAC1/3 +HOXB13 WT 2

value: shHDAC1/3 +HOXB13 WT


title: LZE11T

source_name: Tumor tissue of esophageal carcinoma


title: shHDAC1/3 +HOXB13 WT 1


title: HD24_2

description: RNA-Seq for H929 treated with DMSO (83 nM) - 24Hr

value: DMSO (83 nM)


title: LZE11N

source_name: Non-tumor esophgeal epithelium


title: DamOnly - 15-somite embryo (KIN6213_KIN6284_index02)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Raw data files include both DamID and CEL-seq reads

library_source: genomic

data_processing:
Library strategy: scDam&T-seq
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq reads are aligned using GRCm38 (v. 89) transcript models and tophat2 (v. 2.1.1) with the following paramters: : “--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: celseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; damid count table: count table containing UMI-unique GATC counts per 10-kb interval for all single-cell samples; sample annotation: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. Barcodes follow a 3-NNN-3-NNN format, where "N" positions indicate the barcode-specific sequence, and the "3" indicates positions of a 3nt UMI sequence.

molecule: genomic DNA

organism: Danio rerio

source_name: 15-somite zebrafish embryo

growth_protocol: Adult zebrafish (Danio Rerio) were maintained and embryos raised and staged as previously described (PMID: 31510859).

extract_protocol:
At 15-somite stage, embryos were transferred to 2ml Eppendorf tubes and digested with 0.1% Collagenase type II from Cl. Histolyticum (Gibco) in Hanks Balanced Salt Solution without Mg2+/Ca2+ (Thermofisher) for 20-30 mins at 32oC with constant shaking. Once embryos were noticeably digested, cell solution was spun at 2000g 5mins at room temperature and the supernatant was removed. Cell pellet was resuspended with TrypLE Express (Thermofisher) and digested for 10mins at 32oC with constant shaking. Cell solution was inactivated with 10% Fetal Bovine Serum (Thermofisher) in Hanks Balanced Salt Solution without Mg2+/Ca2+ and filtered through a 70um cell strainer (Greiner BIo-One). Cells were pelleted at 2000g 5min room temperature and washed twice with 10% Fetal Bovine Serum (Thermofisher) in Hanks Balanced Salt Solution without Mg2+/Ca2+. Hoescht at a final concentration of 16.8ug/ml was added to the cell solution and incubated for 30mins at 28oC in the dark. Solution was then filtered through a 40um cell strainer (Greiner BIo-One), Propidium iodide was added at a final concentration of 5ul/ml and immediately sorted on a FACS Influx (BD) gating for alive cells in the G2M phase into 384well plates containing primer solution.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: Tübingen longfin (WT) pairs were set up and the following morning, approximately 1nL of 1ng/ul Dam-Mphosph8 mRNA or 0.5ng/ul Dam-GFP mRNA was injected into the yolk at the 1 cell stage. Embryos were slowed down overnight at 23oC and the following morning all embryos were manually dechorionated.

tag: developmental stage

value: 15-somite embryo

tag: dam-fusion protein

value: untethered Dam

tag: molecule subtype

value: genomic DNA; mRNA


title: DamOnly - 15-somite embryo (KIN6213_index15)


title: pGIPZ-Ethl-2

value: pGIPZ Ethl


title: plko.1 +HOXB13 WT 2

value: plko.1 +HOXB13 WT


title: HY24_1


title: LZE11D


title: LZE1T


title: LZE1D


title: DamOnly - 15-somite embryo (KIN5600_index09)


title: T26_2


title: HD24_3


title: HD24_1


title: pGIPZ-Ethl-1


title: DamOnly - 15-somite embryo (KIN5600_index04)


title: LZE10T


title: DamMphosph8 - 15-somite embryo (KIN6213_index16)

value: Mphosph8 (chromodomain trimer)


title: MY6_1

description: RNA-Seq for MM1S treated with YKL-5-124 (98 nM) - 6Hr


title: MY6_2


title: MD6_3

description: RNA-Seq for MM1S treated with DMSO (98 nM) - 6Hr


title: shHDAC1/3 1

value: LNCaP


title: plko.1 1


title: LZE10N


title: DamMphosph8 - 15-somite embryo (KIN6213_index07)


title: shHOXB13+G84E-2


title: plko.1 2


title: LZE10D


title: DamMphosph8 - 15-somite embryo (KIN6213_index14)


title: MD6_1


title: DamMphosph8 - 15-somite embryo (KIN6213_index08)


title: shHOXB13+G84E-1


title: HY6_3

description: RNA-Seq for H929 treated with YKL-5-124 (83 nM) - 6Hr


title: DamMphosph8 - 15-somite embryo (KIN6213_index03)


title: HY6_2


title: RNA_COVSP014

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: Monocytes CD14+ Covid19: Recovery 6Mo

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters: Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Reads were then mapped to the reference genome GRCh38 by using STAR_2.5.3a software with default parameters
GRCh38
Assembly: GRCh38
Supplementary files format and content: Normalized counts and statistics

source_name: PBMC

extract_protocol:
15.000 to 200.000 CD14hi monocytes from 11 healthy controls, 13 acute and 20 convalescent patients were isolated by FACS directly in TRIzol reagent (ThermoFisher scientific). After chloroform extraction, RNA isolation was performed using a RNeasy kit (Qiagen) and sample quality was tested on a Fragment Analyzer (Agilent)
Indexed cDNA libraries were obtained  using the Ovation Solo RNA-Seq System (Tecan) following manufacturer’s recommendations

value: Monocytes CD14+

tag: disease state

value: Covid19:Recovery 6Mo


title: RNA_COVSP001

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: RNA_COVSP012

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: shHDAC1/3 2


title: plko.1 +HOXB13 WT 1


title: shHOXB13+WT-1


title: MD6_2

value: multiple myeloma


title: DamMphosph8 - 15-somite embryo (KIN5600_index15)


title: RNA_COVER001

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: RNA_COVSP007

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: HD6_3

description: RNA-Seq for H929 treated with DMSO (83 nM) - 6Hr


title: DamMphosph8 - 15-somite embryo (KIN5600_index02)


title: DamMphosph8 - 15-somite embryo (KIN5600_index08)


title: shHOXB13-2


title: HD6_2


title: RNA_COVSP009

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: RNA_COVSP008

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: DamMphosph8 - 15-somite embryo (KIN5600_index01)


title: shHOXB13-1


title: pGIPZ-2


title: shHOXB13+WT-2


title: RNA_COVSP005

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: HD6_1


title: DamMphosph8 - 15-somite embryo (KIN5600_index03)


title: RNA_COVSP010

description: Monocytes CD14+ Covid19: Recovery 3Mo

value: Covid19:Recovery 3Mo


title: HY6_1


title: AMO1_YKL_High_24hr_2

description: RNA-Seq for AMO1 treated with YKL-5-124 (1000 nM) - 24hr

source_name: AMO1 MM Cell Line

treatment_protocol: Treatment with DMSO or YKL for 24 Hr


title: DamMphosph8 DamOnly - 15-somite embryo (KIN5938_index12)

value: Mphosph8 (chromodomain trimer); untethered Dam


title: RNA_COVSP004

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: DamMphosph8 DamOnly - 15-somite embryo (KIN5938_index11)


title: RNA_ICOV6-006

description: Monocytes CD14+ Covid19: Recovery 3Mo


title: AMO1_YKL_High_24hr_3


title: AMO1_YKL_High_24hr_1


title: AMO1_YKL_Low_24hr_3

description: RNA-Seq for AMO1 treated with YKL-5-124 (100 nM) - 24hr


title: RNA_ICOV6-007

description: Monocytes CD14+ Covid19: Recovery 3Mo


title: MY6_3


title: AMO1_YKL_Low_24hr_2


title: RNA_ICOV6-005

description: Monocytes CD14+ Covid19: Recovery 3Mo


title: AMO1_YKL_Low_24hr_1


title: AMO1_DMSO_24hr_3

description: RNA-Seq for AMO1 treated with DMSO - 24hr

value: DMSO


title: pGIPZ-1

value: pGIPZ

value: WT


title: RNA_ICOV6-013

description: Monocytes CD14+ Covid19: Recovery 3Mo


title: E47_T

type: RNA

city: Jinan

first: Qing

last: Sun

address: JINGSHI Road 16766

institute: The First Affiliated Hospital of Shandong First Medical University

description: E47_T.sst-rma-combined-dabg.chp Signal

hyb_protocol: The Affymetrix GeneChip® Hybridization, Wash, and Stain Kit(900720) is used for hybridization at 45℃ for 16h.

scan_protocol: After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix)

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Genesrping software (version 13.1; Agilent Technologies) was employed to finish gene expression analysis.

label: biotin

source_name: Mucinous adenocarcinoma

label_protocol: The Affymetrix WT Terminal Labeling and Controls Kit (901524) is used for the fragmentation and labeling of the cDNA.

extract_protocol: RNA was extracted by RecoverAll™ Total Nucleic Acid Isolation Kit (AM1975) following the manufacturer's instructions.

treatment_protocol: The paraffin tissue was cut at 7μm on the anti-slip slide, and the microdissection was performed after precise positioning by the Applied Biosystems-Arcturus XT machine

value: Mucinous adenocarcinoma


title: AMO1_DMSO_24hr_2


title: RNA_AGER013

description: Monocytes CD14+ Covid19: Acute infection

value: Covid19:Acute infection


title: RNA_AGER010


title: RNA_AGER012


title: AMO1_DMSO_24hr_1


title: rMSC-ISB-P_3

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

country: South Korea

institute: Dankook University

data_processing:
Illumina bcl2fastq  v2.20.0.422 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18
mapped to rn5 whole genome using TopHat v2.0.13 and calculate abundance using cuffdiff v2.2.1
Assembly: rn5
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: rat bone marrow

growth_protocol: rMSCs were cultured in growth medium (alpha MEM supplemented with 10% FBS and 1% P/S) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated by using RibospinTM according to the manufacturer`s protocol.
RNA libraries were prepared for sequencing according to Illumina's protocols using the Truseq Stranded mRNA Prep Kit.

treatment_protocol: 2 × 10^4 rMSCs were seeded on PCL and ISB-P films (16 mm in diameter) sterilized by EO gas and TCP.

