title: WT_MAIT_Input

description: CD3+ CD161+ TCR Vα7.2+

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the hg19 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated from Macs2 output

extract_protocol:
Isolated cells were fixed with 1% formaldehyde in PBS for 10 minutes, then quenched with glycine.  After washing, DNA was extracted using the Illumina SimpleChIP Enzymatic ChIP kit (#9003S). Briefly, nuclei were isolated by incubating in 1ml buffer A for 10 min on Ice, followed by centrifugation and resuspension in 1 ml Buffer B.  Chromatin was sheared to roughly 200-1000bp. Samples were centrifuged to clear lysates, and the supernatant containing the DNA was transferred to a fresh tube for overnight antibody complexing.  Next day, protein G dynabeads were added to each tube, incubated, washed, and isolated with magnet.  DNA complexes were then released from the beads, decrosslinked, and phenol:choloroform:isolamyl alcohol extracted for library prep.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina.  Briefly, DNA ends were repaired, followed by ligation of adapter sequences.  DNA was cleaned with AMPure XP beads, and then DNA was PCR amplified with 7-8 cycles.  After final cleaup with AMPure XP Beads, libraries were quantified using Agilent Bioanalyzer high sensitivity DNA kit and were subsequently sequenced.

value: MAIT


title: WT_Mm_Stritum_scRNASeq

status: Public on Mar 22 2021

type: SRA

city: Esch-sur-Alzette

first: Dimitrios

last: Kyriakis

address: 6, avenue du Swing

country: Luxembourg

institute: LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE (LCSB)

library_source: transcriptomic

data_processing:
Quality control of the Reads (FastQC)
Alignment (STAR)
Quality control mapping (FastQC)
Filtering low quality cells(Seurata.v.3)
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: [TSV] tab-separated value file include count values for each cell, UMAP projection and Clsuter asssignment

molecule: total RNA

organism: Mus musculus

source_name: Striatum

extract_protocol:
Drop-Seq
Libraries were prepared according to Drop-seq methods (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002). After cDNA tagmenation, PCR amplification was performed using Illumina primers (N701,N702, A501). The purified cDNA fragments of ~600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.

tag: tissue

value: Striatum

tag: strain

tag: age

value: Four to six months-old


title: RNAseq_ZFSssI_T2_line1_plus_rep2

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

description: RNAseq data for ZFSssI_T2_line1_plus_rep2

data_processing:
BS-PCR-seq analysis was conducted as previously described (Gallego-Bartolome et al., 2019). Briefly, raw sequencing reads with designed BS-PCR primers were first filtered and trimmed based on the primer sequence with customized scripts. Trimmed reads were then mapped to the reference TAIR10 genome with BSMAP (Xi et al., 2009) (v.2.74) by allowing maximal two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described 19. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were excluded for further analysis. To visualize the BS-PCR-seq data, only cytosines within amplified regions were kept and plotted with R (ggplot2 package, https://ggplot2.tidyverse.org/).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
WGBS analysis was performed as previously described (Gallego-Bartolome et al.,2019). Raw reads were first aligned to the reference TAIR10 genome using BSMAP (Xi  et al., 2009) (v2.74) by allowing up to two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described (Cokus  et al.,2008). Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between ZF-SssI and Col-0 were defined similar to before using the R package DMRcaller (Gallego-Bartolome et al.,2019). To increase coverage for DMR analysis, biological replicates were merged for each genotype (ZF-SssI + and ZF-SssI -), each generation (T2 to T5) and each transgenic lines (line 1 and line 2). In general, the whole TAIR10 genome was divided into 200 bp bins, and only bins with at least four cytosines, with each cytosine covered at least four times, more than 10% more methylation in ZF-SssI than Col-0, and a significance level of less than 0.05 were kept. To define hCG DMRs for T2 and T3, the intersect hCG DMRs of two transgenic lines in each generation were first calculated, then the union set of T2 and T3 in the same genotype (either ZF-SssI + or ZF-SssI -) were kept. DMRs overlapping with 200 bp bins in each cluster were considered as DMRs specific for certain clusters. Genomic location for DMRs and mCG equivalent control were annotated using the Homer (Heinz  et al.,2010) ‘annotatePeaks’ function with default parameters. For T4 and T5, two transgenic lines were separated in order to trace the heritable hCG DMRs. To define heritable hCG DMRs, T2 ZF-SssI – were compared with T2 ZF-SssI + and the shared hCG DMRs were considered as heritable hCG DMRs in T2 ZF-SssI –. For T3 ZF-SssI + and ZF-SssI -, hCG DMRs were overlapped with T2 ZF-SssI +. For T4 ZF-SssI – heritable hCG sites, DMRs were first intersected with T3 ZF-SssI + and then intersected with T2 ZF-SssI + while T5 ZF-SssI – heritable hCG sites were further intersected with T4 ZF-SssI – hCG DMRs.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al., 2019, Buenrostro et al., 2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmead et al., 2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al., 2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al., 2014) or deepTools (Ramirez et al., 2014).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
For ChIP-seq data, raw reads were first mapped to the reference TAIR10 genome with Bowtie (Langmead et al.,2009) (v0.12.8) by allowing uniquely mapped reads and maximal two mismatches. PCR-duplicated reads were then filtered with SAMTools (Li  et al.,2009) (v 1.19) . To call ZF-SssI FLAG peaks, the MACS2 calldiff function (Zhang et al.,2008) (v 2.1.2) was used to compare ZF-SssI FLAG ChIP-seq and Col-0 FLAG ChIP-seq data with default parameters. Genomic location and enriched motifs of ZF-SssI FLAG-specific peaks were then annotated with Homer (Heinz et al.,2010) ‘annotatePeaks’ and ‘findMotifGenome’ functions using 100 bp flanking the summit of the peaks. Promoter regions were defined as default in homer (upstream 1kb and downstream 100bp of TSS). ChIP-seq data visualizations were performed using ngs.plot (Shen  et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al.,2019, Buenrostro et al.,2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmeadet al.,2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al.,2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

