title: PDCL#24_input_DNA

city: Hong Kong

first: Zhi-Jie

last: Xiao

state: Hong Kong

address: Pokfulam

department: Pathology

country: Hong Kong

institute: the University of Hong Kong

data_processing:
Adapters were trimmed from raw reads by Trimmomatic.
Clean reads were aligned to hg19 by bowtie2
samtools,bedtools and were used for the file formate transfer.
Peaks were called using Homer(findPeaks,FDR rate threshold = 0.05).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using bedGraphToBigWig

source_name: Lung cancer cell line

growth_protocol: lung cancer cell line(PDCL#24, which from HongKong patients) were cultivated in RPM1640 medium

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-Chromatin Complexes were isolated with SOX2 antibody.
Libraries were prepared by the company(BGI, HongKong) according to Illumina's instructions accompanying the DNA Sample Kit.

value: non-small-lung cancer cells from Hong Kong patient

tag: antibody


title: PDCL#24_SOX2_ChIPSeq

status: Public on Apr 10 2020

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

value: SOX2(abcam, ab59776)


title: Blood, Smoker_3378

type: genomic

city: Hangzhou

first: Yi

last: Xu

state: Zhejiang

address: No. 17, Dazhi Road, old Zhejiang, Shangcheng District

department: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases

country: China

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48 °C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: All samples were genotyped using the Infinium Human Exome-12 v1.1 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol.

data_processing:
After genotyping, we performed the following quality control analyses on all genotyped SNPs. First, among 242 901 genotyped variants, we excluded all insertions and deletions to ensure that all base pair positions were unique and referred to the same variant. Second, any SNP with a call rate of <95% was excluded. Third, we removed those SNPs that were not in Hardy–Weinberg equilibrium at a p value of < 1.0 × 10−6. Finally, we used a 5% minor allele frequency (MAF) as a threshold to define rare and common variants, and any SNP with an MAF of <0.05 was excluded from the analysis.
[value definition]  Genotype: AA,AB,BB,or NC (no call)

label: cy3, cy5

source_name: Blood

label_protocol: The concentration of each DNA sample was first measured using the QuantiT™ dsDNA assay kit (Life Technologies, Carlsbad, CA) and then 50 DNA samples were pooled in equimolar amounts, as suggested by the manufacturers.

extract_protocol: Genomic DNA was extracted from EDTA-treated peripheral venous blood of each subject using the Qiagen DNA purification kit. All DNA samples were treated with RNase A to remove potential contaminating RNA, and DNA quality and the concentration of each sample was determined by the A260/A280 absorbance ratio.

tag: ethnicity

value: African-American

tag: age

tag: gender

value: Male

tag: cpd

tag: hsi

tag: ftnd

value: Smoker

value: Blood


title: Blood, Smoker_3377

value: Female


title: Blood, Smoker_3376


title: LTS-IR01_299bp: PAPm

city: Taipei

first: John

last: WANG

address: Academia Rd sec 2

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

library_source: transcriptomic

data_processing:
Genome-based pipeline: We mapped reads onto gnH and went through Tuxedo pipeline to generate a common assembled gene set (3ampClontech_pool) and tested DEGs with Cuffdiff
Transcriptome-based pipeline: We mapped reads onto the OGS-plus genes using Bowtie2
We estimated gene expression using RSEM
We tested differentially expressed gene using EBSeq
Genome_build: Si_gnH (NCBI access number AEAQ00000000)
Supplementary_files_format_and_content: gtf file contains gene loci
Supplementary_files_format_and_content: Tab-delimited files contain expression level and DEG test
Supplementary_files_format_and_content: Tab-delimited files with 4Nugenpool prefix were generated by the Tuxedo pipeline
Supplementary_files_format_and_content: Tab-delimited files with Nugen-IR prefix were generated by RSEM
Supplementary_files_format_and_content: Spreadsheet file summary DEG test results by EBSeq

molecule: polyA RNA

organism: Solenopsis invicta

extract_protocol:
We used a droplet of honey to attract workers in the forage area and collected workers of ca. 1.5 cm in length. Workers were decapitated one-by-one on a pre-chilled -20oC metal block sitting on ice. Worker heads were placed individually in 5 ul cold RNAlater ICE (AM7023, ThermoFisher) in a numbered 0.2 ml PCR-tube and temporarily stored in liquid nitrogen. Worker bodies were put in 2 ml tubes containing 50 ul QuickExtract solution (QE09050, Epicenter) and processed for Gp-9 genotyping. The processing of each individual, from sampling to head storage in liquid nitrogen was less than a minute. We sampled 96 individuals/polygyne and 50 individuals/monogyne colony each time. The head samples were stored in a -80oC freezer for subsequent antennae dissection. We sampled polygyne workers until we obtained at least 45 individuals of each genotype. We dissected the antennae of workers of the same genotype on a metal block sitting on ice, under a dissecting microscope (Leica, 20X magnification). We used a clean sheet of Kimwipe tissue to blot away any remaining RNAlater ICE on the samples before placing them into 200 ul cold TRIzol (15596018, Invitrogen). To minimize RNA degradation, we processed at most five heads at once. To minimize cross-sample contamination, we cleaned the metal block and forceps with RNase-Zap after each dissection. Antennae were stored in a -80oC freezer until RNA extraction.
We extracted RNA using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch) following a modification of the manufacturer's instructions (Zhang et al. 2013). Frozen antennae in 200 ul Trizol were homogenized using a FastPrep-24 bead homogenizer (MP Biomedicals). Tissue destruction was checked under a microscope. If extra homogenization was required, we re-froze the sample in liquid nitrogen and repeated the homogenization (three times was the maximum needed). After the tissue was completely homogenized, we added an additional 400 ul Trizol into each sample, followed by vortexing for 10 secs and incubation at room temperature for 15 minutes. Samples were then phase separated with 120 ul chloroform. The aqueous phase was kept for RNA purification using the Direct-zol column with on-column DNase I treatment. RNA was eluted once in 25 ul RNase-free water.
cDNA was amplified from each RNA samples using the Nugen Ovation V.2 kit (M01206, NuGEN Technologies), following the manufacturer’s instructions.
To prepare sequencing samples, we mixed four bioreplicates of amplified cDNA of the same genotype. Samples of the same bioreplicate contributed same amount of cDNA.
follow the manufacturer's instructions of Illumina

value: Antennae

tag: caste

value: worker

tag: colony organization type

value: polygyne

tag: colony name

value: Rui9, Gui3, Bang3, Bo5

tag: genotype

value: SB/Sb


title: LTS-IR02_295bp: PAMm

value: SB/SB


title: LGC-IL03_508bp: MAamp_mix

data_processing:
Genome-based pipeline: We mapped reads onto gnH and went through Tuxedo pipeline to generate a common assembled gene set (3ampClontech_pool) and tested DEGs with Cuffdiff
Transcriptome-based pipeline: We mapped reads onto the OGS-plus genes using Bowtie2
We estimated gene expression using RSEM
We tested differentially expressed gene using EBSeq
Genome_build: Si_gnH (NCBI access number AEAQ00000000)
Supplementary_files_format_and_content: gtf file contains gene loci
Supplementary_files_format_and_content: Tab-delimited files contain expression level and DEG test
Supplementary_files_format_and_content: Tab-delimited files with 3ampClontech prefix were generated by the Tuxedo pipeline
Supplementary_files_format_and_content: Tab-delimited files with Clontech-IL prefix were generated by RSEM
Supplementary_files_format_and_content: Spreadsheet file summary DEG test results by EBSeq

extract_protocol:
We used a droplet of honey to attract workers in the forage area and collected workers of ca. 1.5 cm in length. Workers were decapitated one-by-one on a pre-chilled -20oC metal block sitting on ice. Worker heads were placed individually in 5 ul cold RNAlater ICE (AM7023, ThermoFisher) in a numbered 0.2 ml PCR-tube and temporarily stored in liquid nitrogen. Worker bodies were put in 2 ml tubes containing 50 ul QuickExtract solution (QE09050, Epicenter) and processed for Gp-9 genotyping. The processing of each individual, from sampling to head storage in liquid nitrogen was less than a minute. We sampled 96 individuals/polygyne and 50 individuals/monogyne colony each time. The head samples were stored in a -80oC freezer for subsequent antennae dissection. We sampled polygyne workers until we obtained at least 45 individuals of each genotype. We dissected the antennae of workers of the same genotype on a metal block sitting on ice, under a dissecting microscope (Leica, 20X magnification). We used a clean sheet of Kimwipe tissue to blot away any remaining RNAlater ICE on the samples before placing them into 200 ul cold TRIzol (15596018, Invitrogen). To minimize RNA degradation, we processed at most five heads at once. To minimize cross-sample contamination, we cleaned the metal block and forceps with RNase-Zap after each dissection. Antennae were stored in a -80oC freezer until RNA extraction.
We extracted RNA using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch) following a modification of the manufacturer's instructions (Zhang et al. 2013). Frozen antennae in 200 ul Trizol were homogenized using a FastPrep-24 bead homogenizer (MP Biomedicals). Tissue destruction was checked under a microscope. If extra homogenization was required, we re-froze the sample in liquid nitrogen and repeated the homogenization (three times was the maximum needed). After the tissue was completely homogenized, we added an additional 400 ul Trizol into each sample, followed by vortexing for 10 secs and incubation at room temperature for 15 minutes. Samples were then phase separated with 120 ul chloroform. The aqueous phase was kept for RNA purification using the Direct-zol column with on-column DNase I treatment. RNA was eluted once in 25 ul RNase-free water.
cDNA was amplified from each RNA samples using the SMARTer Stranded RNA-Seq kit, following the manufacturer’s instructions.
To prepare samples for amplification, we mixed three bioreplicates of RNA of the same genotype. Samples of the same bioreplicate contributed same amount of RNA.
follow the manufacturer's instructions of Illumina

value: monogyne

value: Rui7, Zhuang3,Tan1, Rui1


title: Blood, Smoker_3375


title: LGC-IL02_509bp: PAMamp_mix


title: LGC-IL01_498bp: PAPamp_mix


title: Blood, Smoker_3374


title: MA7amp1

data_processing:
We mapped reads onto gnH NCBI with accession number AEAQ00000000 and went through Tuxedo pipeline to generate a common assembled gene set (Tux-genes)
We combined the Tux-genes and OGS and selected putative protein coding genes to generate the OGS-plus genes
We mapped reads onto the OGS-plus genes using Bowtie2
We estimated gene expression using RSEM
We tested differentially expressed gene using EBSeq
Genome_build: gnH NCBI with accession number AEAQ00000000
The genes in the processed data have two prefixes. Genes with SINV prefix are in the Solenopsis invicta Official Gene Set (OGS), published in the Dryad database: doi:10.5061/dryad.n60k3t5. Genes with XLOC prefix were generated by the Tuxedo pipeline.
Supplementary_files_format_and_content: Tab-delimited text files showed raw read counts of each gene in each sample, estimated by RSEM, and expression pattern of each gene tested by EBSeq