value: Primary mesenchymal stem cells

tag: cell source

value: Bone marrow

tag: culture condition

value: cultured at ISB-P film for 4 hours


title: rMSC-ISB-P_2


title: XG1_YKL_High_24hr_3

description: RNA-Seq for XG1 treated with YKL-5-124 (1000 nM) - 24hr

source_name: XG1 MM Cell Line


title: XG1_YKL_High_24hr_2


title: RNA_ICOV6-017

description: Monocytes CD14+ Covid19: Recovery 3Mo


title: rMSC-ISB-P_1


title: XG1_YKL_High_24hr_1


title: RNA_AGER007


title: RNA_AGER008


title: E45_N

description: E45_N.sst-rma-combined-dabg.chp Signal

source_name: normal mucinous adenocarcinoma

value: normal mucinous adenocarcinoma


title: rMSC-PCL_3

value: cultured at PCL film for 4 hours


title: E45_T

description: E45_T.sst-rma-combined-dabg.chp Signal


title: E41_T

description: E41_T.sst-rma-combined-dabg.chp Signal


title: E47_N

description: E47_N.sst-rma-combined-dabg.chp Signal


title: E30_T

description: E30_T.sst-rma-combined-dabg.chp Signal


title: E43_T

description: E43_T.sst-rma-combined-dabg.chp Signal


title: E41_N

description: E41_N.sst-rma-combined-dabg.chp Signal


title: XG1_YKL_Low_24hr_3

description: RNA-Seq for XG1 treated with YKL-5-124 (100 nM) - 24hr


title: RNA_AGER004


title: E30_N

description: E30_N.sst-rma-combined-dabg.chp Signal


title: E43_N

description: E43_N.sst-rma-combined-dabg.chp Signal


title: XG1_YKL_Low_24hr_1


title: rMSC-PCL_1


title: RNA_AGER003


title: rMSC-PCL_2


title: XG1_YKL_Low_24hr_2


title: rMSC-TCP

value: cultured at TCP for 4 hours


title: XG1_DMSO_24hr_3

description: RNA-Seq for XG1 treated with DMSO - 24hr


title: RNA_ICOV1-287

description: Monocytes CD14+ Healthy

value: Healthy


title: XG1_DMSO_24hr_2


title: E28_N

description: E28_N.sst-rma-combined-dabg.chp Signal


title: E26_N

description: E26_N.sst-rma-combined-dabg.chp Signal


title: E28_T

description: E28_T.sst-rma-combined-dabg.chp Signal


title: E26_T

description: E26_T.sst-rma-combined-dabg.chp Signal


title: RNA_ICOV1-114

description: Monocytes CD14+ Healthy

value: Monocytes CD14+


title: RNA_ICOV1-102

description: Monocytes CD14+ Healthy


title: XG1_DMSO_24hr_1


title: RNA_ICOV1-452

description: Monocytes CD14+ Healthy


title: RNA_ICOV1-130

description: Monocytes CD14+ Healthy


title: AMO1_YKL_High_6hr_3

description: RNA-Seq for AMO1 treated with YKL-5-124 (1000 nM) - 6hr

treatment_protocol: Treatment with DMSO or YKL for 6 Hr


title: RNA_ICOV1-007

description: Monocytes CD14+ Healthy


title: AMO1_YKL_High_6hr_2


title: FOCAD-3 MZ focad-/- liver

city: SINGAPORE

first: Tze Shin

last: Teoh

address: 8A, BIOMEDICAL GROVE

country: Singapore

institute: Genome Institute of Singapore

data_processing:
HiSeq/Novaseq Control Software for base calling
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited text files include fpkm for each sample for each gene
Supplementary_files_format_and_content: matrix table with gene readcount, fold change and adjusted p-value for each mutant vs wt.

source_name: liver

extract_protocol:
Zebrafish livers were harvested, snap freeze with liquid nitrogen. Total RNA were extracted using QiaShredder and RNAeasy mini kit (Qiagen). 1 μg total RNA with RIN value above 6.5 was used for following library preparation
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (Illumina).

tag: organ

value: liver

value: maternal zygotic null focad-/-


title: E25_N

description: E25_N.sst-rma-combined-dabg.chp Signal


title: E25_T

description: E25_T.sst-rma-combined-dabg.chp Signal


title: RNA_ICOV1-208

description: Monocytes CD14+ Healthy


title: E24_T

description: E24_T.sst-rma-combined-dabg.chp Signal


title: RNA_ICOV1-075

description: Monocytes CD14+ Healthy


title: Ino80_siRNA_rep1

city: Wakayama

first: Tsuyoshi

last: Morita

address: Mikazura 580

department: Department of Biology

country: Japan

institute: Wakayama Medical University

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

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

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Normalized signal values were calculated by the following method using the Feature Extraction Software: (1) control probes were excluted by setting control type to 0  (2) averaged sigal intensity values were calculated after excluding the top and bottom 2% of Processed Signal(3) scaling factors (SF) were calculated using the formula SF=target signal constant (2500) / the trimmed mean values. (4) normalized singal intensities Scale Signal were obtained by multiplying the SF value by the individula probe signal values

source_name: Ino80 siRNA in RD cells

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

growth_protocol: RD cells were cultured with a Dulbecco Modified Eagle medium supplemented with 20% foetal bovine serum.

extract_protocol: Total RNAs were extracted using  RNAiso plus, and purified using NucleoSpin RNA Plus.

treatment_protocol: RD cells were transfected with siRNAs using Lipofectamine RNAiMAX for 2 days

value: RD

value: human rhabdomyosarcoma cells

tag: genotype/variation

value: Ino80 knockdown


title: Ies6_siRNA_rep1

source_name: Ies6 siRNA in RD cells

value: Ies6 knockdown


title: Actr5_siRNA_rep1

source_name: Actr5 siRNA in RD cells

value: Actr5 knockdown


title: E23_T

description: E23_T.sst-rma-combined-dabg.chp Signal

value: Mucinous adenocarcinoma


title: control_siRNA_rep1

source_name: control siRNA in RD cells

value: control


title: E21_T

description: E21_T.sst-rma-combined-dabg.chp Signal


title: AMO1_YKL_Low_6hr_1

description: RNA-Seq for AMO1 treated with YKL-5-124 (100 nM) - 6hr

value: multiple myeloma


title: AMO1_YKL_Low_6hr_2


title: E23_N

description: E23_N.sst-rma-combined-dabg.chp Signal


title: PDIA6-2 MZ pdia6-/- liver

tag: age

value: 3.5 month-old

value: maternal zygotic null pdia6-/-


title: RNA_ICOV6-008

description: Monocytes CD14+ Healthy


title: PDIA6-3 MZ pdia6-/- liver


title: AMO1_YKL_Low_6hr_3

tag: cell line


title: FOCAD-1 MZ focad-/- liver


title: PDIA6-1 MZ pdia6-/- liver


title: E21_N

description: E21_N.sst-rma-combined-dabg.chp Signal

value: normal mucinous adenocarcinoma


title: RNA_ICOV1-017

description: Monocytes CD14+ Healthy

tag: cell type


title: D45_T

description: D45_T.sst-rma-combined-dabg.chp Signal

source_name: secretory adenocarcinoma

value: secretory adenocarcinoma


title: AMO1_DMSO_6hr_2

description: RNA-Seq for AMO1 treated with DMSO - 6hr

tag: treatment

value: DMSO


title: AMO1_DMSO_6hr_3

tag: treatment time


title: AMO1_DMSO_6hr_1


title: FOCAD-2 MZ focad-/- liver


title: RNA_ICOV6-023

description: Monocytes CD14+ Healthy

value: Healthy


title: AGER010

data_processing:
Adapters were removed with TrimmomaticPE with the following parameters : LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to hg38 by Bowtie2 with the following parameters: –X 2000 –fr –very-sensitive –no-discordant –no-mixed –non-deterministic
Reads from the alignment were sorted and indexed according to chromosomes
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping within the blacklist of the ENCODE project were removed with a custom script and samtools view
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Assembly: hg38
Supplementary files format and content: txt: peaks and fold change and p-value, bigwig: signal

extract_protocol:
20 000 to 50 000 sorted CD14+ monocytes were collected in 1mL of RPMI media supplemented with 10% FCS at 4°C.Cells were centrifuged, then cell pellets were resuspended in 50 μL of lysis buffer (Tris HCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0,1%) and centrifuged (500 g) for 10 minutes at 4°C. Supernatant was discarded and nuclei were resuspended in 50 μL of reaction buffer (Tn5 transposase 2,5 μL, TD buffer 22,5 μL and 25 μL H2O – Nextera DNA sample preparation kit, Illumina). Tagmentation was performed for 30 minutes at 37°C. DNA was purified using the MinElute purification kit (QIAGEN).
Purified DNA was amplified and indexed by PCR using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs) with 10-12 cycles. Llibraries were purified using MinElute PCR Purification Kit (Qiagen) and quality controlled using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).

value: Monocytes CD14+

value: Covid19:Acute infection


title: E24_N

description: E24_N.sst-rma-combined-dabg.chp Signal


title: D43_T

description: D43_T.sst-rma-combined-dabg.chp Signal


title: AB-3 wt liver

value: liver

value: wildtype


title: D45_N

description: D45_N.sst-rma-combined-dabg.chp Signal

source_name: normal secretory gland cells

value: normal secretory gland cells


title: AB-1 wt liver


title: XG1_YKL_High_6hr_2

description: RNA-Seq for XG1 treated with YKL-5-124 (1000 nM) - 6hr


title: RNA_COVSP002

description: Monocytes CD14+ Covid19: Recovery 6Mo

value: Covid19:Recovery 6Mo


title: XG1_YKL_High_6hr_3


title: AGER003


title: AB-2 wt liver


title: COVSP007

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: D41_T

description: D41_T.sst-rma-combined-dabg.chp Signal


title: AGER013


title: XG1_YKL_High_6hr_1


title: ICOV1-007

description: Monocytes CD14+ Healthy


title: XG1_YKL_Low_6hr_3

description: RNA-Seq for XG1 treated with YKL-5-124 (100 nM) - 6hr


title: D41_N

description: D41_N.sst-rma-combined-dabg.chp Signal


title: COVSP012

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: XG1_YKL_Low_6hr_1


title: XG1_YKL_Low_6hr_2


title: COVER001

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: D43_N

description: D43_N.sst-rma-combined-dabg.chp Signal


title: Nip_Emb_10DAP_rep3

city: Yokohama

first: Hiroki

last: Nagata

state: Kanagawa

address: 641-12 Maioka, Totsuka

department: Kihara Institute for Biological Research

institute: Yokohama City University

hyb_protocol: The Cy3-labeled cRNAs were fragmented and hybridized to the microarray slides at 65 °C for 17 hrs. One-color spike mix was added to total RNAs before reactions and used for monitoring efficiency of the labeling reactions and hybridizations. Hybridization and washing conditions of the hybridized slides were used according to Agilent protocol.