molecule: polyA RNA

organism: Arabidopsis thaliana

growth_protocol: Plant materials  All plants in this study were grown under long-day conditions (16 h light/8 h dark). The fwa-4 mutant has been described previously (Johnson et al.,2014), as have the fwa nrpd1, fwa drm1 drm2 and fwa nrpe1 lines (Gallego-Bartolome et al., 2019). The pMDC123-ZF-3xFLAG-SssI plasmid was transformed into Agrobacterium AGLO and transformed into the different backgrounds by Agrobacterium-mediated floral dipping. T1 transgenic plants were grown on 1/2 MS medium + Glufosinate 50 μg/mL (Goldbio) in growth chambers under long-day conditions and transplanted to soil. The selection of transgenic lines for experiments was based on i) early flowering T1 plants for the lines in the fwa backgrounds and  ii) protein expression by WB for the lines in the Col-0 background. Following transgenic generations were germinated directly on soil and presence of the transgene was done by genotyping. Plants were not selected for homozygocity except for the T4 populations used for the ChIP experiment. Controls in this study correspond to untransformed plants of the different backgrounds used coming from the same seed stock. Flowering time was scored by counting the total number  rosette and caulinar leaves. In the flowering time dot plots, each dot represents the flowering time of individual plants. Plants with 20 or fewer leaves were considered early flowering. The samples used for all our genomics data correspond to inflorescence tissue collected during the day.

extract_protocol:
Total RNA from inflorescences was extracted using Direct-zol kit (ZYMO research).
1 μg of total RNA was used to prepare libraries using the TruSeq Stranded mRNA kit (Illumina).

value: inflorescence

tag: genotype

tag: ecotype

value: Columbia 0


title: Human_H3K27ac_Input_2

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

country: USA

institute: Moffitt Cancer Center

description: CD3+ CD161+ TCR Vα7.2+

library_source: genomic

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the hg19 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2
High confidence peaks were determined using IDR with a threshold IDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated from Macs2 output

molecule: genomic DNA

organism: Homo sapiens

source_name: MAIT cells

extract_protocol:
Chromatin was immunoprecipitated using the Active Motif Low Cell ChIP-seq kit (53084) using 100,000 cells. Chromatin was sheared using a Diagenode Bioruptor Pico (B01060002)
Libraries were generated using the Active Motif Low Cell ChIP-seq kit (53084).

value: peripheral blood

tag: cell type

value: MAIT cells

tag: group

value: Input

tag: chip antibody

value: none (input)


title: WT_MAIT_Bcl11b

description: CD3+ CD161+ TCR Vα7.2+

value: Bcl11b ChIP


title: WT_Mm_Midbrain_scRNASeq

source_name: Midbrain

value: Midbrain


title: RNAseq_ZFSssI_T2_line1_plus_rep1

description: RNAseq data for ZFSssI_T2_line1_plus_rep1


title: RNAseq_ZFSssI_T3_line2_plus_rep4

description: RNAseq data for ZFSssI_T3_line2_plus_rep4


title: MAIT_SS_KO_2

description: Bcl11b KO SS

data_processing:
Fastq files were trimmed using Seqtk
Trimmed fastq files were aligned to the mm10 genome via Hisat2
Raw counts were extracted from bam files using htseq
Differential analysis was performed on raw counts with DESeq2
Normalized counts were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts extracted from bam files using htseq

extract_protocol:
WT and Bcl11b KO MAIT cells were sorted from naïve or salmonella infected mouse lungs. Cells were lysed and RNA was isolated using Qiagen Rneasy Plus Micro Kit (Qiagen #74034). RNA quality was determined on a bioanalyzer (Agilent RNA 6000 Nano #5067-1511)
Libraries were prepared using New England Biolabs NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (cat# E7770S) according to the manufacturer's instructions. Library quality and concentration was checked on a bioanalyzer (Agilent High Sensitivity DNA Kit #5067-4626) and by Qubit (Qubit™ dsDNA HS Assay Kit #Q32854). Libraries were sequenced on a NextSeq500.