molecule: total RNA

extract_protocol:
We used a droplet of honey to attract workers in the forage area and collected workers of ca. 1.5 cm in length. Workers were decapitated one-by-one on a pre-chilled -20oC metal block sitting on ice. Worker heads were placed individually in 5 ul cold RNAlater ICE (AM7023, ThermoFisher) in a numbered 0.2 ml PCR-tube and temporarily stored in liquid nitrogen. Worker bodies were put in 2 ml tubes containing 50 ul QuickExtract solution (QE09050, Epicenter) and processed for Gp-9 genotyping. The processing of each individual, from sampling to head storage in liquid nitrogen was less than a minute. We sampled 96 individuals/polygyne and 50 individuals/monogyne colony each time. The head samples were stored in a -80oC freezer for subsequent antennae dissection. We sampled polygyne workers until we obtained at least 45 individuals of each genotype. We dissected the antennae of workers of the same genotype on a metal block sitting on ice, under a dissecting microscope (Leica, 20X magnification). We used a clean sheet of Kimwipe tissue to blot away any remaining RNAlater ICE on the samples before placing them into 200 ul cold TRIzol (15596018, Invitrogen). To minimize RNA degradation, we processed at most five heads at once. To minimize cross-sample contamination, we cleaned the metal block and forceps with RNase-Zap after each dissection. Antennae were stored in a -80oC freezer until RNA extraction.
We extracted RNA using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch) following a modification of the manufacturer's instructions (Zhang et al. 2013). Frozen antennae in 200 ul Trizol were homogenized using a FastPrep-24 bead homogenizer (MP Biomedicals). Tissue destruction was checked under a microscope. If extra homogenization was required, we re-froze the sample in liquid nitrogen and repeated the homogenization (three times was the maximum needed). After the tissue was completely homogenized, we added an additional 400 ul Trizol into each sample, followed by vortexing for 10 secs and incubation at room temperature for 15 minutes. Samples were then phase separated with 120 ul chloroform. The aqueous phase was kept for RNA purification using the Direct-zol column with on-column DNase I treatment. RNA was eluted once in 25 ul RNase-free water.
cDNA was amplified from each RNA samples using the Nugen Ovation V.2 kit (M01206, NuGEN Technologies), following the manufacturer’s instructions.
follow the manufacturer's instructions of Illumina


title: Blood, Smoker_3373


title: Blood, Smoker_3372


title: Blood, Smoker_3369


title: Blood, Smoker_3370


title: PAP7amp1


title: PAM7amp1


title: MA6amp


title: Blood, Non-smoker_482

value: Non-smoker


title: Blood, Smoker_3379


title: PAM6amp


title: Blood, Smoker_3368


title: Blood, Smoker_3366


title: Blood, Smoker_3367


title: MA3amp


title: Blood, Smoker_3381


title: MA2amp1


title: Blood, Smoker_3364


title: PAM3amp


title: Blood, Smoker_3363


title: PAP3amp


title: PPRV control  CD-4 pbmc subset_R2

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

description: Gene expression in CD-4 cells

data_processing: Initially, the quality-filtered reads from control and infected samples (0 days and 9 dpi) were mapped to Capra hircus genome using Bowtie2. The mapped reads were then assembled using RNA-Seq by expectation maximization (RSEM).

organism: Capra hircus

source_name: CD-4 cells at 0day post infection from infected group

extract_protocol:
Total RNA from each subset of PBMCs of control and PPRV infected goats were isolated using the RNeasy Mini kit (Qiagen GmbH, Germany). The integrity and quantity of isolated RNA were assessed  based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples were found greater than 8, which is considered suitable for further processing. protocol. The integrity and quantity of isolated RNA were assessed  based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 8, which is considered suitable for further processing.
Library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NewEngland Biolabs Inc.) following the manufacturer’s protocol. Approximately, 100ng of RNA from each sample was used for RNA library preparation. The quality of the libraries was assessed on Bioanalyzer and further quantified using a Qubit 2.0 Fluorometer (Life technologies) and by qPCR. Libraries were sequenced on Illumina – NextSeq500  following manufacturer’s protocol.

treatment_protocol: Two groups including one control and one treated were used in the study. For both the group (control and infected) blood was collected from goats and pbmcs were isolated.The PBMCs subsets(T helper cells, T cytotoxic cells, B lymphocytes, and monocytes)were enriched by positive selection using indirect MACS technology.were collected and screened for the absence of PPRV antigen, and for the infected group tissues were isloated from goat infected with Izatnagar 94 PPRV at 9 day post infection. The tissues of both groups were collected in RNase free 1.5 ml centrifuge tube in RNA later.

tag: cell type

value: CD-4 cells

tag: infection status

value: control


title: Blood, Smoker_3362


title: PAP2amp1


title: PAM2amp1


title: Blood, Smoker_3371


title: Blood, Smoker_3365


title: PAP6amp


title: Blood, Smoker_3360


title: Blood, Smoker_3358


title: Blood, Smoker_3359


title: Blood, Smoker_3357


title: PPRV control  CD-21 pbmc subset_R1

description: Gene expression in CD-21 cells

source_name: CD-21 cells at 0day post infection from infected group

value: CD-21 cells


title: PPRV control CD-21 pbmc subset_R2

description: Gene expression in CD-21 cells


title: PPRV control  CD-14 pbmc subset_R1

description: Gene expression in CD-14 cells

source_name: CD-14 cells at 0day post infection from infected group

value: CD-14 cells


title: PPRV control  CD-4 pbmc subset_R1

description: Gene expression in CD-4 cells


title: Blood, Smoker_3356

value: African-American

value: Male


title: Blood, Smoker_3354

value: Smoker

value: Blood


title: Blood, Smoker_3353

value: Female


title: Blood, Smoker_3361


title: Blood, Smoker_3355


title: Blood, Smoker_3352


title: PPRV infected CD-4 pbmc subset_R2

description: Gene expression in CD-4 cells

source_name: CD-4 cells at 9day post infection from infected group

value: infected


title: PPRV control CD-8 pbmc subset_R1

description: Gene expression in CD-8 cells

source_name: CD-8 cells at 0day post infection from infected group

value: CD-8 cells


title: PPRV control  CD-8 pbmc subset_R2

description: Gene expression in CD-8 cells


title: Blood, Smoker_3351


title: Blood, Smoker_3350


title: PPRV infected CD-21 pbmc subset_R1

description: Gene expression in CD-21 cells

source_name: CD-21 cells at 9day post infection from infected group


title: Blood, Smoker_3349


title: PPRV infected CD-14 pbmc subset_R2

description: Gene expression in CD-14 cells

source_name: CD-14 cells at 9day post infection from infected group


title: PPRV infected CD-4 pbmc subset_R1

description: Gene expression in CD-4 cells


title: PPRV infected CD-21 pbmc subset_R2

description: Gene expression in CD-21 cells


title: PPRV infected CD-14 pbmc subset_R1

description: Gene expression in CD-14 cells


title: Blood, Smoker_3347


title: PPRV control  CD-14 pbmc subset_R2

description: Gene expression in CD-14 cells


title: Blood, Smoker_3348


title: PPRV infected CD-8 pbmc subset_R2

description: Gene expression in CD-8 cells

source_name: CD-8 cells at 9day post infection from infected group


title: Blood, Smoker_3345


title: PPRV infected CD-8 pbmc subset_R1

description: Gene expression in CD-8 cells


title: Blood, Smoker_3344


title: Blood, Smoker_3346


title: Blood, Smoker_3343


title: shKDM3B_ATRA_rep1_RNA-seq

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Filtered reads were aligned to hg38 using HISAT2.
Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Read counts for each gene were carried out using HT-Seq using the hg38 refSeq refFlat GTF file accessed on July 2015
R/Bioconductor package DESeq2 to call differentiall gene expression between CTRL and shRNA treatment.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count for each Sample

source_name: NB4 cell line

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA prepared was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).Double-strand cDNA libraries were prepared and constructed using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq experiments, NB4 cells with the stable transduction of shRNA against KDM3B or empty vector (pLVX-shRNA2-puro) were grown in regular medium and collected. NB4 were treated with 1µM ATRA for 24 or 48 hours

tag: cell line

value: Leukemic cells

tag: shRNA

tag: Stage

value: differentiated


title: shNC_ATRA_rep1_RNA-seq

value: empty vector


title: shKDM3B_ATRA_rep2_RNA-seq


title: shNC_ATRA_rep2_RNA-seq


title: Blood, Smoker_3342


title: shKDM3B_rep2_RNA-seq

value: undifferentiated


title: Blood, Smoker_3341


title: Blood, Smoker_3340


title: Blood, Smoker_3339


title: shNC_rep1_RNA-seq


title: shNC_rep2_RNA-seq


title: shKDM3B_rep1_RNA-seq


title: Blood, Smoker_3338


title: shKDM3B_INPUT_DNA

data_processing:
All reads were mapped to the human genome (hg38) using the Bowtie2 alignment software
Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
The profile and correlation plots were made with DeepTools.
Genome_build: hg38
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in bigwig format.

extract_protocol:
Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor Diagenode, immunoprecipitated using the indicated antibody, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
Libraries were created from successful large-scaled ChIP experiments using Illumina’s TruSeq Library Prep Kit following instructions in the user manual (Illumina, San Diego, CA, USA). The library size was estimated using a Bioanalyzer 2100

treatment_protocol: For ChIP-seq experiments, NB4 cells with the stable transduction of shRNA against KDM3B or empty vector (pLVX-shRNA2-puro) were grown in regular medium and collected.

tag: chip antibody


title: Blood, Smoker_3335

tag: tissue


title: Blood, Smoker_3337

tag: ethnicity


title: Blood, Smoker_3336

tag: age


title: Blood, Smoker_3334

tag: gender


title: shKDM3B_H3K9me1_ChIP-seq


title: Blood, Smoker_3333

tag: cpd


title: shNC_H3K9me3_ChIP-seq


title: shNC_INPUT_DNA


title: Blood, Smoker_3331

tag: hsi


title: Blood, Smoker_3332

tag: ftnd


title: Blood, Smoker_3330


title: shNC_H3K9me1_ChIP-seq


title: shNC_H3K9me2_ChIP-seq


title: Ctrl_2nd_mRNA

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1  -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cell