scan_protocol: Scanning the slides were performed by the Agilent G2565BA microarray scanner (Agilent). The background corrections of raw Cy3 signals were performed using the Agilent Feature Extraction software (version 9.5.1; Agilent). All microarray analyses were performed with three independent biological samples of the embryo and endosperm.

data_processing: Data analysis was performed using the R software package (version 3.5.2). The Raw signal data were normalized by Quantile method in limma package (version 3.38.3). The normalized signal densities were log2-transformed normalized signal densities that were deducted the signals of negative-control probes.

organism: Oryza sativa Japonica Group

source_name: Embryo, 10 DAP

label_protocol: The 44k Agilent microarray slides in this study were prepared according to the previously published literature (Ishiguro et al., 2014). The labeling reactions were performed using a Quick Amp Labeling kit (Agilent).

growth_protocol: Rice plants (Oryza sativa cv. Nipponbare) were grown in a biotron chamber (NC-350HC; Nihon Ikakikai) according to described protocol (Ohnishi et al., 2011) except for short day condition and temperature (day light condition for 11 hours at 30 ºC and night condition for 13 hours at 25 ºC).

extract_protocol: Rice endosperm was harvested at 24 hr intervals from 2 to 7 days after pollination (DAP), and at 10 DAP. For isolation of liquid endosperm from the coenocytic (2 DAP) and just after cellularized (3 DAP) stages, a cut was made on the surface of seed coat using a scalpel under a binocular microscope described previously (Tonosaki et al., 2021). The squished out liquid endosperm from a cut was collected using a pipette and transferred into 50 µL of the extraction buffer of PicoPure RNA isolation kit (Applied Biosystems). From 70 to 100 seeds at 2 DAP, and 50 seeds at 3 DAP were used for isolation of liquid endosperm, respectively. After 4 DAP, endosperm tissues were directly dissected from the ovaries under a binocular microscope, and then those are homogenized with RNA isolation cocktail; 350 µL of RLC buffer (RNeasy; Qiagen), 100 µL of Fruit-mate (TAKARA) and 4.5 µL of 2-mercaptoethanol (Wako) (Lee et al., 2016) using micro pestles and 1.5 mL plastic tubes. From 10 to 30 ovaries were used for isolation of endosperm from 4 to 7 DAP. Total RNAs were extracted according to manufacturer’s instructions of RNeasy Plant Mini Kit (Qiagen). For 10 DAP, dissected endosperm tissue from three ovaries were directly transferred to 1.5 mL plastic tubes and immediately frozen by liquid nitrogen. The frozen endosperm was homogenized by multi-beads shocker MB755U (Yasui Kikai) at 1500 rpm for 2 seconds. The resultant homogenized endosperm in a 1.5 mL microcentrifuge tube was immediately added with 1.3 mL of Fruit-mate. The mixture was subdivided into 650 µL aliquot and centrifuged at 12000 g for 5 minutes at 4 ºC. 250 µL of the supernatants was mixed with 400 µL of the RLT buffer in RNeasy Plant Mini Kit (Qiagen) and with 4 µL of 2-mercaptoethanol (Wako). For DNase treatment, RNase-Free DNase Set (Qiagen) was used according to the manufacturer’s instructions. Rice embryo was dissected from the developing ovaries at 5, 7 and 10 DAP under the binocular microscope. Since the early stage of embryo is small and difficult to harvest materials under the binocular microscope, two protocols of the RNeasy Plant Mini Kit (Qiagen) and the PicoPure RNA isolation kit (Thermo Fischer Science) were tested to isolate RNA form the embryo at 5 DAP. For the RNeasy Plant Mini Kit (Qiagen), 15 embryos were collected from the developing ovaries and were immediately frozen by liquid nitrogen. The frozen embryos were homogenized by the multi-beads shocker at 1500 rpm for 2 seconds, the subsequent steps were followed by protocol of RNeasy Plant Mini Kit described above. For the PicoPure RNA isolation kit (Thermo Fischer Science), 3 embryos at 5 DAP were homogenized with 10 µL of the extraction buffer of PicoPure RNA isolation kit using a micro pestle and 1.5 mL microcentrifuge tube. The homogenate was incubated at 42 °C for 30 minutes. Total RNA was extracted followed by the manufacturer’s instructions. At 7 and 10 DAP, 3 embryos were used for total RNA extraction using RNeasy Plant Mini Kit. Quality of total RNAs were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cultivar

value: Nipponbare

value: Embryo

tag: dap


title: D39_T

description: D39_T.sst-rma-combined-dabg.chp Signal


title: D39_N

description: D39_N.sst-rma-combined-dabg.chp Signal


title: Nip_Emb_10DAP_rep2


title: XG1_DMSO_6hr_3

description: RNA-Seq for XG1 treated with DMSO - 6hr


title: D35_T

description: D35_T.sst-rma-combined-dabg.chp Signal


title: XG1_DMSO_6hr_2

description: RNA-Seq for XG1 treated with DMSO - 6hr


title: XG1_DMSO_6hr_1

description: RNA-Seq for XG1 treated with DMSO - 6hr


title: Nip_Emb_7DAP_rep3

source_name: Embryo, 7 DAP


title: COVSP014

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: ICOV6-007

description: Monocytes CD14+ Covid19: Recovery 3Mo

value: Covid19:Recovery 3Mo


title: ICOV1-130

description: Monocytes CD14+ Healthy


title: AGER012


title: Nip_Emb_10DAP_rep1


title: Nip_Emb_7DAP_rep2


title: D35_N

description: D35_N.sst-rma-combined-dabg.chp Signal


title: ICOV1-287

description: Monocytes CD14+ Healthy


title: D33_T

description: D33_T.sst-rma-combined-dabg.chp Signal


title: D31_N

description: D31_N.sst-rma-combined-dabg.chp Signal


title: D31_T

description: D31_T.sst-rma-combined-dabg.chp Signal


title: Nip_Emb_7DAP_rep1


title: C42-shRB Input DHT

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
Alignment to hg19 genome using bowtie2
peak calling with MACS2 with a 0.01 q-value cutoff
Genome_build: hg19
Supplementary_files_format_and_content: BED file

growth_protocol: C4-2 cells (shCon and shRB) were cultured in hormone proficient media

extract_protocol:
ChIP was performed as previously described (Mandigo et al. 2021)
Illumina library prep kit was utilyzed according to manufacturer's instructions

treatment_protocol: C4-2 cells (shCon and shRB) were moved to hormone deficient media for 72 hours followed by treatment with 10 nm DHT for 3 hours prior to harvest

tag: knockdown

value: shRB

value: 72 hrs CDT, 3 hrs 10 nM DHT

tag: ip


title: ICOV6-006

description: Monocytes CD14+ Covid19: Recovery 3Mo


title: C42-shCon Input DHT

value: shCon


title: Nip_Emb_5DAP_rep2

source_name: Embryo, 5 DAP

tag: tissue


title: D29_T

description: D29_T.sst-rma-combined-dabg.chp Signal


title: C42-shRB AR ChIP-seq DHT Rep 1

value: AR


title: ICOV6-005

description: Monocytes CD14+ Covid19: Recovery 3Mo


title: D33_N

description: D33_N.sst-rma-combined-dabg.chp Signal


title: D29_N

description: D29_N.sst-rma-combined-dabg.chp Signal


title: Nip_Emb_5DAP_rep3


title: C42-shCon AR ChIP-seq DHT Rep 1


title: AGER008


title: Nip_End_10DAP_rep3

source_name: Endosperm, 10 DAP

value: Endosperm


title: C42-shRB AR ChIP-seq DHT Rep 2


title: C39_N

description: C39_N.sst-rma-combined-dabg.chp Signal

source_name: normal bronchial epithelial

value: normal bronchial epithelial


title: AGER007

source_name: PBMC


title: ICOV1-114

description: Monocytes CD14+ Healthy


title: ICOV1-452

description: Monocytes CD14+ Healthy


title: AGER004


title: C42-shCon AR ChIP-seq DHT Rep 2


title: Nip_End_7DAP_rep3

source_name: Endosperm, 7 DAP


title: C37_T

description: C37_T.sst-rma-combined-dabg.chp Signal

source_name: Bronchial epithelial carcinoma

value: Bronchial epithelial carcinoma


title: C39_T

description: C39_T.sst-rma-combined-dabg.chp Signal


title: J82_CTRL_RNAseq_rep3

city: Alhambra

first: Yi-Tsung

last: Lu

state: CA

address: 516 SAN PASQUAL DR

institute: University of Southern California

data_processing:
Illumina Casava1.8 was used for basecalling.
After adaptor trimming, we used STAR for alignment to hg19 using gencode v19.
Counts for each gene from the gencode19 were assigned using the Subread package’s featureCounts program with BAM files as inputs
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: J82 bladder cancer cell

growth_protocol: J82 is cultured in DMEM, 10% FBS

extract_protocol:
RNA was extracted using Trizol method
Libraries were constructed using the KAPA mRNA HyperPrep Kit.
RNA-seq, paired-ended 75bp reads

treatment_protocol: LentiCRISPRv2 was used to knock-out FOXC1. The confirmation of FOXC1 knock-out was confirmed by western.