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion) and was further purified with two phenol-chloroform treatments.The purified RNA was then treated with RQ1 DNase (RNase free) (Promega, Madison, WI, USA) and its quality and quantity were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: Plasmids transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

value: HeLa cell control plasmid


title: Blood, Smoker_3329


title: Ctrl_1st_mRNA


title: Blood, Smoker_3328


title: Prdx1_1st_mRNA

value: Prdx1 overexpression in HeLa cell


title: Prdx1_2nd_mRNA


title: Blood, Smoker_3327


title: Blood, Smoker_3326


title: shKDM3B_H3K9me2_ChIP-seq


title: ECA109 LV-LEF1C (S146)

first: Yue

last: Zhao

address: 168 Changhai Road, Shanghai 200433, China

department: Department of Thoracic Surgery

institute: Changhai Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contains counts for each sample

source_name: esophageal squamous cell carcinoma cells

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately, The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LEF1 overexpression

tag: cell line source

value: esophageal squamous cell carcinoma (ESCC)


title: Blood, Smoker_3325


title: ECA109 LV-LEF1A (S144)


title: shKDM3B_H3K9me3_ChIP-seq


title: Blood, Smoker_3323


title: ECA109 LV-GFP3 (S143)

value: NC


title: ECA109 LV-LEF1B (S145)


title: Blood, Smoker_3320


title: ECA109 LV-GFP2 (S142)


title: Blood, Smoker_3322


title: Blood, Smoker_3321


title: Blood, Smoker_3319


title: Blood, Smoker_3317


title: Blood, Smoker_3318


title: Blood, Smoker_3316


title: Blood, Smoker_3324


title: Control-2

type: RNA

first: Shen

last: si

address: No. 500 Chengdu North Road

institute: Shanghai Changzheng hospital

description: Gene expression after cultured for 24h

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section.

scan_protocol: After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: human hepatocellular carcinoma

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: For 3 dimensional (3D) culture the cells were resuspended in 1XAccutase enzymes (Innovative Cell Technologies, Santiago, American), and the concentration of the cell suspension was adjusted to 6×106cells/ml.Then 37.6ul cell suspension,22.8ul water, 6.2ul 10×CBpH5.5 and 13.4ul Mal-Dextran were gently mixed and the mixture was fully mixed with 20ul PEG-link. After 3 times of speed blow, the mixture was rested for 5min.After the hydrogel solidified, a proper amount of DMEM containing 10% FBS was added and cultured for 4h.Then replace the culture medium for new before the pressure test began.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit (Cat # 217004，QIAGEN, GmbH, Germany) ,following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Pressure loading of 3D cultured cells was performed (30mmHg, 24h) using the compression system Flexcell 5000C (Flexcell International,McKeesport,PA;see their Web site at www.flexcelllint.com for a description). Three dimensional cell gel was placed in Flexcell BioPress compression culture 6-well plates,and set pressure parameters on the computer,including compressive strength(1.995kpa/15mmHg) and intervention time(24h). The cells in gel were detached by 1XAccutase enzymes, and centrifuged 10min at 1000rpm. Then the cells were collected for follow-up experiments.

tag: treatment


title: Blood, Smoker_3315


title: Pressure-treated-3

description: Gene expression after 15mmHg pressure-treated for 24h

value: pressurized, 15mmHg, 24h


title: Blood, Non-smoker_3313

value: African-American

value: Non-smoker


title: Control-1

description: Gene expression after cultrued for 24h


title: Blood, Smoker_3312

value: Smoker


title: Blood, Non-smoker_3314

value: Blood


title: Control-3

description: Gene expression after cultured for 24h


title: ECA109 LV-GFP1 (S141)


title: Blood, Non-smoker_3311

value: Female


title: Blood, Smoker_3310


title: Blood, Smoker_3307

value: Male


title: Blood, Smoker_3309


title: Blood, Smoker_3306


title: Blood, Smoker_3308


title: Pressure-treated-2


title: Pressure-treated-1


title: Blood, Smoker_3305


title: Blood, Smoker_3304


title: C3aR_STZ-3: Renal_C3aR-/- Diabetic_rep3

city: Zhengzhou

first: Xiao-Qian

last: Li

state: Henan

address: No. 1, East of Jianshe Street, Erqi District

department: Nephrology Hospital

institute: the First Affiliated Hospital of Zhengzhou University

description: C57BL/6, sacrificed 26 weeks after STZ induction

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2.0 (8×60K) 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Mus musculus

source_name: Renal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Eight-week-old C57BL/6J mice were fed with high fat diet (HFD; 60% of total calories from fat, D12492, Keao Xieli, Beijing, China), while the control group was fed with normal chow diet (NCD; 10% of total calories from fat). After four weeks, mice in the HFD group were intraperitoneally injected with streptozotocin (STZ, S0130, Sigma Aldrich, St Louis, USA) dissolved in 50 mM sodium citrate buffer (pH 4.5, Solarbio, Beijing, China) at 60 mg/kg for three consecutive days, while the NCD group were injected with equivalent amount of vehicle.

tag: strain

value: Renal cortical

tag: gendel


title: Wt_STZ-3: Renal_WT Diabetic_rep3


title: C3aR-KO-ctrl-3: Renal_C3aR-/- Control_rep3

description: C57BL/6, sacrificed 20 weeks after STZ induction


title: C3aR-KO-ctrl-1: Renal_C3aR-/- Control_rep1


title: C3aR_STZ-2: Renal_C3aR-/- Diabetic_rep2


title: Wt_STZ-1: Renal_WT Diabetic_rep1


title: Blood, Smoker_3301


title: Blood, Smoker_3303


title: Blood, Non-smoker_3299


title: Blood, Smoker_3300


title: Blood, Non-smoker_3302


title: Blood, Smoker_3297


title: C3aR-KO-ctrl-2: Renal_C3aR-/- Control_rep2


title: C3aR_STZ-1: Renal_C3aR-/- Diabetic_rep1


title: Blood, Smoker_3298


title: TM3: Small RNAs from ovaries of w1118; CyRoi/+;TM3, Sb Ser/+  strain

city: Moscow

first: Pavel

last: Komarov

address: Kurchatov sq. 2

country: Russia

institute: Institute of Molecular Genetics of the Russian Academy of Sciences

data_processing:
smallRNA-seq: Reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie2 to dm3 genome assembly and transgene sequences.
GRO-seq: Reads were clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG), reads smaller than 19 nt were discarded. Reads were mapped to the dm3/R5 genomic assembly of transgene sequence by bowtie2 and deduplexed. Only single-mapped reads were used for the construction the genomic profiles.
Genome_build: dm3
Supplementary_files_format_and_content: smallRNA-seq: Tab-delimited file include the raw counts of clipped read occurrences.  GRO-seq: Genomic profiles of RPM-normalized single-mapped reads.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
smallRNA-seq: Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt).
smallRNA-seq: Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)
GRO-seq: Nuclei were purified from homogenized ovaries, and were used for run-on reacton with Br-UTP in vitro (Rozkov et al. 2013).
GRO-seq: De novo synthesized RNA was subjected to library preparation for RNA-seq.

value: ovaries

value: w1118; CyRoi/+;TM3, Sb Ser/+

tag: molecule subtype

value: small RNAs


title: Blood, Smoker_3296


title: WT2: Renal_WT Control_rep2


title: ko1

city: Düsseldorf

first: Katja

last: Merches

address: Auf'm Hennekamp 50

country: Germany

institute: Leibniz Institute for Environmental Medicine

hyb_protocol: After fragmentation labeled cDNA was hybridized to Applied Biosystems™ Clariom™ S Mouse Gene Expression Microarrays for 16 hr at 45°C and stained by streptavidin/phycoerythrin conjugate, according to the manufacturer's protocol. Fluidics Station 450 was used.

scan_protocol: Using the Affymetrix Calvin Scan Acquisition on the Affymetrix GeneChip Scanner 3000 7G with the Affymetrix GeneChip Command Console Scan Control Version 4.0.0.1567.

data_processing: Data analyses on Affymetrix CEL files was performed using R (3.5.2); quality control of hybridization data was performed with ArrayQualityMetrix (3.38.0), a Bioconductor package under R. One of the Ahr+/- arrays did not pass the quality control and was identified as an outlier by Kolmogorov-Smirnov statistic Ka between each array's distribution and the distribution of the pooled data. The abnormal hybridization correlated with a poor RNA-quality in this sample. For the further data analysis only the remaining 3 Ahr-/- and 3 Ahr+/- samples were considered. The hybridization intensity values were normalized using the Robust Multichip Average algorithm (RMA) using the oligo (1.46.0) package in R, which allows background subtraction, quantile normalization and summarization (via median-polish). The differentially regulated genes were extracted using limma (3.38.3) package, then annotated using mogene20 package (chip mogene20sttransriptcluster) False Discovery Rate (FDR) was addressed using the Benjamini and Hochberg’s method and FDR has been used to measure the statistical significance, p-value < or = 0.05.

label: biotin labeling

source_name: AHR-knockout homozygote

label_protocol: According to the manufacturer's protocol: 10 ng of total RNA were converted to cDNA, amplified to complementary RNA (cRNA) followed by in vitro transcription and biotin labeling of cDNA.

growth_protocol: B6.129-Ahrtm1Bra/J mice were heterozygously bred under SPF-conditions in our animal facility. Heterozygous littermates were used as control animals.

extract_protocol: RNA from sorted cells was extracted from frozen cell pellets using the NucleoSpin RNA XS kit (Macherey Nagel, Düren) according to manufacture's protocol.

treatment_protocol: Epidermal cells were isolated from female and male Ahr-ko and Ahr-het mice at the age of 2 weeks from the back and belly skin. The skin was freed from fat and incubated dermal-site down on 0.75% trypsin in PBS (PAN biotech) for 1.5 h at 37 °C. The epidermis was gently peeled off from the dermis using forceps and further incubated in 0.05 % trypsin / 0.05 % EDTA in PBS (PAN biotech) for 1 h at 37 °C followed by rigorous pipetting. The cell-solution was filtered through a 70 µm strainer, diluted with medium (DMEM, 10% FCS, 1% Penicillin/Streptomycin; PAN biotech), subsequently washed with FACS-buffer (PBS, 2 % FCS, 2 mM EDTA) and stained for FACS-sorting. Before staining, Fc-receptors of isolated cells were blocked with 2.5 µg/ml anti-CD16'/32 (clone 93; BioLegend). Antibodies used for the identification of dendritic epidermal T cells (DETC) were anti gdTCR-APC (clone GL3; BioLegend) and ant-Vg3TCR-FITC (clone 536; BD). Cells were stained for 20 min on 4 °C in FACS-buffer. Dead cells were stained by addition of 2 µg/ml DAPI (Roth). DETC were sorted on a BD Aria IIITM using the BD DIVATM 8.0 software. For sorting we used sequential gating in two-dimensional plots. Forward-Scatter and DAPI-staining was used to exclude doublets and dead cells according to flow cytometry guidelines. The 90 - 98 % puresorted cells were pelleted and stored at -20 °C for RNA-isolation.

tag: cell type

value: dendritic epidermal T cells

tag: genotype

value: AHR-knockout homozygote

value: 2 weeks


title: ko3


title: wk: Small RNAs from ovaries of wk strain

value: wk


title: het1

source_name: AHR-knockout heterozygote

value: AHR-knockout heterozygote


title: WT3: Renal_WT Control_rep3


title: het2


title: Blood, Non-smoker_3293

source_name: Blood


title: 2_4_pat: Small RNAs from ovaries of 2.4 pat transgenic strain

value: 2.4 pat


title: Blood, Non-smoker_3294


title: ko2


title: het3


title: WT1: Renal_WT Control_rep1


title: Blood, Non-smoker_3292


title: 2_4_mat: Small RNAs from ovaries of 2.4 mat transgenic strain

value: 2.4 mat


title: Blood, Non-smoker_3291

value: African-American


title: 2_1_mat: Small RNAs from ovaries of 2.1 mat transgenic strain

value: 2.1 mat


title: Blood, Non-smoker_3289

value: Non-smoker


title: Blood, Smoker_3288

value: Smoker

value: Blood


title: Blood, Smoker_3295

value: Male


title: 2_1_pat: Small RNAs from ovaries of 2.1 pat transgenic strain

value: 2.1 pat


title: Blood, Smoker_3286

value: Female


title: Blood, Non-smoker_3287


title: Blood, Non-smoker_3281


title: Blood, Smoker_3282


title: Blood, Non-smoker_3283


title: Wt_STZ-2: Renal_WT Diabetic_rep2

value: Renal cortical


title: Blood, Smoker_3279


title: Blood, Non-smoker_3280


title: Blood, Smoker_3278


title: Blood, Smoker_3277


title: Blood, Non-smoker_3276


title: Blood, Non-smoker_3284


title: Blood, Smoker_3285


title: Blood, Smoker_3274


title: Blood, Smoker_3273


title: Blood, Smoker_3272


title: Blood, Smoker_3268


title: Blood, Smoker_3267


title: Blood, Non-smoker_3270


title: Blood, Smoker_3271


title: Blood, Smoker_3269


title: Blood, Smoker_3266


title: Blood, Smoker_3265


title: Sample 20_Fgf20_mut_pre-TRAP

city: St. Louis

first: Lu

middle: M

last: Yang

state: Missouri

address: 660 S. Euclid Avenue Campus Box 8103

department: Developmental Biology

country: USA

institute: Washington University School of Medicine

description: mRNA

data_processing:
RNAseq reads were basecalled with with Illumina RealTimeAnalysis (RTA) software the resulting bcl files were demultiplexed with Illumina’s bclToFastq2
RNAseq reads were mapped to the mouse genome using STAR with default parameters, except for the following: multi-sample 2-pass, with default settings on first pass and sjdbFileChrStartEnd (for novel splice junctions), ScoreMinOverLread=0.4, MatchNminOverLread=0.4, MismatchNmax=5 on second pass
Counting was performed using SummarizedOverlaps method (mode = Union) from the R package GenomicAlignments
Data was filtered with the following criteria: genes in which less than 8 of 24 samples had 25 or more reads were removed
Removal of Unwanted Variation (RUVs) was used to correct for batch effect arising from the two separate experiments (k = 1)
DESeq2 with RUVs correction factors was used for DEG analysis, with alpha = 0.1 and Benjamini-Hochberg multiple-comparisons correction.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: comma-delimited text file of counts generated from data processing step 3 (prior to filtering and normalization)

source_name: Ventral otocyst

extract_protocol:
Ventral otocysts containing the cochlea were dissected from E14.5 mouse embryos and homogenized, followed by centrifugation to isolate ribosomes and immunoprecipitation with anti-GFP antibodies. RNA then purified with Arcturus Picopure RNA Isolation Kit
cDNA libraries were prepared using Clontech SMARTer kit

value: C57BL/6J x 129X1/SvJ

value: ventral otocyst

tag: developmental stage

value: embryonic day 14.5

tag: collection method

value: pre-TRAP

tag: batch

value: experiment 1


title: Sample 23_Fgf20_het_pre-TRAP

description: mRNA

tag: tissue

value: experiment 2


title: Sample 22_Fgf20_mut_pre-TRAP

description: mRNA


title: Sample 18_Fgf20_mut_pre-TRAP

description: mRNA


title: Sample 21_Fgf20_het_pre-TRAP

description: mRNA


title: Sample 19_Fgf20_het_pre-TRAP

description: mRNA


title: Sample 24_Fgf20_mut_pre-TRAP

description: mRNA


title: Blood, Non-smoker_3264

tag: ethnicity


title: Sample 17_Fgf20_het_pre-TRAP

description: mRNA


title: Sample 14_Fgf20_mut_TRAP

description: TRAP mRNA

data_processing:
Library strategy: TRAP-seq
RNAseq reads were basecalled with with Illumina RealTimeAnalysis (RTA) software the resulting bcl files were demultiplexed with Illumina’s bclToFastq2
RNAseq reads were mapped to the mouse genome using STAR with default parameters, except for the following: multi-sample 2-pass, with default settings on first pass and sjdbFileChrStartEnd (for novel splice junctions), ScoreMinOverLread=0.4, MatchNminOverLread=0.4, MismatchNmax=5 on second pass
Counting was performed using SummarizedOverlaps method (mode = Union) from the R package GenomicAlignments
Data was filtered with the following criteria: genes in which less than 8 of 24 samples had 25 or more reads were removed
Removal of Unwanted Variation (RUVs) was used to correct for batch effect arising from the two separate experiments (k = 1)
DESeq2 with RUVs correction factors was used for DEG analysis, with alpha = 0.1 and Benjamini-Hochberg multiple-comparisons correction.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: comma-delimited text file of counts generated from data processing step 3 (prior to filtering and normalization)

value: TRAP


title: Sample 16_Fgf20_mut_TRAP

description: TRAP mRNA


title: Blood, Non-smoker_3263

tag: age


title: Sample 15_Fgf20_het_TRAP

description: TRAP mRNA


title: Blood, Non-smoker_3275

tag: gender


title: Sample 13_Fgf20_mut_TRAP

description: TRAP mRNA


title: Blood, Non-smoker_3262

tag: cpd


title: Sample 12_Fgf20_het_TRAP

description: TRAP mRNA


title: Sample 10_Fgf20_mut_TRAP

description: TRAP mRNA


title: Sample 9_Fgf20_het_TRAP

description: TRAP mRNA


title: Blood, Smoker_3259

tag: hsi


title: Sample 11_Fgf20_het_TRAP

description: TRAP mRNA


title: Sample 8_Fgf20_mut_TRAP

description: TRAP mRNA


title: Sample 6_Fgf20_mut_TRAP

description: TRAP mRNA


title: Blood, Non-smoker_3261

tag: ftnd


title: Sample 7_Fgf20_het_TRAP

description: TRAP mRNA


title: Blood, Smoker_3290


title: Blood, Smoker_3258


title: Blood, Smoker_3256


title: Sample 3_Fgf20_het_TRAP

description: TRAP mRNA


title: Sample 1_Fgf20_het_TRAP

description: TRAP mRNA


title: Blood, Smoker_3254


title: Blood, Smoker_3255


title: Blood, Smoker_3260


title: Blood, Smoker_3253


title: Sample 4_Fgf20_mut_TRAP

description: TRAP mRNA


title: Blood, Smoker_3257


title: Sample 5_Fgf20_het_TRAP

description: TRAP mRNA


title: Blood, Smoker_3251


title: Blood, Smoker_3250


title: Sample 2_Fgf20_mut_TRAP

description: TRAP mRNA


title: Blood, Smoker_3249


title: Blood, Smoker_3248


title: Breast_AH_61

city: Amherst

first: D.

middle: Joseph

last: Jerry

state: MA

address: 661 North Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts

description: Gene expression from laser capture microdissection of breast epithelium

hyb_protocol: The biotin labeled cDNA was hybridized to GeneChip® Human Gene 1.0 ST Arrays (Affymetrix) for 16 hrs. Chips were washed and stained with phycoerythrein-conjugated streptavidin (Life Technologies, Carlsbad, CA) in a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures.

scan_protocol: Arrays were scanned and fluorescence intensities determined using the GeneChip Scanner 3000 7G with autoloader instrument system and Affymetrix GeneChip Command Console (AGCC) Scan Control Software (v 4.0.0.1567), producing CEL files.

data_processing: Analysis of microarray data: The data were normalized using the Single-Channel Array Normalization (SCAN) and Universal exPression Codes (UPC) methods from the BioConductor R package “SCAN.UPC” (Gentleman et al., 2004). This package produces standardized expression measures that are used to estimate whether a given gene or probe is active in a specific sample (Piccolo et al., 2012; Piccolo et al., 2013). “ComBat”, an empirical Bayesian framework for adjusting data for batch effects (Johnson et al., 2007), was applied. Limma (Smyth, 2004) was used to identify differentially expressed genes in a paired-sample model, with HNB and AH samples paired by patient. A total of 1039 probesets were selected with adjusted p<0.05. Two methods were employed to identify gene signatures distinguishing AH and normal benign tissue. Agglomerative clustering was performed using AGNES (Kaufman, 2005a) to visualize gene expression patterns. Prediction Analysis of Microarrays (PAM) was used as an alternative approach to define a minimal gene expression signature (Kaufman, 2005b).

label: Biotin

source_name: Laser capture microdissection of breast epithelium_Atypia

label_protocol: cDNA synthesis, amplification, and labeling: The Ovation® FFPE WTA System (NuGEN San Carlos, CA) was used to prepare amplified cDNA from FFPE-derived total RNA because amplification is initiated at the 3´ end as well as randomly throughout the whole transcriptome in the sample which makes this system ideal for amplification of RNA obtained from FFPE samples.  50 ng of RNA was used to prepare the cDNA according to the manufactures instructions. The cDNA was then purified using columns from the QIAquick PCR Purification kit (Qiagen). Buffer PB from the purification kit was added to the cDNA reaction, loaded on to the column, and centrifuged for 1 min at 13,000xg. The flow through was discarded and 80% EtOH was added to the column and centrifuged for 1 min at 13,000xg. The 80% EtOH wash step was repeated and the purified cDNA was eluted with nuclease free water.  An aliquot containing 5 g of cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN) according to the manufacturer’s instructions. The biotin labeled cDNA was hybridized to Affymetrix 1.0 ST microarrays by Genome Explorations.