value: J82 bladder cancer cell line

tag: genotype

value: control


title: Nip_Emb_5DAP_rep1


title: Nip_End_7DAP_rep2


title: Nip_End_10DAP_rep2


title: Nip_End_10DAP_rep1


title: J82_FOXC1_KO_RNAseq_rep2

value: FOXC1 KO


title: J82_FOXC1_KO_RNAseq_rep3


title: Nip_End_7DAP_rep1


title: J82_FOXC1_KO_RNAseq_rep1


title: ICOV1-075

description: Monocytes CD14+ Healthy

value: Monocytes CD14+

value: Healthy


title: ICOV6-008

description: Monocytes CD14+ Healthy


title: J82_CTRL_RNAseq_rep2


title: C35_N

description: C35_N.sst-rma-combined-dabg.chp Signal


title: C35_T

description: C35_T.sst-rma-combined-dabg.chp Signal


title: C37_N

description: C37_N.sst-rma-combined-dabg.chp Signal


title: C33_T

description: C33_T.sst-rma-combined-dabg.chp Signal


title: J82_CTRL_RNAseq_rep1


title: C23

description: Monocytes CD14+ Healthy


title: J82_input_rep2

data_processing:
Illumina Casava1.8 was used for basecalling.
After adaptor trimming, we used BWA for alignment to hg19.
All ChIP-seq data were mapped to hg19 and peaks were called using MACS2 2.2.7.1 with the IDR 2.0.2 according to the ENCODE3 ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/).
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak files were generated by MACS2, bw were generated using bedtools and  bedGraphToBigWig

extract_protocol:
Lysates were clarified from sonicated nuclei and FOXC1-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using KAPA HyperPrep Kit (Roche) and the NEXTflex DNA Barcodes (Bioo Scientific).
ChIP-seq, single-ended 75-bp reads

tag: chip antibody


title: AMO1_YKL_High_6hr_1

source_name: AMO1 MM Cell Line

value: multiple myeloma


title: ICOV6-017

description: Monocytes CD14+ Covid19: Recovery 3Mo

tag: disease state


title: COVSP009

description: Monocytes CD14+ Covid19: Recovery 6Mo

value: Covid19:Recovery 6Mo


title: C29_T

description: C29_T.sst-rma-combined-dabg.chp Signal


title: C33_N

description: C33_N.sst-rma-combined-dabg.chp Signal


title: Nip_End_6DAP_rep3

source_name: Endosperm, 6 DAP

value: Nipponbare


title: J82_input_rep1


title: Nip_End_6DAP_rep2


title: Nip_End_5DAP_rep2

source_name: Endosperm, 5 DAP


title: J82_ChIPseq_rep2

value: anti-FOXC1 (D8A6)


title: ICOV1-208

description: Monocytes CD14+ Healthy


title: J82_ChIPseq_rep1


title: Nip_End_4DAP_rep3

source_name: Endosperm, 4 DAP


title: COVSP008

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: T47D D538G FOXA1

city: Boston

first: Zheqi

last: Li

state: Massachusetts

address: 450 Brookline Avenue, Smith Building SM1006

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq reads were aligned to hg19 genome assembly using Bowtie 2.0
Peaks were called using MACS 2.0 with q value below 0.05
DiffBind R package was used to perfrom prinicple component analysis, peak intersections and identify binding sites with differential binding intensities
Genomic feature distribution were called using ChIPseeker R package, taking the promoter region as +/- 3000 bp of the transcriptional start site (TSS).
Genome_build: Hg19

source_name: T47D cell line

growth_protocol: Individual clones were maintained in RPMI 1640, supplemented with 10 % FBS, 100 μg/mL penicillin and 100 mg/mL streptomycin, at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and FOXA1-bound DNA complexes were isolated with antibody (Abcam, ab23738).
ChIP was performed according to our in-house protocols. A minimum of 10ng DNA was sent to Health Sciences Sequencing Core at Children's Hospital of Pittsburgh. The library was prepared using TruSeq ChIP Library Preperation kit (Illumina) and was sequenced on Nextseq  (Illumina). Over 50M single end 150bp reads were allocated for each sample.

treatment_protocol: Cells were washed with pheno-red-free charcoal-stripped serum with 10% CSS for 3 days, then treated with 1 nM E2 for 45 minutes for one of the WT cell group.

tag: esr1 genotype

tag: treatments


title: Nip_End_5DAP_rep1


title: Nip_End_6DAP_rep1


title: C27_T

description: C27_T.sst-rma-combined-dabg.chp Signal


title: T47D D538G Input


title: COVSP005

description: Monocytes CD14+ Covid19: Recovery 6Mo


title: ICOV1-017

description: Monocytes CD14+ Healthy


title: Nip_End_4DAP_rep1


title: ICOV6-013

description: Monocytes CD14+ Covid19: Recovery 3Mo

value: Covid19:Recovery 3Mo


title: T47D Y537S Input


title: Nip_End_4DAP_rep2


title: T47D WT E2 FOXA1

value: Wild-type

value: 1nM estroadiol


title: human  nevus sebaceous-04

city: NANJING

first: Xianhong

last: Yang

address: 12 JIANGWANGMIAO ROAD

department: dermatopathology

institute: Hospital of Skin Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina NovaSeq 6000 was applied for sequencing.
The trimmed data was compared by String Tie software to the known transcriptome.
The transcription abundance was then  calculated by Ballgown
Supplementary_files_format_and_content: The unit of expression is expressed as fragments per kilobase of gene transcript model per million mapped fragments (FPKM).

source_name: skin

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen, California, USA) from frozen  tissues according to the manufacturer’s standard protocol. The NanoDrop ND2000  (Thermo Fisher Scientific Inc, Waltham, MA) instrument was used to quantify total  RNA and standard denaturing agarose gel electrophoresis was used to evaluate the  quality of the RNA.
An RNA Sequencing library was conducted by Reagent test kit according to the manufacturer’s instructions. The RNA Sequencing library was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies Inc, Santa Rosa, CA) and quantified by quantitative polymerase chain reaction (qPCR). Illumina NovaSeq 6000 was applied for sequencing.

tag: race

value: Asian

value: human  nevus sebaceous

value: skin


title: C27_N

description: C27_N.sst-rma-combined-dabg.chp Signal

value: normal bronchial epithelial


title: T47D Y537S FOXA1


title: C25_T

description: C25_T.sst-rma-combined-dabg.chp Signal

value: Bronchial epithelial carcinoma


title: T47D WT E2 Input


title: human  nevus sebaceous-03


title: Nip_End_3DAP_rep3

source_name: Endosperm, 3 DAP

value: Endosperm


title: C25_N

description: C25_N.sst-rma-combined-dabg.chp Signal


title: Nip_End_2DAP_rep3

source_name: Endosperm, 2 DAP


title: C23_T

description: C23_T.sst-rma-combined-dabg.chp Signal


title: human  nevus sebaceous-02


title: T47D WT FOXA1


title: Nip_End_3DAP_rep1


title: Nip_End_2DAP_rep2


title: 15-adkdm2b-vegf-4h

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description: Gene expression data of human endothelial cells

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the human reference genome hg19 with HISAT2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary_files_format_and_content: bigwig

source_name: human umblical vein endothelial cells (HUVECs)

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs) were used as human ECs in this work. HUVECs were purchased from Lonza Japan Ltd. (Tokyo, Japan) and cultured in EBM-2 complete medium composed of EBM-2 Basal Medium (Lonza), supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza) and 3% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA).

extract_protocol:
Total RNA was isolated from HUVECs by using a miRNeasy micro Kit (Qiagen) with the DNase digestion step, according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: HUVEC plates (80-90% confluent) were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 50 ng/ml VEGF (Peprotech, Rocky Hill, NJ) for the indicated periods thereafter.

value: KDM2B overexpression

value: VEGF 4h


title: C21_N

description: C21_N.sst-rma-combined-dabg.chp Signal


title: C23_N

description: C23_N.sst-rma-combined-dabg.chp Signal


title: Nip_End_3DAP_rep2


title: normal human scalp skin tissue-05

value: normal human scalp skin tissue


title: T47D WT Input


title: C21_T

description: C21_T.sst-rma-combined-dabg.chp Signal


title: Nip_End_2DAP_rep1


title: PL_SNU_WT

city: Oxford

first: Jane

last: Mellor

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description:
Sample 1 (PL_SNU_WT repeat 1), aka 17
Sample 2 (PL_SNU_WT repeat2), aka 18

data_processing:
After quality control with fastqc, single-end fastq files were trimmed with Trimmomatic (Bolger et al., 2014) to remove reads with a quality score below 20 in a sliding window of 5 bp. The poly(A) signals were removed with the clip option. Sequences were then aligned with hisat2 with the same settings as for TT-Seq. Sorted bam files were generated using samtools. Calibration of samples was achieved by calculating scaling factors of spike-in counts between samples based on counts tables generated by the bioconductor package featureCounts. Bedgraph and bigwig files were generated from bam files using bedtools, and wigTobigWig (UCSC Genome Browser), respectively. 3’end single basepair resolution was achieved by using the bedtools -bg -3 option. In order to remove potential signals arising from internal priming due to intragenic poly-A stretches, peak-calling on the SNU-Seq bedgraph files (separately for each strand) was performed using macs2 with the narrowpeaks and no-model options. DNA sequences of these peaks were retrieved using the bedtools getfasta command before generating a bed file containing all peak coordinates with sequences containing at least 8 consecutive As (or Ts on the reverse strand). Finally, the ’bedtools intersect -wa’ option was used to filter out any SNU-Seq signals that lie within these peaks.
genome build: hg38
Supplementary_files_format_and_content: The six processed files report (i) the complete SNU-seq signal generated by sequencing from the artificial polyA tract on both the forward and reverse strand, (ii) the 3' end reads only to yield single nucleotide resolution data on both the forward and reverse strand (the standard SNU-seq readout) and (iii) the same 3' end single nucleotide resolution data but lacking any signal from internal priming at polyA tracts 8nt or longer which was removed bioinformatically on both the forward and reverse strands.

source_name: Human Embryonic Kidney

growth_protocol: HeLa and HEK293 cells were cultured in DMEM supplemented with 10 % (v/v) FBS and 1 % (v/v) Penicillin-Streptomycin. The incubator was set at 37 ◦C at 5 % CO2. Cells were passaged 24 hours before harvesting for next-generation sequencing ex- periments at which point they were grown to 80 % confluency. Cells were counted on a Nexcelom Biosciences Auto 2000 Cell Counter

extract_protocol:
Cells were washed rapidly in PBS before adding 0.7 mL QIAZOL per 10 million cells. The cells were scraped off into 2mL Eppendorffs, vortexed for 10 s and placed on ice for 10 minutes. If required for comparative calibration, 2.4 ng of thio-labelled RNA spike-ins per 1 million cells were added at this stage. Total RNA was purified by adding 320 µL chloroform, vortexing for 10 s, incubating at room temperature for 3 minutes, and centrifugation at 4◦C for 15 minutes at 12000 rpm. The upper phase was transferred to a new Eppendorf with 800 uL isopropanol. The sample was left at room temperature for 5 minutes before centrifugation at 4 ◦C for 15 minutes at 15000 rpm. After removing the supernatant, the pellet was washed 3 times in 320 uL 75% ethanol (prepared freshly), with centrifugation at 4 ◦C for 15 minutes at 15000 rpm. The pellet was then air-dried for 10 minutes before dissolving in 160 µL RNAse-free water. At this stage samples were frozen at -80 ◦C. RNA amounts were checked with Nanodrop. 300 µg of total RNA in 400 µL water were chilled on ice for 10 minutes. Samples were split equally into two Eppendorfs, incubated at 65 ◦C for 10 minutes, and then on ice for 5 minutes. After quick-spinning, 300 µL RNase-free water, 100 µL 10x Biotinylation Buffer (100 mM Tris pH 7.5, 1m mM EDTA pH 8.0), 200 µL DMF, and 200 mL EZ-link HPDP Biotin in DMF (1mg / mL, stored in the dark at 4 ◦C). Incubate in the dark at room temperature for 2 hours with shaking at 800 rpm. RNA was purified using Phase-Lock tubes and resuspended in 100 µL RNase-free water. Samples were pooled back together. Following purification, the RNA was not sonicated but carried through to biotinylation and streptavidin purification.For thio-labelled RNA separation, a wash buffer (100 mM Tris pH 7.5, 10 mM EDTA pH 8.0, 1 M NaCl, 0.1 % Tween-20) was prepared freshly – one kept at room temperature (RT-WB), and one at 65 ◦C (65-WB). 100 µL uMACS streptavidin beads were added to 200 µL RNA-Biotin and incubated in a thermomixer at 4 ◦C for 15 minutes at 800 rpm. During this time, the uMACS magnetic stand and rack were prepared alongside a drainer. uMACS columns were placed into the magnetic rack and equilibrated with 900 µL RT-WB for 10 minutes.The biotin-RNA-bead mix was added to the uMACS column. The flow-through was collected and re-loaded to the columns. The second flow-through was discarded. Columns were washed 3 times with 900 µL of 65-WB and then 3 times with 900 µL RT- WB. Elution of labelled RNA was carried out with 100 µL 100 mM DTT. After 5 minutes, elution was performed again with an additional 100 uL 100 mM DTT. Samples were then immediately carried through for RNA purification using the miRNeasy kit. RNA was eluted with 15 µL RNase-free water. Quality and quantity of thiolabelled RNA was checked using the Agilent Bioanalyzer with an RNA pico chip. RNAs were polyadenylated using the NEB Poly A Polymerase kit following the kit instructions. The reaction with 150 ng thiolabeled RNA was left for 45 minutes at 37 ◦C before isopropanol precipitation. The pellet was resuspended in 11 µL RNase-free water. Qualities and amounts were checked on the Qbit fluoremeter and Agilent bioanalyzer.
Libraries were prepared following the Quant-Seq Lexogen 3’ mRNA kit instructions with 13 PCR cycles. Following the manufacturer’s instructions, the chips loaded by the Ion Chef were then sequenced on an Ion Proton Sequencing platform
Thiolabelled spike-ins were generated by amplifying 3 1000-bp long DNA frag- ments from genomic yeast DNA with a 42 % GC content, covering the genes bat2, hxt1, and gal1 using forward primers containing the T7 promoter sequence. The PCR product was purified and then transcribed in vitro following the MEGAscript T7 tran- scription kit instructions, using a thio-UTP to UTP ratio of 1:5.

treatment_protocol: For SNU-Seq labelling, 60 million cells per sample were incubated with 500 µM 4sU for 10 mins

value: Untreated

tag: protocol

value: SNU-Seq

tag: fraction

value: Nascent RNA


title: 14-adkdm2b-vegf-1h

value: human umblical vein endothelial cells (HUVECs)

value: VEGF 1h


title: normal human scalp skin tissue-04

tag: age


title: normal human scalp skin tissue-03


title: 12-mock-vegf-4h

tag: cell type

value: mock

value: control (for KDM2B overexpression)


title: 13-adkdm2b-vegf-0h

value: untreated


title: E13.5, input

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: Louisiana

address: 1430 Tulane Avenue

department: Pediatric Nephrology

institute: Tulane University

data_processing:
Sequencing was performed on an Illumina HiSeq 2500, running HiSeq Control Software 2.2.58. Quality control of sequencing reads was performed using FastQC.
Reads were then aligned to the reference genome using BWA v. 0.7.5a. Samples were filtered for regions blacklisted by the ENCODE project. Subsequently samples were deduplicated using SAMtools v. 1.3.1.
Alignment coordinates were converted to BED format using BEDTools v.2.17 and peak calling was performed using Sicer.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Mus musculus

source_name: Embryonic Kidneys

growth_protocol: E13 and P0 MACS(Magnetic Aactivated Cell Sorting-cells) were expanded in nephron progenitor expansion medium (NPEM) for two passages to obtain near pure populations of Cited1+-enriched NPC.

extract_protocol:
Chromatin was prepared from E13.5 and P0 NPCs using the Diagenode iDeal ChIP-seq kit for Histones. Samples corresponding to 0.5 million cells were resuspended in 100 µl of shearing buffer iS1 and sheared during eight cycles of 30 s ‘ON’/30 s ‘OFF’ with the Bioruptor Pico combined with the Bioruptor Water cooler.The shearing efficiency was analyzed using an automated capillary electrophoresis system Fragment Analyzer (High sensitivity NGS fragment kit) after RNAse treatment, reversal of the crosslinking and purification of DNA.
500 pg of DNA was  used for library preparation using the MicroPlex v2 protocol. The ChIP samples (eight samples in total) were processed together. A control library was processed in parallel of the samples using the same amount of a control Diagenode ChIP's DNA.
12 cycles of amplification were performed to amplify the libraries. After amplification, 1 µl of each library was loaded on BioAnalyzer for quality and quantified using the Qubit ds DNA HS kit.

tag: strain

value: Embryonic Kidneys


title: C16_T

description: C16_T.sst-rma-combined-dabg.chp Signal


title: 11-mock-vegf-1h


title: 10-mock-vegf-0h


title: E13.5, H3K4me1

value: Diagenode antibody, C15410194, lot A1862D


title: normal human scalp skin tissue-02

value: Asian

value: skin


title: E13.5, H3K27me3

value: Diagenode antibody, C15410195, lot A1811-001P


title: B39_T

description: B39_T.sst-rma-combined-dabg.chp Signal

source_name: Alveolar epithelial carcinoma

value: Alveolar epithelial carcinoma


title: B39_N

description: B39_N.sst-rma-combined-dabg.chp Signal

source_name: normal alveolar epithelial

value: normal alveolar epithelial


title: p21kD_1: MCV LT p21KD 1

city: Hershey

first: Hyun Jin

last: Kwun

address: 500 University Drive

department: Microbiology and Immunology

institute: Penn State Milton S. Hershey Medical Center

data_processing:
Base-calling software
NovaSeq paired-end 150-bp reads from Total RNA-Seq data files were first adaptor trimmed using Trim Galore! v0.6.6
Then analyzed using the STAR program (version 2.6.1d) for alignment of short reads to the GRCh38 genome
Transcript counts were inferred from alignment files
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table containing raw gene counts for each sample and gene

source_name: Human Foreskin Fibroblasts

growth_protocol: Cells were grown in 10cm^3 dishes and were supplemented in 10% FBS in DMEM

extract_protocol:
Cells expressing empty vector, MCV LT, MCV dMUR were trypsinized and harvested at day 14. p21 knockdown cells were trypsinized and harvested at day 21.
Total RNA-Seq libraries were constructed from 300 ng of total RNA. To remove rRNA, a method described by Bogdanova et al. (2011) was followed with some modifications. Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat # R3000) according to the manufacturer’s instructions (https://www.zymoresearch.com/products/zymo-seq-ribofree-total-rna-library-kit). RNASeq libraries were sequenced on an Illumina NovaSeq to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.

treatment_protocol: Cells were transduced with lentivirus encoding empty vector, MCV LT, or MCV LT dMUR and grown for 14 days. 14 day old MCV LT expressing cells were transduced with p21 shRNA and grown for 1 week.

tag: cell line

value: BJhTERT

value: Human Foreskin

value: 21 days

value: Human Foreskin Fibroblasts

tag: treatment

value: Lentiviral Transduction, puromycin selection, G418 selection


title: PO, input

source_name: Neonatal NPCs

value: Neonatal NPCs


title: C16_N

description: C16_N.sst-rma-combined-dabg.chp Signal

source_name: normal bronchial epithelial

value: normal bronchial epithelial


title: 9-sikdm2b-oligo2-vegf-4h

value: human umblical vein endothelial cells (HUVECs)

value: KDM2B knockdown

value: VEGF 4h


title: p21kD_2: MCV LT p21KD 2


title: B37_T

description: B37_T.sst-rma-combined-dabg.chp Signal


title: B35_T

description: B35_T.sst-rma-combined-dabg.chp Signal


title: S349_3: MCV LT dMUR 3

value: 14 days

value: Lentiviral Transduction, puromycin selection


title: 8-sikdm2b-oligo2-vegf-1h

value: VEGF 1h


title: p21kD_3: MCV LT p21KD 3


title: PO, H3K27ac

value: Diagenode antibody, C15410196, lot A1723-0041D


title: E13.5, H3K27ac

value: Embryonic Kidneys


title: 7-sikdm2b-oligo2-vegf-0h

value: untreated


title: 6-sikdm2b-oligo1-vegf-4h


title: B33_T

description: B33_T.sst-rma-combined-dabg.chp Signal

value: Alveolar epithelial carcinoma


title: S349_2: MCV LT dMUR 2

value: BJhTERT


title: PO, H3K4me1

value: Diagenode antibody, C15410194, lot A1862D


title: B37_N

description: B37_N.sst-rma-combined-dabg.chp Signal

value: normal alveolar epithelial


title: B35_N

description: B35_N.sst-rma-combined-dabg.chp Signal


title: 5-sikdm2b-oligo1-vegf-1h


title: S348_2: MCV LT 2

value: Human Foreskin

value: Human Foreskin Fibroblasts


title: B31_N

description: B31_N.sst-rma-combined-dabg.chp Signal


title: B33_N

description: B33_N.sst-rma-combined-dabg.chp Signal


title: B31_T

description: B31_T.sst-rma-combined-dabg.chp Signal


title: 4-sikdm2b-oligo1-vegf-0h


title: S348_3: MCV LT 3


title: B29_T

description: B29_T.sst-rma-combined-dabg.chp Signal


title: E13.5, H3K27ac

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine


title: E13.5, input


title: S348_1: MCV LT 1


title: S350_3: Empty Vector_GFP 3


title: E13.5, H3K4me1


title: 3-sicontrol-vegf-4h

value: sicontrol

value: control (for KDM2B knockdown)


title: B29_N

description: B29_N.sst-rma-combined-dabg.chp Signal


title: 2-sicontrol-vegf-1h

value: human umblical vein endothelial cells (HUVECs)