growth_protocol: Samples microdissected from H&E stained FFPE tissue samples

extract_protocol: Microdissection and RNA isolation: The H&E stained sections of the atypical hyperplasias (AH) samples were used to estimate the total area for microdissection. A minimum area of 10 x 106 μm2 was required to ensure a minimum of 50 ng total RNA.  Consecutive tissue sections  (8-μm thick) were cut using RNase-free conditions and mounted on membrane slides (MMI). The first and every 10th section were H&E stained for microscopic evaluation of AH tissue. The AH lesion and benign glandular tissue were marked by a breast pathologist (GMC) for microdissection. The benign glandular areas were selected to be at least 1 cm away from the AH lesion. The tissues on membrane slides were deparaffinized in 3 changes of Xylene, and allowed to air dry under a vacuum in a desiccator for 30 min prior to the LCM procedure. The unstained sections were oriented for microdissection aided by landmarks defined on the H& stained slides. Using MMI Cell Tools software (Version Celltools-4.4 #261, Rockledge FL), areas to be microdissected were circumscribed on the monitor using the MMI system stylus. Microdissected AH and benign tissues were collected separately onto caps using the MMI Cell Cut laser capture system (MMI Inc., Rockledge FL). The microdissected tissue was collected in 150 l digestion buffer containing 10 l proteinase K (miRNeasey FFPE Kit, Qiagen), was kept overnight at 55C and stored at -80C until further processing.  Total RNA was isolated from LCM tissue using the miRNeasey FFPE Kit (Qiagen) according to the manufacturer’s instructions and quantified using a NanoDrop1000 (Thermo Fisher Scientific).

treatment_protocol: Microscopic evaluation: Atypical hyperplasias (AH) arise in the terminal duct lobular units of the breast and are divided into ductal and lobular subtypes based on cytomorphologic characteristics. Ductal lesions included in the study are atypical ductal hyperplasia (ADH) and flat epithelial atypia (FEA); lobular lesions included atypical lobular hyperplasia (ALH) and lobular carcinoma in situ (LCIS). Patients with either ductal or lobular atypia were included in the analysis to assess differences in transcriptional features. To assure consistency of diagnoses, the specimens were reviewed by a single breast pathologist (GMC) and marked for microdissection. Sufficient RNA was obtained from 21 AH lesions (from 20 patients).  The tissues included 8 lobular lesions (ALH and/or LCIS), 11 ductal lesions (ADH and/or FEA), and 2 that were a mixture of ductal and lobular lesions (sampled separately). The mean age was 51.9 years (SD=7.9 years).

tag: patient age

tag: r/l breast

value: R

tag: histology

value: AH

tag: copathology report

value: FEA


title: Breast_Benign_66

source_name: Laser capture microdissection of breast epithelium_Benign

value: Benign


title: Breast_Benign_61


title: Breast_Benign_64


title: Breast_Benign_46


title: Blood, Smoker_3252

value: African-American

value: Smoker


title: Blood, Smoker_3247

value: Blood


title: Breast_AH_66

value: L

value: ADH/DCIS LG


title: Breast_AH_64

value: Female

value: ADH/FEA


title: Breast_AH_49

value: ALH


title: Breast_AH_46


title: Breast_AH_53/54

value: ADH severe


title: Breast_Benign_53/54


title: Breast_AH_98-15-8

value: LCIS/ALH


title: Breast_Benign_49


title: Breast_B9_98-15-8


title: Breast_AH_43


title: Blood, Non-smoker_3246

value: Non-smoker


title: Blood, Smoker_3245

value: Male


title: Breast_B9_W4/S04-C


title: Breast_AH_W4/S04-C

value: ADH


title: Breast_Benign_43


title: Breast_AH_W6/S01-C

value: LCIS


title: Breast_B9_W6/S01-C


title: Breast_normal_HaoS09

value: normal


title: Breast_normal_HaoS10


title: Blood, Non-smoker_3244


title: Blood, Smoker_3243


title: Blood, Smoker_3241


title: Blood, Non-smoker_3242


title: Blood, Non-smoker_3240


title: Blood, Smoker_3238


title: Blood, Smoker_3239


title: Breast_Benign_S-10-8


title: Blood, Smoker_3237


title: Breast_Atypia_S-10-17

value: Atypia


title: Breast_Atypia_S-10-8


title: Blood, Smoker_3236


title: C3698

city: East Lansing

first: Karen

last: Liby

state: MI

address: 1355 Bogue Street

department: Pharmacology&Toxicology

institute: Michigan State University

data_processing:
After removal of adaptors and low quality reads, reads were mapped to the mm10 mouse reference genome using TopHat2
Reads that mapped to genes were counted and normalized to gene length, then reported in FPKM (Fragments Per Kilo bases per Million reads)
Routine identification of differentially expressed genes was performed using DESeq2
Supplementary_files_format_and_content: FPKM

source_name: tumor

extract_protocol:
Tumors were dissected, flash frozen in liquid nitrogen. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumors from Brca1Co/Co;MMTV-Cre;p53+/- mice treated with saline, free Talazoparib (i.v.), or NanoTLZ for five doses (0.33mg/kg, three times a week) were harvested. Three samples were collected for each group.

value: mammary gland tumor

tag: treatment

value: Nano-Talazoparib (i.v., 0.33mg/kg)


title: Breast_Atypia_S-10-1

value: FEA


title: Breast_Benign_S-10-12

value: Benign


title: Breast_Atypia_S-10-11

value: L


title: Blood, Smoker_3235

data_processing:
After genotyping, we performed the following quality control analyses on all genotyped SNPs. First, among 242 901 genotyped variants, we excluded all insertions and deletions to ensure that all base pair positions were unique and referred to the same variant. Second, any SNP with a call rate of <95% was excluded. Third, we removed those SNPs that were not in Hardy–Weinberg equilibrium at a p value of < 1.0 × 10−6. Finally, we used a 5% minor allele frequency (MAF) as a threshold to define rare and common variants, and any SNP with an MAF of <0.05 was excluded from the analysis.
[value definition]  Genotype: AA,AB,BB,or NC (no call)

value: African-American

value: Smoker

value: Blood


title: Breast_Normal_S-10-10

value: Female

value: Normal


title: Breast_Normal_S-10-14

value: ADH, FEA


title: Breast_Benign_S-10-1


title: Breast_ADH_HaoS09

value: R

value: ALH/FEA


title: Breast_Atypia_S-10-12


title: Breast_Benign_S-10-17


title: Breast_Benign_S-10-4


title: Breast_ADH _HaoS10

value: ADH

value: ADH, ALH


title: Breast_Atypia_S-10-4


title: Breast_Atypia_S-10-14


title: C3519


title: Breast_Benign_S-10-3


title: Blood, Non-smoker_3234

value: Non-smoker


title: B3700

value: Talazoparib (i.v., 0.33mg/kg)


title: B3684

value: mammary gland tumor


title: Breast_Benign_S-10-11


title: Blood, Non-smoker_3233


title: B3638


title: A3688

value: saline


title: Blood, Smoker_3232

value: Male


title: A3673


title: Breast_Atypia_S-10-3

value: Atypia

value: LCIS


title: C3669

value: Nano-Talazoparib (i.v., 0.33mg/kg)


title: Blood, Smoker_3231

value: African-American

value: Smoker


title: Blood, Smoker_3230

value: Female

value: Blood


title: whole_root_Heatshock

city: Seattle

first: Christine

last: Queitsch

state: WA

address: 3720 15th Ave NE, Foege Hall

department: Genome Sciences

institute: University of Washington

data_processing:
Illumina Nextseq 500 base caller is used
10X reads were aligned to TAIR10 genome (using ARAPORT annotation) using Cellranger (version 2.1.0)
whole_root_Control_2 and whole_root_Heatshock datasets were aggregated using Cellranger (version 2.1.0)
Data was parsed into R (version 3.5.0) to be Analyzed using Monocle (version 2.99.1)
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression matrix files were generated using Cellranger. Rds files were generated by parsing into R. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.

organism: Arabidopsis thaliana

source_name: Whole Root Protoplast Cell_heat shock

growth_protocol: plant protoplast extracted from the roots 7-8 day old Arabidopsis thaliana seedlings

extract_protocol:
Protoplast isolation was done according to Bargmann and Birnbaum (2010), with slight modifications.
10X genomics protocol
single cell RNA-Seq (10X Genomics)

treatment_protocol: plants were transferred from 22C to 38C for 45 min and roots were extracted for protoplasting immediately afterwards

tag: cell type

value: protoplast cells

tag: ecotype

value: whole root

value: HeatShock


title: whole_root_Control_2

source_name: Whole Root Protoplast Cell_control

value: Control


title: ChIP-seq_input_EPrec

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Read quality was evaluated using FastQC. Raw reads were mapped against the human reference genome (hg19 build) using Bowtie allowing up to 2 mismatches.
Sample quality was evaluated using the cross-correlation analysis implemented in spp R package.
ChIP-seq peak calling was performed using MACS2. Input data were used to model the background noise.
Genome_build: hg19
Supplementary_files_format_and_content: fold-enrichment bigWig obtained with MACS2 bdgcmp function

source_name: erythroid precursors (E-Prec)

growth_protocol: Erythroid differentiation was performed as described in Roselli et al. (Roselli et al., 2010). CD36+ erythroid progenitors (E-Prog) were selected after 5 days of culture. Differentiated erythroid precursors (E-Prec) were collected after 11 days of culture.

extract_protocol:
Chromatin from E-Prog and E-Prec was prepared after cross-linking for 10’ at RT with 1% formaldehyde-containing medium. Nuclear extracts were sonicated using the Bioruptor Pico Sonication System (Diagenode) to obtain DNA fragments around 150-200 bp in length. For histone modifications, chromatin obtained from 107 cells was immunoprecipitated overnight with 10 µg of antibody. For transcription factors, chromatin obtained from 3x107 cells was immunoprecipitated overnight with 30 µg of antibody.  ChIP assay was performed as previously described (Romano, Sci Reports, 2016; Cui et al., 2009).
ChIP-seq libraries for E-Prog and E-Prec were prepared from 1 ng of immunoprecipitated DNA (IP) and 5 ng of control DNA (Input: non-immunoprecipitated chromatin fragments) following the Diagenode Microplex Library preparation kit. Libraries were checked by capillary electrophoresis by Tape Station Agilent with the High sensitivity D1000 assay and quantified by Real Time q-PCR using the kit from KAPA Biosystems (Roche). Each library was sequenced in one MiSeq Illumina RUN and 50 bp single-end reads were generated.

value: human HSPC-derived late erythroid precursors

value: Human umbilical cord blood

tag: antibody

value: none (non-immunoprecipitated chromatin fragments)


title: Blood, Smoker_3229

extract_protocol: Genomic DNA was extracted from EDTA-treated peripheral venous blood of each subject using the Qiagen DNA purification kit. All DNA samples were treated with RNase A to remove potential contaminating RNA, and DNA quality and the concentration of each sample was determined by the A260/A280 absorbance ratio.


title: Blood, Non-smoker_3225

value: Non-smoker


title: Blood, Smoker_3227


title: Blood, Non-smoker_3228


title: ChIP-seq_H3K27ac_EPrec

value: H3K27ac (ab4729, Abcam)


title: ChIP-seq_GATA1_EPrec

value: GATA1 (ab11852, Abcam)


title: ChIP-seq_H3K27me3_EPrec

value: H3K27me3 (07-449, Millipore)


title: ChIP-seq_H3K4me1_EPrec

value: H3K4me1 (ab8895, Abcam)


title: ChIP-seq_GATA2_EPrec

value: GATA2 (sc-9008, Santa Cruz Biotechnology)


title: Blood, Non-smoker_3224

value: African-American


title: ChIP-seq_GATA1_EProg

source_name: erythroid progenitors (E-Prog)

value: human HSPC-derived early erythroid progenitors


title: ChIP-seq_GATA2_EProg


title: ChIP-seq_H3K27me3_EProg


title: ChIP-seq_H3K4me3_EPrec

value: H3K4me3 (ab8580, Abcam)


title: Blood, Non-smoker_3223

value: Female

value: Blood


title: ChIP-seq_H3K4me1_EProg


title: ChIP-seq_H3K4me3_EProg


title: ChIP-seq_H3K27ac_EProg


title: Blood, Non-smoker_3221


title: whole_root_Control_1

value: protoplast cells

value: whole root


title: Blood, Smoker_3226

value: Male

value: Smoker


title: CI-AKI Rep3_miRNA

city: Fuzhou

first: Zhiqing

state: Fujian

address: NO. 156, North Xierhuan Road

department: Department of Cardiology

institute: 900 Hospital of the Joint Logistics Team

data_processing:
Raw reads were preprocessed with Fastx (Ver 0.0.13) to filter out adapter sequences in reads, bases near 3'-end with quality value lower than 10, and reads of length smaller than 10.
Clean reads were aligned to reference genome (rn6) by Bowtie (Ver0.12.7) with one mismatch allowed. After that, miRNA and other small RNAs were identified considering miRNA location from miRBase.
For expression quantification of miRNA, reads number of each miRNA was normalized into TMM (trimmed mean of M values),  and then transformed into TPM (Transcripts per Million).
Genome_build: rn6
Supplementary_files_format_and_content: text file with abundance measurements

organism: Rattus norvegicus

source_name: kidney

growth_protocol: Rats were pretreated with water dehydration for 48 hours before the experiment, and were allowed to recover with free access to tap water after surgical procedure. Standard chow was allowed throughout the study.

extract_protocol:
Total RNA was extracted with mirVana miRNA Isolation Kit (Cat #. AM1561, Austin TX, US) and its Standard Operating Protocol(SOP), which then experienced quality control with 2100 Bioanalyzer (Agilent Technologies Santa Clara, US).
Library was constructed in steps: 3'-end  adapter ligation, 5'-end adapter ligation, reverse transcription, PCR amplification, size selection of cDNA library, and purification. These steps were completed with TruSeq Small RNA Sample Prep Kit (Illumina), T4 RNA Ligase 2 Truncated (BioLabs), SuperScript II Reverse Transcriptase (Invitrogen), 6% TBE Gel (1.0mm x 10well)(Invitrogen), Novex TBE Running Buffer (5X)(Invitrogen), Pellet Paint NF Co-precipitant (Novagen), Qubit dsDNA HS Assay Kit(Invitrogen), and Agilent High Sensitivity DNA Kit(Agilent).

treatment_protocol: Rats were pretreated with intravenous injection of indomethacin (10mg/kg) and N-ω nitro-L-arginine methyl ester (10mg/kg) before contrast medium administration.

tag: strain

value: SD

value: kidney

value: three-month-old

tag: Sex

value: male

tag: disease state

value: contrast-induced acute kidney injury (CI-AKI)


title: ChIP-seq_input_EProg

tag: tissue

value: Human umbilical cord blood

value: none (non-immunoprecipitated chromatin fragments)


title: CI-AKI Rep1_miRNA

tag: age


title: Blood, Smoker_3220

tag: ethnicity

tag: gender


title: Blood, Non-smoker_3219

tag: cpd

tag: hsi

value: Non-smoker


title: Control Rep1_miRNA

value: control


title: Control Rep2_miRNA


title: Blood, Non-smoker_3216

value: African-American

tag: ftnd


title: Blood, Smoker_3218


title: Blood, Non-smoker_3217


title: Control Rep3_miRNA


title: 0030348590T

city: Guangzhou

first: neng

last: jiang

state: Guangdong

address: No. 58, ZhongShan Second Road

department: Department of Pathology

institute: The First Affiliated Hospital, Sun Yat-sen University

description: Patient 4 (tumor)

hyb_protocol: After stopping the labeling procedure, briefly spin the reaction and leave it at 4°C. The labeled sample is now ready for hybridization on the array. Hybridization should preferably occur within 1-2h. Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.

scan_protocol: The hybridized chips were scanned with an Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background. subtraction and four Replicated spots of each probe on the same slide have been averaged.
We use Median Normalization Method to obtain "Normalized Data", Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.

source_name: primary lung cancer

label_protocol: miRNAs were  labeled with the miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) according to the manufacturer’s guideline for miRNAs labelling.

extract_protocol: Total RNA was extracted from fresh tissue samples by TRIzol Reagent (Invitrogen life technologies).

value: primary lung adenocarcinoma

value: lung cancer tissue

tag: status after 5 years

value: Alive

value: AD

value: 52 years

tag: Stage

value: IB


title: Blood, Smoker_3215

first: Yi

address: No. 17, Dazhi Road, old Zhejiang, Shangcheng District

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

value: Male

value: Smoker

value: Blood


title: Blood, Smoker_3222

value: Female


title: 0030340180T

description: Patient 1 (tumor)

value: Dead

tag: histology

value: 57 years

value: IIIA


title: 001156551T

description: Patient 2 (tumor)

value: 65 years

value: IA


title: Blood, Smoker_3214


title: CI-AKI Rep2_miRNA

value: SD

value: kidney

value: three-month-old

value: male

value: contrast-induced acute kidney injury (CI-AKI)


title: Blood, Non-smoker_3213

value: African-American

value: Non-smoker


title: 0001164948N

description: Patient 4 (non-tumor)

value: primary lung adenocarcinoma

value: adjacent non-tumor tissue

value: Alive

value: AD

value: 52 years

value: IB


title: 001162111T

description: Patient 3 (tumor)

value: lung cancer tissue

value: 60 years

value: Female

value: IIB


title: 0030338793T

description: Patient 5 (tumor)

value: 54 years

value: Male


title: Sample 6_I030

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
hg19 AmpliSeq transcriptome ERCC v1 was used as a reference genome for alignment of raw sequencing reads.
Read count normalization was performed using the regularized logarithm (rlog) method provided in DESeq2 (PMID: 25516281).
Differentially expressed genes were identified using DESeq2, and p-values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Genome_build: hg19 AmpliSeq transcriptome
Supplementary_files_format_and_content: Ion Suite

source_name: iPSC-CMs

growth_protocol: iPSCs were differentiated into iPSC-cardiomyocytes (iPSC-CMs) using a monolayer small molecule-based method.

extract_protocol:
RNA was extracted using a miRNeasy Mini Kit, and collected total RNA was used for RNA-sequencing.
AmpliSeq sequencing data was performed using the AmpliSeq plugin available for Ion Torrent™ sequencing platforms

treatment_protocol: iPSC-CMs were cultured until day 30, as well as long-term until day 90 and day 200.

tag: cell line source

value: iPSC line 2

value: iPSC-cardiomyocytes (iPSC-CMs)

tag: culture period

value: Day 200


title: Sample 5_I029

value: iPSC line 1

tag: cell type


title: Sample 4_I028

value: Day 90


title: Blood, Smoker_3212

last: Xu

value: African-American

value: Smoker

value: Blood


title: Sample 2_I026

value: Day 30


title: Sample 3_I027


title: 0030338793N

description: Patient 5 (non-tumor)

value: primary lung adenocarcinoma

value: adjacent non-tumor tissue

value: Alive

value: AD


title: 0001156551N

description: Patient 2 (non-tumor)

value: Dead

value: 65 years

value: Female

value: IA


title: Blood, Smoker_3211


title: Sample 1_I025


title: Blood, Non-smoker_3210

value: Non-smoker


title: Blood, Non-smoker_3209


title: 0001162111N

description: Patient 3 (non-tumor)

value: 60 years

value: IIB


title: Blood, Smoker_3208

value: Male


title: Blood, Smoker_3202


title: Blood, Smoker_3203


title: Blood, Smoker_3201


title: Blood, Smoker_3204


title: Blood, Non-smoker_3207


title: Blood, Smoker_3206


title: Blood, Non-smoker_3205


title: Blood, Non-smoker_3200


title: 568386N

description: Patient 1 (non-tumor)

value: 57 years

value: IIIA


title: Blood, Non-smoker_3199

value: African-American


title: H3K4me3_WT_ChIP_rep2

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

description: ChIP-seq of mus musculus

data_processing:
Peakcalling performed using MACS2 version 2.1.1 with parameters -q 0.05 --nomodel --extsize 300 -B -SPMR
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.6
Genome_build: mm10

source_name: th17 cells

growth_protocol: Naive CD4+ T cells (CD4+CD25-CD62LhiCD44lo) were purified by FACS Aria II flow cytometer or sorted by Mouse CD4 Naïve T cell Enrichment Kit (Invitrogen, # 8804-6824-74). Naive CD4+T cells were cultured with irradiated (30 Gy) APC sorted from spleen at a ratio of 1:3, and were activated with 2µg/ml anti-CD3 and 3 µg/ml anti-CD28 in 48-well plate (5×105 T cells/well). T cells were cultured in RPMI 1640 medium supplemented with 10% FBS, sodium pyruvate, penicillin/streptomycin, and 2-mercaptoethanol.For Th17 cell differentiation, culture medium was supplemented with IL-6 (20 ng/mL), TGF-β1 (5 ng/mL), anti-IL-4 (10 ng/mL), anti-IL-12(10 ng/mL), anti-IFNγ (10 ng/mL).