title: C29_N

description: C29_N.sst-rma-combined-dabg.chp Signal

value: normal bronchial epithelial


title: S349_1: MCV LT dMUR 1


title: human  nevus sebaceous-05

value: Asian

value: human  nevus sebaceous

value: skin


title: S350_2: Empty Vector_GFP 2

value: 14 days

value: Lentiviral Transduction, puromycin selection


title: 1-sicontrol-vegf-0h


title: B27_T

description: B27_T.sst-rma-combined-dabg.chp Signal


title: B27_N

description: B27_N.sst-rma-combined-dabg.chp Signal


title: PO, H3K27me3

value: Neonatal NPCs

value: Diagenode antibody, C15410195, lot A1811-001P


title: B25_T

description: B25_T.sst-rma-combined-dabg.chp Signal

value: Alveolar epithelial carcinoma


title: PO, H3K27ac

value: Diagenode antibody, C15410196, lot A1723-0041D


title: COVSP010

description: Monocytes CD14+ Covid19: Recovery 3Mo

source_name: PBMC

value: Monocytes CD14+

value: Covid19:Recovery 3Mo


title: Nip_End_5DAP_rep3

tag: cultivar

value: Nipponbare

value: Endosperm

tag: dap


title: PO, H3K4me1

value: Diagenode antibody, C15410194, lot A1862D


title: 4-vegf-1h-input

description: ChIP-seq data of human endothelial cells during VEGF-signaling

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the human reference genome hg19 with Bowtie2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (PMID: 32125007). In brief, 10 million HUVECs were cross-linked with 1% formaldehyde for 10 min and then neutralized with 0.2 M glycine for 5 min. Collected cell pellets were re-suspended in SDS lysis buffer (10 mM Tris-HCl, 150 mM NaCl, 1% SDS, 1 mM EDTA) with cOmplete™ EDTA-free Protease Inhibitor Cocktail (Sigma-Aldrich), and fragmented by a Picoruptor (40 cycles, 30 sec on/30 sec off; Diagenode, Liege Science Park, Belgium). The sonicated solution was diluted with ChIP dilution buffer (20 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100) to achieve 1 to 5 dilution. The specific antibody was bound to magnetic Dynabeads M-280 (Thermo Fisher Scientific) and applied to the diluted, sonicated solution for immunoprecipitation. Antibody against H3K36me3 (MAB Institute, Inc. Hokkaido, Japan) was used. DNA sonicated to an average size of 0.5 kb was used for the ChIP-seq library preparation. ChIP samples were processed for library preparation with a KAPA Hyper Prep Kit (Kapa Biosystems Inc., Wilmington, MA), according to the manufacturer’s instructions. Deep sequencing was performed on a HiSeq 2500 sequencer (Illumina Inc., San Diego, CA) as single-end 50 base reads.
Libraries were prepared according to Illumina's instructions.

value: VEGF 1h


title: 3-vegf-0h-input

value: human umblical vein endothelial cells (HUVECs)

value: untreated


title: PO, input


title: 2-vegf-1h-H3K36me3


title: S350_1: Empty Vector_GFP 1

value: BJhTERT

value: Human Foreskin

value: Human Foreskin Fibroblasts


title: samAx81

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

data_processing:
The normalized cDNA libraries were pooled and sequenced on Illumina Novaseq 6000 with pair-end 100 cycles in 50M reads sequencing depth.
Image analysis and bases calling were conducted in real-time by the Illumina analysis pipeline.
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab delimited gene expression data of each sample

extract_protocol:
Total RNA was extracted from  skin biopsies by the Qiagen miRNeasy Mini Kit (Valencia, CA, USA). DNA was removed with on-column DNase digestion by the Qiagen RNase-free DNase Set. The quality of extracted RNA was examined using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
Libraries were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA), according to the manufacture’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina Novaseq 6000 with pair-end 100 cycles in 50M reads sequencing depth. Image analysis and bases calling were conducted in real-time by the Illumina analysis pipeline.

tag: timepoint

tag: subytpe

value: Nonlesional

tag: skin condition

value: hidradenitis suppurativa


title: samAx80

value: Perilesional


title: Labeled fraction alpha-amanitin replicate 2

city: Cologne

first: Achim

last: Tresch

state: North Rhine-Westphalia

address: Paul-Schallueck-Str. 10

department: Institute of Medical Statistics and Computational Biology

country: Germany

institute: University of Cologne

data_processing:
Library strategy: TT-seq
Read mapping with STAR 2.3.0 for RNA-seq.
Differential expression analysis with DESeq2 1.30.1 for R 4.0.2.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: GTF with the differential expression and associated statistics of the examined RNA types.
Supplementary_files_format_and_content: countmatrix.csv: Matrix of the raw read counts per annotated feature.

source_name: K562 erythroleukemia cells

extract_protocol:
Cell lysis (QIAgen, #79306) followed by RNA precipitation and fragmentation (Covaris S220).
NuGEN Ovation Library kit (Ovation Universal RNA-seq System): DNase (QIAgen) treatment was performed on column before the library preparation. cDNA fragmentation was performed using Covaris S220 with the following settings: 145 W, 10% duty cycle, 200 cycle/burst, 50 sec, water level 12. Strand selection purification was performed in a cDNA to beads ratio of 1:0.9.

treatment_protocol: 8 hour treatment with 5 µg/mL alpha-amanitin.

value: alpha-amanitin

tag: rna fraction

value: labeled fraction

tag: barcode

value: GTCGTA


title: ATAC_10k_fpkm

city: Debrecen

first: Lajos

last: Széles

address: Egyetem tér 1.

country: Hungary

institute: University of Debrecen

description:
unstimulated CD8-positive dendritic cells
GSM3569295

data_processing:
read trimming with Trimmomatic using SE and -phread33 parameters, TruSeq3-SE.fa:2:30:10 adapter and LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 values
alignment with bwa v0.7.17 using default parameters
bam generation with Picard tools v2.8.1 using SortSam, AddOrreplaceReadGroups, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, MarkDuplicates with default parameters
tag directory generation with homer v4.9.1 makeTagDirectory using -checkGC and -single parameter
peak calling with MACS2 using -B, -q 0.001, --call-summits parameters
mm10 ENCODE blacklist were subtracted from the peak list
in case of ATAC-seq: calculating FPKM values from the previously created BAM and BED files
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (continuous-valued data in track format), bed (position of peaks)
Supplementary_files_format_and_content: table (tsv) of expression values

source_name: dendritic cells from the spleen

growth_protocol: CD8-positive dendritic cells were cultured in IMDM-glutamax medium supplemented with 10% FCS, 1% penicillin + streptomycin and 0,1% β-mercaptoethanol

extract_protocol:
Cells were double cross-linked with DSG (40 min) and  formaldehyde (10 min). Nuclei were isolated using lysis buffer containing 150 mM NaCl, 1 nM EDTA pH 8, 20 mM Tris-HCl pH 8, 1% Triton x-100, 1% SDS with EDTA-free protease inhibitor (Roche). Chromtain was sheared with sonication and immunoprecipitated overnight using antibodies against IRF3 (D83B9, Cell Signaling), IRF5 (ab21689, Abcam), IRF9 (AF5629, R&D Systems). Chromatin-antibody complexes were washed and eluted after pull-down by superparamagnetic beads (ThermoFisher Scientific). Eluted complexes were decrosslinked overnight and purified by NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel). ChIP-DNA was quantified by Qubit fluorometer. In case of unstimulated cells for ATAC-seq after lysis, nuclei were subjected to tagmentation.
Indexed cDNA libraries were prepared from 1-10 ng ChIP-DNA using TruSeq ChIP Library Preparation Kit (Illumina) or Ovation Ultralow System V2 (Tecan Genomics) according to manufacturer’s instructions. Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol (Illumina) for ATAC-seq. RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England BioLabs) according to the manufacturer’s protocol. Libraries were sequenced on NextSeq 500 or HiSeq 2500.

treatment_protocol: Cells were left unstimulated or stimulated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG)  or 10U IFN-beta for 90 min.

value: CD8-positive dendritic cell line

tag: stimulation

tag: chip antibody


title: B25_N

address: JINGSHI Road 16766

institute: The First Affiliated Hospital of Shandong First Medical University

description: B25_N.sst-rma-combined-dabg.chp Signal

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Genesrping software (version 13.1; Agilent Technologies) was employed to finish gene expression analysis.

extract_protocol: RNA was extracted by RecoverAll™ Total Nucleic Acid Isolation Kit (AM1975) following the manufacturer's instructions.

tag: tissue

value: normal alveolar epithelial


title: Labeled fraction alpha-amanitin replicate 1

value: AAGCCT


title: samAx78


title: ATAC_15k_fpkm

description:
unstimulated CD8-positive dendritic cells
GSM3574316


title: Labeled fraction control replicate 1

value: ACCTCA


title: 1-vegf-0h-H3K36me3


title: samAx79

value: Lesional


title: samAx77


title: Labeled fraction control replicate 2

value: GTGCTT


title: B23_T

description: B23_T.sst-rma-combined-dabg.chp Signal

value: Alveolar epithelial carcinoma


title: B21_N

description: B21_N.sst-rma-combined-dabg.chp Signal


title: mm_DC_PIC_ChIP-seq_cRel_rep1

description: pIC-stimulated dendritic cell (90 min)

value: 90 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)

value: cRel (sc-71x, Santa Cruz Biotechnology)


title: B21_T

description: B21_T.sst-rma-combined-dabg.chp Signal


title: B23_N

description: B23_N.sst-rma-combined-dabg.chp Signal


title: mm_DC_PIC_ChIP-seq_Junb_rep1

description: pIC-stimulated dendritic cell (90 min)

value: Junb (sc-46x, Santa Cruz Biotechnology)


title: mm_DC_CpG_ChIP-seq_Junb_rep1

description: CpG-stimulated dendritic cell (90 min)

value: 90 min; 1 mM class B CpG oligonucleotide (1826)


title: A39_N

description: A39_N.sst-rma-combined-dabg.chp Signal

source_name: normal terminal bronchiolar epithelium

value: normal terminal bronchiolar epithelium


title: samAx76

value: hidradenitis suppurativa


title: A39_T

description: A39_T.sst-rma-combined-dabg.chp Signal

source_name: Bronchoalveolar carcinoma

value: Bronchoalveolar carcinoma


title: Total fraction alpha-amanitin replicate 1

value: alpha-amanitin

value: total fraction

value: AGTGAG


title: Total fraction alpha-amanitin replicate 2

value: GCACTA


title: samAx75

value: Baseline

value: Nonlesional


title: mm_DC_UT_ChIP-seq_Junb_rep1

description: unstimulated CD8-positive dendritic cells

value: CD8-positive dendritic cell line


title: samAx74

value: Perilesional


title: Total fraction control replicate 1

value: AACCAG


title: mm_DC_CpG_ChIP-seq_p300_rep2

description: CpG-stimulated dendritic cell (90 min)

value: p300 (sc-585, Santa Cruz Biotechnology)


title: mm_DC_UT_ChIP-seq_cRel_rep1


title: samAx72


title: samAx73

value: Lesional


title: mm_DC_CpG_ChIP-seq_cRel_rep1

description: CpG-stimulated dendritic cell (90 min)

value: cRel (sc-71x, Santa Cruz Biotechnology)


title: Total fraction control replicate 2

value: TGGTGA


title: A35_N

description: A35_N.sst-rma-combined-dabg.chp Signal


title: A35_T

description: A35_T.sst-rma-combined-dabg.chp Signal


title: A37_T

description: A37_T.sst-rma-combined-dabg.chp Signal


title: A37_N

description: A37_N.sst-rma-combined-dabg.chp Signal


title: mm_DC_UT_ChIP-seq_p300_rep2


title: mm_DC_CpG_ChIP-seq_p300_rep1

description: CpG-stimulated dendritic cell (90 min)

value: 90 min; 1 mM class B CpG oligonucleotide (1826)


title: samAx70


title: A33_T

description: A33_T.sst-rma-combined-dabg.chp Signal


title: samAx71


title: RNA-Seq CD4_withMHE_PC154

city: Paterna

first: Ana

last: Conesa

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: CSIC

description:
gender: Man
Gene expression in human CD4 T-cells

data_processing:
Illumina Sequencer Software HiSeq Control Software 2.2.58 used for basecalling.
Sequenced reads were trimmed and masked for low-quality sequence, then mapped to hg38 whole genome using STAR v2.6.1c with default parameters.
Sequencing reads were counted to obtain the gene expression matrix with HTSeq v0.9.1 using intersection-strict mode. Conditional quantile normalization (Hansen et al., Biostatistics, 2012) was applied to remove technical variability in RNA-seq data.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and samples withouth and with MHE.
Supplementary_files_format_and_content: Matrix table with normalized values for samples withouth and with MHE.

source_name: CD4 T-cell, with Minimal Hepatic Encepalopathy

extract_protocol:
CD4 T cells were isolated using EasySep™ Human CD4+ T Cell Isolation Kit (STEMCELL Technologies Inc.) and RNA isolation was made with miRNeasy Micro Kit (QIAGEN). HiSeq Sequencing v4 Chemistry was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral CD4 T-cells

tag: disease state

value: withMHE

tag: gender

value: Male


title: RNA-Seq CD4_withMHE_PC145

tag: age


title: samAx69

value: hidradenitis suppurativa


title: E13.5, H3K27me3

value: Embryonic Kidneys

value: Diagenode antibody, C15410195, lot A1811-001P


title: RNA-Seq CD4_withMHE_PC144

tag: cell type


title: mm_DC_UT_ChIP-seq_p300_rep1


title: samAx68


title: samAx67


title: A33_N

city: Jinan

first: Qing

last: Sun

description: A33_N.sst-rma-combined-dabg.chp Signal

value: normal terminal bronchiolar epithelium


title: RNA-Seq CD4_withMHE_PC134


title: RNA-Seq CD4_withMHE_PC126


title: A31_T

description: A31_T.sst-rma-combined-dabg.chp Signal

value: Bronchoalveolar carcinoma


title: mm_DC_UT_ChIP-seq_PU.1_rep2

value: PU.1 (sc-352, Santa Cruz Biotechnology)


title: RNA-Seq CD4_withMHE_PC122


title: samAx66

value: Nonlesional


title: mm_DC_UT_ChIP-seq_PU.1_rep1

value: CD8-positive dendritic cell line


title: mm_DC_UT_ChIP-seq_IRF8_rep2

value: IRF8 (sc-6058, Santa Cruz Biotechnology)


title: RNA-Seq CD4_withoutMHE_PC149

source_name: CD4 T-cell, without Minimal Hepatic Encepalopathy

value: withoutMHE


title: RNA-Seq CD4_withoutMHE_PC135


title: mm_DC_UT_ChIP-seq_IRF8_rep1


title: samAx64

value: Lesional


title: A31_N

description: A31_N.sst-rma-combined-dabg.chp Signal


title: RNA-Seq CD4_withoutMHE_PC132


title: mouse glioblastoma, AAE9

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
fastp 0.20.1 used for trimming and filtering
STAR 2.7.2a used for alignment to the GRCm38 assembly
DESeq2 1.30.1 used for normalization of count data
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for each sample
Supplementary_files_format_and_content: Supplementary tab-delimited text files including normalized counts for all samples, compressed using gzip

source_name: mouse glioblastoma

growth_protocol: Mouse glioblastomas were induced by lentiviral vector expressing PDGFB and shRNA against p53. Tumor tissues were isolated from mice reached clinical endpoints. Normal brain tissue was trimmed away from GFP+ tumor tissue using a dissecting microscope.

extract_protocol:
RNA was isolated using the Rneasy kit according to manufacturer's protocol with the addition of Dnase (Qiagen).
cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina).

value: glioblastoma

tag: strain

value: GFAP-Cre transgenic

tag: lentiviral vector


title: A29_T

description: A29_T.sst-rma-combined-dabg.chp Signal


title: samAx63

value: Baseline


title: A27_T

description: A27_T.sst-rma-combined-dabg.chp Signal


title: mouse glioblastoma, AAE7


title: PO, H3K27me3

value: Neonatal NPCs


title: samAx65

value: Perilesional


title: A27_N

description: A27_N.sst-rma-combined-dabg.chp Signal


title: mouse glioblastoma, AAE8


title: samAx61


title: samAx60


title: RNA-Seq CD4_withoutMHE_PC130

description:
gender: Woman
Gene expression in human CD4 T-cells

value: Peripheral CD4 T-cells

value: Female


title: RNA-Seq CD4_withoutMHE_PC127

value: Male


title: normal mouse brain, AAE5

source_name: normal mouse brain

value: brain


title: RNA-Seq CD4_withoutMHE_PC131


title: A25_N

description: A25_N.sst-rma-combined-dabg.chp Signal

value: normal terminal bronchiolar epithelium


title: A25_T

description: A25_T.sst-rma-combined-dabg.chp Signal

value: Bronchoalveolar carcinoma


title: samAx59

value: hidradenitis suppurativa


title: samAx62


title: A23_N

description: A23_N.sst-rma-combined-dabg.chp Signal


title: RNA-Seq CD4_control_CR219

source_name: CD4 T-cell, control

value: control


title: A21_T

description: A21_T.sst-rma-combined-dabg.chp Signal


title: A29_N

description: A29_N.sst-rma-combined-dabg.chp Signal


title: samAx58


title: normal mouse brain, AAE4


title: samAx57

value: Nonlesional


title: RNA-Seq CD4_control_CR215


title: A23_T

description: A23_T.sst-rma-combined-dabg.chp Signal


title: mouse glioblastoma, AAE6


title: RNA-Seq CD4_control_CR216


title: hen1fbw2_3

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
We trimmed adapters and low-quality reads using Cutadapt v2.9 software (Martin, 2011) and retaining only reads between 18- and 20-nt long.
Reads were then mapped to the Arabidopsis genome version 10 (available at www.arabidopsis.org/download/) and its corresponding TAIR10 cDNAs, using Bowtie2 (Langmead and Salzberg, 2012).
Analysis of the PARE data vas done using CleaveLand v4.5
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Count files

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized using ethanol and plated on MS agar (MES-buffered MS salts medium [Duchefa, Murashige & Skoog medium inc. vitamins/MES- MO255)], 1% sucrose, and 0.8% agar, pH 5.7). The seeds were then stratified for 2 days at 4°C in the dark and then transferred in 16h-light/8h-dark (20,5/17°C, 70% humidity) growth chamber, under fluorescent light (Osram Biolux 58W/965).

extract_protocol:
RNA was extracted in Tri-Reagent according to the manufacturer’s protocol, and aqueous phase was left in 1 volume of isopropanol over-night at -20°C, precipitated 30 minutes at 16000g (4°C). Pellets were rinsed in 1 ml 70% ethanol and centrifuged an additional 10 minutes. For AGO1-loaded small RNA samples, IPs were performed as described above from 500mg of 1-week-old Arabidopsis seedlings grown on MS-agar plates. AGO1-loaded small RNA were then extracted by adding Tri-Reagent directly on the magnetic beads and extraction of RNA was then performed according to the manufacturer’s instructions.
Small RNA libraries were constructed using Real-Seq-AC kit (RealSeq®-AC, USA) according to manufacturer’s instructions with 500ng as starting material. Libraries were sequenced using Illumina Next-Seq 500 technology at University of Delaware (Delaware, USA).

treatment_protocol: No treatment

tag: ecotype

value: Columbia 0

tag: replicate

tag: genotype


title: hen1_3


title: samAx56

tag: timepoint


title: samAx55

tag: subytpe


title: normal mouse brain, AAE3


title: hyl1fbw2_3


title: RNA-Seq CD4_control_CR214


title: samAx54

tag: skin condition


title: samAx53


title: RNA-Seq CD4_control_CR199


title: samAx52


title: RNA-Seq CD4_control_CR201


title: RNA-Seq CD4_control_CR208


title: hyl1_3


title: RNA-Seq CD4_control_CR211


title: samAx51


title: samAx50


title: hen1fbw2_2


title: LN-Cap MDV3100 resistant Rano, 150µM 3

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

hyb_protocol: Labelled samples were hybridized on the Human Clariom D gene chip at the Human Microarray Core at the University of Colorado Anshutz Medical campus, according to Thermofisher protocols : https://www.thermofisher.com/search/browse/category/us/en/603372/DNA+%26+RNA+Microarray+Analysis

scan_protocol: Chips scanned at the Human Microarray Core at the University of Colorado Anshutz Medical campus.