extract_protocol:
ChIP assays were performed according to the manufacturer’s instructions with modifications using the ChIP-IT kit (Active Motif, USA). In brief, the Th17 cells were fixed with 1% formaldehyde, and then the crosslinked chromatin was sonicated in a 4°C water bath using a Bioruptor Pico sonicator (Diagenode) to obtain DNA fragments between 150 and 500 bp in size. For Cxxc1 ChIP-seq, 5×106 Th17 cells and 6 µg of Cxxc1 antibody were used for each sample. For H3K4me3 ChIP-seq, 3×106 Th 17 cells and 4 µg of H3K4me3 antibody were used for each sample.
The immunoprecipitated DNA was purified and subjected to sequencing library preparation using a VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (Vazyme Biotech Co., Ltd) according to the manufacturer’s protocol. The DNA libraries were then sequenced with an Illumina HiSeq X ten system at Veritas Genetics in Hangzhou.

tag: chip antibody

value: naive CD4-derived th17 cells


title: Blood, Non-smoker_3197

city: Hangzhou

value: Blood


title: Blood, Smoker_3198

value: Smoker


title: intestine_pups from high fat diet dams_3week_rep3 [G8]

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: gene expression data from intestine from maternal high fat diet

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

label: biotin

source_name: pups from high fat diet dams, 3 weeks

label_protocol: biotin

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

tag: strain background

value: Sprague Dawley

tag: mouse group

value: pups from high fat diet dams

value: 3 week

value: intestine


title: HK34me3_KO_ChIP_rep2

description: ChIP-seq of mus musculus


title: Cfp1_KO_ChIP_rep2

description: ChIP-seq of mus musculus


title: Cfp1_WT_ChIP_rep2

description: ChIP-seq of mus musculus


title: Blood, Non-smoker_3196


title: Cfp1_KO_input_rep2

description: ChIP-seq of mus musculus


title: intestine_pups from high fat diet dams_3week_rep2 [D8]


title: intestine_pups from sitagliptin-treated dams_3week_rep2 [E8]

description: gene expression data from intestine from maternal sitagliptin treatment

source_name: pups from sitagliptin-treated dams, 3 weeks

value: pups from sitagliptin-treated dams


title: intestine_pups from sitagliptin-treated dams_3week_rep3 [F8]


title: Cfp1_WT_input_rep2

description: ChIP-seq of mus musculus


title: Series5_A549_SARS-CoV-2_1

city: New York

first: Daniel

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
CoV_A549-SARSCoV2-3
processed data file: RawReadCounts_Human.tsv

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or Ferret genome (MusPutFur1.0) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.

source_name: SARS-CoV-2 infected A549 cells

extract_protocol:
TruSeq Stranded mRNA LP
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

tag: cell line

tag: tissue/cell type

value: Lung adenocarcinoma

tag: treatment

value: SARS-CoV-2 infected (MOI 2)

tag: strain

tag: time after treatment

value: 24 hours


title: Blood, Smoker_3195

tag: ethnicity

tag: age

tag: gender

value: Female

tag: cpd

tag: tissue


title: intestine_pups from sitagliptin-treated dams_3week_rep1 [B9]


title: HK34me3_KO_ChIP_rep1

description: ChIP-seq of mus musculus


title: Blood, Smoker_3194

tag: hsi

tag: ftnd


title: intestine_pups from high fat diet dams_3week_rep1 [B1]


title: Cfp1_WT_ChIP_rep1

description: ChIP-seq of mus musculus


title: Cfp1_KO_ChIP_rep1

description: ChIP-seq of mus musculus


title: Blood, Non-smoker_3192

value: Non-smoker


title: Cfp1_KO_input_rep1

description: ChIP-seq of mus musculus


title: Blood, Non-smoker_3190


title: Cfp1_WT_input_rep1

description: ChIP-seq of mus musculus


title: Blood, Smoker_3189


title: PAX7-B cDNA rep2

city: Durham

first: Charles

last: Gersbach

address: 101 Science Dr

institute: Duke University

description: Sample 11

data_processing:
All RNA-seq samples were first validated for consistent quality using FastQC v0.11.2 (Babraham Institute).
Raw reads were trimmed to remove adapters and bases with average quality score (Q) (Phred33) of < 20 using a 4bp sliding window (SLIDINGWINDOW:4:20) with Trimmomatic v0.32
Trimmed reads were subsequently aligned to the primary assembly of the GRCh38 human genome using STAR v2.4.1a, removing alignments containing non-canonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical).
Aligned reads were assigned to genes in the GENCODE v19 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4).
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: .counts.txt file

source_name: Differentiated iPSCs

growth_protocol: Human iPSCs were dissociated into single cells and plated on Matrigel-coated plates at 2.3 - 3.3 x 104/cm2 in mTeSR medium supplemented with 10 μM Y27632. The following day, mTeSR medium was replaced with E6 media supplemented with 10 μM CHIR99021 to initiate mesoderm differentiation. After 2 days, CHIR99021 was removed and cells were maintained in E6 media with 10 ng/mL FGF2 and 1 μg/mL of doxycycline. Cells were grown without passaging for 14 days with media refreshed daily. At day 14, cells were dissociated and sorted by mCherry expression from the lentiviral vector. Sorted cells were immediately processed for RNA isolation.

extract_protocol:
RNA was extracted from freshly sorted cells at day 14 of differentiation using the Total RNA Purification Plus Micro Kit (Norgen)
Library preparation and sequencing was performed by GENEWIZ.

treatment_protocol: Human iPSCs were transduced with lentivirus prior to differentiation.

value: PAX7-B cDNA

value: differentiated iPSCs

tag: collection time

value: Day 14 differentiated iPSCs


title: PAX7-A cDNA rep2

description: Sample 8

value: PAX7-A cDNA

tag: cell type


title: PAX7-B cDNA rep1

description: Sample 10


title: PAX7-A cDNA rep3

description: Sample 9


title: PAX7-A cDNA rep1

description: Sample 7


title: PAX7-B cDNA rep3

description: Sample 12


title: VP64dCas9VP64 +gRNA rep2

description: Sample 5

value: VP64dCas9VP64 +gRNA


title: VP64dCas9VP64 +gRNA rep3

description: Sample 6


title: Blood, Non-smoker_3193

source_name: Blood

value: African-American

value: Male

value: Blood


title: H3K4me3_WT_ChIP_rep1

description: ChIP-seq of mus musculus

tag: chip antibody

value: naive CD4-derived th17 cells


title: VP64dCas9VP64 +gRNA rep1

description: Sample 4


title: Blood, Smoker_3191

value: Smoker


title: PAX7-targeting gRNA only rep2

description: Sample 2

value: PAX7-targeting gRNA only


title: PAX7-targeting gRNA only rep3

description: Sample 3


title: siCon rep 2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from mouse primary hepatocytes

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-1_0-type from Affymetrix. A Custom CDF Version 16 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: primary hepatocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Primary hepatocytes were prepared from 12 week old C57BL/6 mice via the two-step collagenase perfusion method.Then, isolated hepatocytes were plated on 6-well plates and cultured in Williams E medium with 1% l-glutamine, 1% Penicillin/Streptomycin, 0.1% dexamethasone and 10% fetal bovine serum. After hepatocyte attachment (~4 h), culture medium was changed to starvation medium (no dexamethasone and fetal bovine serum).

extract_protocol: Total RNA was isolated using InviTrap Spin Universal RNA Mini Kit from all sample groups according to the manufacturer’s instruction.

treatment_protocol: After attachment, primary hepatocytes were transfected overnight with 10 nM siRNA targeting CAV1 or a negative control siRNA using RNAiMAX transfection reagent according to the manufacturer’s instructions. Next day, the hepatocytes were treated with/without 5 ng/ml recombinant TGF-β1 and cultured additional 48 h in starvation medium.

tag: sirna

value: Ctrl


title: siCon+TGF-β rep 2

description: Gene expression data from mouse primary hepatocytes treated with TGFBeta

value: TGFBeta


title: siCon rep 3


title: siCon rep 1


title: siCAV1 rep 2

description: Gene expression data from mouse primary hepatocytes treated with Cav1 siRNA


title: siCAV1 rep 3

source_name: primary hepatocytes treated with Cav1 siRNA


title: siCAV1 rep 1


title: siCon+TGF-β rep 1

source_name: primary hepatocytes treated with TGFBeta


title: PAX7-targeting gRNA only rep1

description: Sample 1


title: siCon+TGF-β rep 3


title: HaCaT_unstimulated_HiC

city: Manchester

first: Paul

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

country: United Kingdom

institute: Univeristy of Manchester

description:
This Sample represents 1 replicate
Hi-C, HaCaT Keratinocyte cells, unstimulated, replicate 1

data_processing:
CHi-C: Fastq files were filtered and mapped to the hg19 genome by the Hi-C User Pipeline (HiCUP) v0.5.8. The filtered files for two biological replicates were simultaneously run through the Capture Hi-C Analysis of Genomic Organisation (CHiCAGO) v1.1.8, with a score threshold of 5. Interactions were limited to same-chromosome (cis) and to psoriasis-specific loci.
Hi-C: Fastq files were filtered and adapters removed using fastp v0.19.4. Reads were mapped to the GRCh38 genome with Hi-C Pro v2.11.0 using default settings. Hi-C interaction matrices were normalised within Hi-C Pro using iterative correction and eigenvector decomposition (ICE). Topologically associating domains (TADs) were then called in TADtool software using insulation score with the normalised Hi-C contact matrices, binned with 40 kb resolution. For comparison, TADs were lifted over to the hg19 genome using UCSC LiftOver.
Hi-ChIP: Fastq files were filtered and the adapters were removed using fastp v0.19.4. The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0, using default settings. Genome-wide anchors for H3K27ac were called in hichipper v0.7.3 using the self-circle and dangling end reads for the first replicate, extended for 147 bp. For interactions, two replicates were merged and loops were identified using FitHiChIP using the following settings: Coverage normalisation, stringent background with merging enabled, peaks generated from HiChIP data using the included tool and 5kb bin size.
RNA-seq: Reads were quality trimmed using Trimmomatic v0.38 using a sliding window of 5 with a mean minimum quality of 20. Adapters and poly A/poly G tails were removed using Cutadapt v1.18 and then UMIs were extracted from the 5’ of the reads using UMI-tools v0.5.5. Reads were then mapped using STAR v2.5.3a on the GRCh38 genome with GENCODE annotation v29. Reads were de-duplicated using UMIs with UMI-tools and then counted using HTSeq v0.11.2. Count matrixes were analysed in R 3.5.1 and normalisation and differential expression analysis was conducted using DESeq2 v1.22.2.
Genome_build: hg19
Supplementary_files_format_and_content: TADs.bed.gz: TAD coordinates (chromosome, start, end)
Supplementary_files_format_and_content: Ps_bait_fragments.bed.gz: HindIII fragments tagged by psoriasis-associated GWAS SNPs (chromsosome, start, end, SNP)
Supplementary_files_format_and_content: CHi-C_interactions.txt.gz: Significant CHi-C interacting HindIII fragments involving psoriasis loci (bait chromosome, bait start, bait end, other-end chromosome, other-end start, other-end end, CHiCAGO score, SNP)
Supplementary_files_format_and_content: HiChIP_9q31_interactions.txt.gz: Significant HiChIP interactions originating from the H3K27ac peak at KLF4 in 9q31 (peak chromosome, peak start, peak end, other-end chromosome, other-end start, other-end end, Hichipper score)
Supplementary_files_format_and_content: combined_RNA-seq_counts.csv: Raw RNA-seq counts for all experimental samples
Supplementary_files_format_and_content: 27ac.anchors.bed.gz: Standard bed files
Supplementary_files_format_and_content: HiChIP_interactions.txt.gz: FitHiChIP interaction files (with header)

source_name: HaCaT Keratinocyte cells

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a dounce homogeniser with a 5 minute break between douncing. The nuclei were pelleted and permeabilised and the chromatin was digested with HindIII. Ends were marked with biotin followed by in-nucleus ligation, decrosslinking and biotin pulldown according to the previously established Hi-C protocol (Dryden et al., 2014; P. Martin et al., 2015)
Sequencing libraries were generated with 6-8 cycles of PCR using Truseq single indexes (Illumina) and Phusion polymerase (NEB)

treatment_protocol: Cells were fixed in 1% formaldehyde for 10 minutes at room temperature, Fixation was quenched by the addition of cold 1M glycine to a final concentration of 0.125M. Pelleted cells were frozen on dry ice and stored at -80C.

value: HaCaT Keratinocyte cell line

tag: stimulation

tag: biomaterial provider

tag: restriction enzyme

value: HindIII


title: siCAV1+TGF-β rep 3

description: Gene expression data from mouse primary hepatocytes treated with Cav1 siRNA and TGFBeta

tag: treatment


title: HaCaT_stimulated_HiC

description:
This Sample represents 1 replicate
Hi-C, HaCaT Keratinocyte cells, stimulated, replicate 1

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2. Cells were stimulated with 100 ng/mL recombinant human IFN-γ (285-IF-100; R&D Systems) for 8 hours.

value: 100 ng/mL recombinant human IFN-γ for 8 hours


title: siCAV1+TGF-β rep 2

source_name: primary hepatocytes treated with Cav1 siRNA and TGFBeta


title: HaCaT_unstimulated_CHiC

description:
This Sample represents 2 replicates
Capture Hi-C, HaCaT Keratinocyte cells, unstimulated, replicate 1 & 2

data_processing:
Library strategy: Capture Hi-C
CHi-C: Fastq files were filtered and mapped to the hg19 genome by the Hi-C User Pipeline (HiCUP) v0.5.8. The filtered files for two biological replicates were simultaneously run through the Capture Hi-C Analysis of Genomic Organisation (CHiCAGO) v1.1.8, with a score threshold of 5. Interactions were limited to same-chromosome (cis) and to psoriasis-specific loci.
Hi-C: Fastq files were filtered and adapters removed using fastp v0.19.4. Reads were mapped to the GRCh38 genome with Hi-C Pro v2.11.0 using default settings. Hi-C interaction matrices were normalised within Hi-C Pro using iterative correction and eigenvector decomposition (ICE). Topologically associating domains (TADs) were then called in TADtool software using insulation score with the normalised Hi-C contact matrices, binned with 40 kb resolution. For comparison, TADs were lifted over to the hg19 genome using UCSC LiftOver.
Hi-ChIP: Fastq files were filtered and the adapters were removed using fastp v0.19.4. The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0, using default settings. Genome-wide anchors for H3K27ac were called in hichipper v0.7.3 using the self-circle and dangling end reads for the first replicate, extended for 147 bp. For interactions, two replicates were merged and loops were identified using FitHiChIP using the following settings: Coverage normalisation, stringent background with merging enabled, peaks generated from HiChIP data using the included tool and 5kb bin size.
RNA-seq: Reads were quality trimmed using Trimmomatic v0.38 using a sliding window of 5 with a mean minimum quality of 20. Adapters and poly A/poly G tails were removed using Cutadapt v1.18 and then UMIs were extracted from the 5’ of the reads using UMI-tools v0.5.5. Reads were then mapped using STAR v2.5.3a on the GRCh38 genome with GENCODE annotation v29. Reads were de-duplicated using UMIs with UMI-tools and then counted using HTSeq v0.11.2. Count matrixes were analysed in R 3.5.1 and normalisation and differential expression analysis was conducted using DESeq2 v1.22.2.
Genome_build: hg19
Supplementary_files_format_and_content: TADs.bed.gz: TAD coordinates (chromosome, start, end)
Supplementary_files_format_and_content: Ps_bait_fragments.bed.gz: HindIII fragments tagged by psoriasis-associated GWAS SNPs (chromsosome, start, end, SNP)
Supplementary_files_format_and_content: CHi-C_interactions.txt.gz: Significant CHi-C interacting HindIII fragments involving psoriasis loci (bait chromosome, bait start, bait end, other-end chromosome, other-end start, other-end end, CHiCAGO score, SNP)
Supplementary_files_format_and_content: HiChIP_9q31_interactions.txt.gz: Significant HiChIP interactions originating from the H3K27ac peak at KLF4 in 9q31 (peak chromosome, peak start, peak end, other-end chromosome, other-end start, other-end end, Hichipper score)
Supplementary_files_format_and_content: combined_RNA-seq_counts.csv: Raw RNA-seq counts for all experimental samples
Supplementary_files_format_and_content: 27ac.anchors.bed.gz: Standard bed files
Supplementary_files_format_and_content: HiChIP_interactions.txt.gz: FitHiChIP interaction files (with header)

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a dounce homogeniser with a 5 minute break between douncing. The nuclei were pelleted and permeabilised and the chromatin was digested with HindIII. Ends were marked with biotin followed by in-nucleus ligation, decrosslinking and biotin pulldown according to the previously established Hi-C protocol (Dryden et al., 2014; P. Martin et al., 2015). Genomic regions of interest were captured using biotinylated RNA baits (Agilent Technologies).
Sequencing libraries were generated with 6-8 cycles of PCR using Truseq single indexes (Illumina) and Phusion polymerase (NEB)


title: HaCaT_stimulated_CHiC

description:
This Sample represents 2 replicates
Capture Hi-C, HaCaT Keratinocyte cells, stimulated, replicate 1 & 2


title: 1510: KO_6

city: Baltimore

first: Jay

last: Baraban

state: MD

address: 725 North Wolfe Street

department: Neuroscience

institute: The Johns Hopkins University School of Medicine

hyb_protocol: Arrays were hybridized for 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in the GeneChip Expression Analysis Technical Manual.

scan_protocol: Arrays were scanned using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in the GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Probeset annotation was from the miRNA-4_0-st-v1.pgf and miRNA-4_0-st-v1.annotations.20160922.csv files.  RMA normalization of the mouse-specific probesets was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analysis.

source_name: Mouse C57BL/6J epididymal white adipose tissue

label_protocol: The total RNA samples were biotin labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit, following manufacturer's instructions.

growth_protocol: Mice were housed in ventilated racks, on a 14-h/10-h light/dark cycle and with standard chow (2018SX Teklad Global, Frederick, MD) and water available ad libitum.

extract_protocol: Total RNA was isolated from epididymal white adipose tissue and liver using the miRNeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: A colony of translin KO mice was established at Johns Hopkins University from the line generated in Dr. Kasai’s laboratory and provided by the JCRB Laboratory Animal Resource Bank of the National Institute of Biomedical Innovation (translin KO: Nbio055). These mice had been backcrossed to C57/BL6 mice for over ten generations. Adult male WT and KO mice were anesthetized, decapitated and epididymal adipose tissue biopsies collected for furthe processing.

tag: strain

value: epididymal white adipose tissue

tag: genotype

value: translin KO


title: siCAV1+TGF-β rep 1


title: Verapamil 3

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
TrimGalore
STAR
RSEM
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression values (TPM) generated by RSEM

source_name: iPSC-CM

growth_protocol: Cardiogenic differentiation of human iPSC was performed using a chemically defined protocol using activator and inhibitors of the Wnt signaling pathway.

extract_protocol: Total RNA was isolated using Direct-zol RNA MiniPrep Plus (Zymo Research) in accordance to manufacturer’s instructions, followed by DNAse treatment.

treatment_protocol: iPSC-CMs were treated with calcium channel blockers or DMSO as a vehicle for a period of 14 days. Each calcium channel blocker was applied at its serum peak concentration.

tag: agent

value: Verapamil

value: iPSC-CM

tag: cell origin

value: Human


title: Vehicle 3

value: Control


title: 1545: KO_3


title: 1546: KO_4


title: 1531: KO_2


title: 1530: KO_1


title: Nifedipine 3

value: Nifedipine


title: Verapamil 2


title: 1573: WT_6

value: WT


title: Amplodipine 3

value: Amplodipine


title: 1526: WT_5


title: 1512: WT_4


title: Nifedipine 2


title: Vehicle 2


title: Diltiazem 2

value: Diltiazem


title: Amplodipine 2


title: Verapamil 1


title: 1548: KO_5


title: 1509: WT_3


title: 1493: WT_2


title: Nifedipine 1


title: Vehicle 1


title: Diltiazem 3


title: 1474: WT_1


title: Diltiazem 1


title: A. viteae M

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: https://parasite.wormbase.org/Acanthocheilonema_viteae_prjeb1697/Info/Index
Supplementary_files_format_and_content: excel, expression profiles: summary of miRNA candidates identified in secretions of A. viteae adult females and males

organism: Acanthocheilonema viteae

source_name: in vitro culture media, secretions

growth_protocol: Females and males were separated and cultured for up to 3 weeks at 1-2 worms per ml RPMI-1640 containing 200 U/ml penicillin and 200 µg streptomycin, and 4 mM L-glutamine, at 37 °C, 5 % CO2.

extract_protocol:
Total RNA purification kit (Norgen Biotek #17200, blood protocol
Illumina Truseq Small RNA Preparation

treatment_protocol: Collected culture media were spun at 1000 x g for 30 min at 4 °C, filtered through 0.22 µm pores, and frozen at -20 °C for several weeks. Upon thawing, media were concentrated over a 3 kDA membrane. Concentrated media were further spun 45 min at 12,000 x g and ultracentrifuged as follws:  2 h at 100,000 x g, 4°C; the pellet was washed once with PBS, and centrifuged again for 2h at 100,000 x g, 4 °C.

tag: Sex

value: Male

tag: Stage

value: adula