data_processing:
Data was analyzed using Transcriptome Analysis Console (TAC) 4.0 (Thermo Fisher Scientific, Waltham, MA). Signal Space Transformation Robust Multi Array Average (SST-RMA) was used for background correction, normalization and log-transformation of signal intensities.
Significance Analysis of Microarrays or SAM {Tusher, 2001 #1036} was used for differential gene expression analysis. Differentially expressed genes were identified using a false discovery rate (FDR) threshold (p<0.05) and a fold-change threshold of 1.2.
Signal Space Transformation Robust Multi Array Average (SST-RMA)

source_name: LN-Cap MDV3100 resistant Rano treatm. 150µM

label_protocol: Sample RNA was amplified and labelled using the GeneChip WT PLUS Reagent Kit according to the manufacturer’s instructions.

growth_protocol: LNCaP MDV-resistant (LNCaP-MDV-res) cells were developed by growing them in increasing concentrations of MDV ranging from 1.25 to 2.5 µM for 6 months. Cells were authenticated by STR profle analysis.

extract_protocol: Sample RNA was amplified and labelled using the GeneChip WT PLUS Reagent Kit according to the manufacturer’s instructions (Thermo Fisher Scientific, Waltham, MA). Labelled samples were hybridized on the Human Clariom D chip.

treatment_protocol: LNCaP-MDV-res were treated with vehicle, MDV3100 (10 μM), ranolazine (150 µM) or etomoxir (100 µM) for 48h and subjected to gene microarray analysis (Clariom D).

value: LNCaP-MDV-resistant cells

tag: agent

value: Rano


title: A21_N

description: A21_N.sst-rma-combined-dabg.chp Signal


title: fbw2_3


title: REH_ETV6-RUNX1_rep1

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

data_processing:
ChIP-seq reads were aligned to the reference human genome version GRCh37 (hg19).
The .sam files were converted to .bam files using SAMtools.
The .bam files were then processed to yield .wig files using MACS.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: wig files

source_name: Pre-B lymphoblast cells

growth_protocol: REH cells were maintained in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) containing 10% heat-inactivated fetal calf serum (FCS) (Eurobio) supplemented with antibiotics (100 U/mL penicillin-G and 100 U/mL streptomycin, Gibco).

extract_protocol:
Cells were fixed in 1% formaldehyde (648336, Polysciences) at room temperature for 10 min and then quenched in 100 mM glycine for 1 min. Cells were washed twice in PBS and lysed 15 min in 50 mM Tris-HCl ph8.1/10 mM EDTA/0.5% Empigen BB/1% SDS. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using TruSeq® ChIP Library Preparation Kit (Illumina) according to the manufacturer’s protocol.

tag: cell line

value: REH

value: Pre-B lymphoblast cells

value: Peripheral blood

value: HPA00026 (Sigma Aldrich)


title: LN-Cap MDV3100 resistant Etomoxir, 100µM 3

source_name: LN-Cap MDV3100 resistant Etomoxir treatm. 100µM

value: Etomoxir


title: hen1_2


title: hyl1fbw2_2


title: LN-Cap MDV3100 resistant Etomoxir, 100µM 1


title: input DNA

city: Hangzhou

first: jiamin

last: he

address: Qingchun East Road

institute: Sir runrun Shaw hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
The reads that passed the prefiltering step were aligned with the Bowtie2 v2.2.5 software to the human genome (hg19). Peak calling was performed with MACS2. Homer software was used to annotate ChIP-seq peaks, and Meme was uesd to find motifs.
Genome_build: hg19

source_name: gastric cancer cel

growth_protocol: MKN45 cells were seeded in 15 cm plate with density of 70-80% supplemented with 10% FBS and incubated at 37℃ for 24h.

extract_protocol: After 48h, approximately 5*10^7 cells were used for each CHIP-seq assay according to the manufacturer’s instructions(Merk, Germany)

treatment_protocol: MKN45 cells were transfected with GV141-HOXC10-Flag or GV141 empty vector using Fugene HD(Roche)

tag: cell typle


title: samAx49

value: Lesional


title: hyl1_2


title: LN-Cap MDV3100 resistant MDV3100, 10µM 2

source_name: LN-Cap MDV3100 resistant MDV3100 treatm. 10µM


title: LN-Cap MDV3100 resistant Rano, 150µM 2


title: samAx48


title: HOXC10-Flag3_ChIPSeq

tag: chip antibody

value: Sigma Aldrich:f1804


title: LN-Cap MDV3100 resistant Etomoxir, 100µM 2


title: HOXC10-Flag4_ChIPSeq


title: Col0_3

value: wildtype


title: samAx47

value: Perilesional


title: LN-Cap MDV3100 resistant Rano, 150µM 1


title: LN-Cap MDV3100 resistant MDV3100, 10µM 3


title: fbw2_2


title: LN-Cap MDV3100 resistant MDV3100, 10µM 1


title: Col0_2


title: LN-Cap MDV3100 resistant CTRL 3

source_name: LN-Cap MDV3100 resistant CTRL

value: CTRL


title: HOXC10-Flag1_ChIPSeq

source_name: gastric cancer cell


title: samAx46


title: LN-Cap MDV3100 resistant CTRL 2


title: TPE-3

city: Chengdu

first: Yanyun

last: Wang

address: No. 20 Ren Min Nan Lu

institute: West China Second University Hospital, Sichuan University

description: circRNA expression in exosomes of TPE

hyb_protocol: One microgram cRNA was then fragmented with 5μl 10 × Blocking Agent and 1μl 25× Fragmentation Buffer at 60°C for 30 min. After diluting the reaction mix with 25μl 2× Hybridization buffer, 50μl solution was dispensed into the gasket slide and assembled into the circRNA expression microarray slide. After incubating for 17h at 65°C in an Agilent Hybridization Oven

scan_protocol: the hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C. The scanned images were imported into Agilent Feature Extraction software

data_processing:
the raw data was quantile normalized and low intensity signals were filtered. The fold change of each circRNA between the two groups was calculated, and the statistical significance was estimated by t-test.
The differentially expressed circRNAs (DECs) were screed based on fold changes ≥ 2 and p-values ≤ 0.05.

source_name: exosomes

label_protocol: Total RNA from each sample was digested with Rnase R (Epicentre, Inc., USA), and amplified with fluorescent-labeled random primers using the Arraystar Super RNA Labeling kit. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Germany), and their concentration and specific activity (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (ThermoFisher Scientific, USA).

extract_protocol: Exosomal RNA was extracted from 7 ml PE fluid using exoRNeasy Serum/Plasma Maxi Kit

treatment_protocol: Fifteen milliliter PE samples were collected into 15 mL tubes and centrifuged at 1600 rpm for 30 min at 4℃ (5810R, Eppendorf, Germany). After removing the debris, the supernatants were filtered through a 0.22 mm membrane and stored at -20℃.

tag: fluid

value: pleural effusion

tag: disease

value: TPE


title: WMJJ control replicate 3

city: Lubbock

first: Mauricio

last: Ulloa

state: Texas

address: 3810 4th Street

department: PA, CSRL

institute: USDA-ARS

description: Mildly RKN-resistant Genotype

data_processing:
We first performed quality assessment of the resulting reads from the Illumina platform using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and processed sequencing libraries using Trimmomatic (version 0.39; ) to remove adapter read sequences.
We then quantified gene expression using the pseudo-alignment RNA-seq quantification program kallisto version 0.46.1. The G. hirsutum TM-1 UTx v2.1 genome release was used as a reference genome to align the reads (www.cottongen.org ; https://doi.org/10.1038/s41588-020-0614-5 )
We then integrated transcript-level abundances from kallisto to  count-based statistical analysis in edgeR (version 3.13) to produce the table of read counts per locus.
Genome_build: The G. hirsutum TM-1 UTx v2.1 genome release was used as a reference genome to align the reads (www.cottongen.org ; https://doi.org/10.1038/s41588-020-0614-5 )
Supplementary_files_format_and_content: The table of counts is a tab-separated plaint text file (.txt) which contains the counts per million reads corresponding to each locus per library (rows), and each RNA-seq library sample (columns) is named according to genotype, condition and biological replicate (for example SJ2_ctl1 would be Acala SJ2-control conditions-replicate 1; rkn means root-knot nematode infested).

organism: Gossypium hirsutum

source_name: Root tissue (23 days-old-plants)

growth_protocol: Cotton plants were grown in a Greenhouse in pots with soil. Air temperatures in the greenhouse were maintained between 280 C and 350 C during the day and 240 C at night.

extract_protocol:
The root samples from each genotype were grounded in liquid nitrogen, and total RNA was isolated three biological replicates following the manufacturer’s instructions using Spectrum TM Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). The yield and purity of RNA were analyzed with a ND-1000 Spectrophotometer (Nano Drop Technology, Wilmington, DE, USA). Only RNA samples with 1.8 - 2.2 ratio of absorbance 260/280 nm were used for analysis.
For each genotype, 2 mg of RNA from each of the three biological-replicates used for cDNA library preparation. The cDNA libraries were prepared following the TruSeq RNA Sample Preparation v2 low sample (LS) protocol guide (Illumina Inc., San Diego, CA USA)
Illumina Platform, MiSeq and HiSeq2500

treatment_protocol: Two treatments control (ctl) and root-knot nematode M. incognita infested (rkn). Control plants were not infested. For root-knot nematode (RKN) infestated plants, the roots of 12 days old seedlings of three genotypes NemX (resistant), SJ2 (susceptible) and WMJJ (moderately resistant) were infected with 5000 J2/plant RKN. The disease progression was noted for 10 days and infected roots from 23-day old plant were collected from each of the five plants, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extraction.

tag: treatment

value: Control (ctl)

value: Wild Mexico Jack Jones (WMJJ)


title: hen1_1

value: Columbia 0


title: samAx45

value: Baseline

value: Nonlesional

value: hidradenitis suppurativa


title: samAx42


title: Acala SJ2 rkn replicate 3

description: RKN susceptible Genotype

value: Root-knot nematode infested (M. incognita) (rkn)

value: Acala SJ2


title: TPE-1

description: circRNA expression in exosomes of TPE

tag: age


title: Acala SJ2 control replicate 3

description: RKN susceptible Genotype


title: hyl1fbw2_1


title: Acala NemX rkn replicate 3

description: RKN-resistant Genotype

value: Acala NemX


title: samAx44


title: WMJJ rkn replicate 3

description: Mildly RKN-resistant Genotype


title: samAx41


title: fbw2_1


title: LA-MPE-3

description: circRNA expression in exosomes of LA-MPE

value: LA-MPE


title: Acala NemX control replicate 3

description: RKN-resistant Genotype


title: LN-Cap MDV3100 resistant CTRL 1

tag: cell type

value: LNCaP-MDV-resistant cells


title: hen1fbw2_1


title: samAx40

value: Lesional


title: LA-MPE-2


title: Col0_1

value: wildtype