value: Bcl11bF/F PlzfCre+

value: Lung

tag: treatment

value: Steady state

value: KO


title: WT_2

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using STAR v2.5.2b.
Raw read counts were extracted using HTSeq-count v0.11.2 and were downsampled such that all samples have the same number of total counts.
Differential expression analysis was performed using DESeq2 v1.26.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: raw_counts.downsampled.txt: Tab-delimited text file storing read counts per gene per sample.

source_name: hESC derived INS-GFP+ cells

growth_protocol: Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 6-well plates in StemFlex medium (Thermo Fisher) and maintained at 37℃ with 5% CO2. MEL-1 cells were differentiated using a previously reported strategy48. Briefly, on day 0, cells were exposed to basal medium RPMI 1640 (Corning) supplemented with 1× glutamax (Thermo Fisher), 50 μg/mL normocin, 100 ng/mL Activin A (R&D systems), and 3 μM of CHIR99021 (Cayman Chemical) for 24 hours. The medium was changed on day 2 to basal RPMI 1640 medium supplemented with 1× glutamax, 50 μg/mL normocin, 0.2% FBS (Corning), 100 ng/mL Activin A for 2 days. On day 4, the resulting definitive endoderm cells were cultured in MCDB131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× glutamax, 10 mM glucose, 2% BSA, 50 ng/ml FGF7, 0.25 mM ascorbic acid for 2 days. On day 6, the cells were differentiated in MCDB131 medium supplemented with 2.5 g/L sodium bicarbonate, 1× glutamax, 10 mM glucose, 2% BSA, 0.25 mM ascorbic acid, 2 μM retinoic acid, 0.25 μM SANT1, 50 ng/ml FGF7, 200 nM TPB, 200 nM LDN and 0.5× ITS-X supplement for 2 days to pancreatic progenitor stage 1 cells. On day8, the cells were induced to differentiate to pancreatic progenitor stage 2 cells in MCDB131 medium supplemented with 2.5 g/L sodium bicarbonate, 1× glutamax, 10 mM glucose, 2% BSA, 0.25 mM ascorbic acid, 0.2 μM retinoic acid, 0.25 μM SANT1, 2 ng/ml FGF7, 100 nM TPB, 400 nM LDN and 0.5× ITS-X supplement for 3 days. On day 11, the cells were induced to differentiate to insulin expressing cells in MCDB131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× glutamax, 20mM glucose, 2% BSA, 0.1 μM retinoic acid, 0.25 μM SANT1, 200 nM LDN, 1 μM T3, 10 μM ALKi5, 10 μM zinc sulfate, 10 μg/mL heparin and 0.5× ITS-X for 3 days. On day 14, the cells were further maturated in MCDB131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× glutamax, 20 mM glucose, 2% BSA, 100 nM LDN, 1 μM T3, 10 μM zinc sulfate, 10 μg/mL heparin, 100 nM GS inh XX and 0.5× ITS-X for 9 days.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. cDNA libraries were sequenced with pair-end 51 bps using an Illumina NovaSeq6000 platform.

value: hESC derived beta cells

value: WT


title: WT_1


title: WT_3


title: Non-Lay rep3 [S6_RNOD28]

city: Honolulu

first: Nirvay

last: Sah

state: HI

address: 1955 East-west raod

department: Human Nutrition, Food and Animal Sciences

institute: University of Hawaii at Manoa

description:
S6_RNOD28
domesticated

data_processing:
Single-end reads in FASTQ format was explored using FastQC (Babraham Institute, Cambridge, UK)
Sequencign reads were cleaned using Prinseq (version 0.20.4). The cleaning procedure included trimming low quality reads from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found and filtering out reads having mean quality score less than 30 and length below 30 nucleotides.
Cleaned reads were aligned against chicken reference genome Galgal 5.0 using Array Studio (version10)
Differential gene expression analysis in layers with respect to non-layers’ groups was performed by the DESeq2 alogrithm
Genome_build: Galgal 5.0
Supplementary_files_format_and_content: .txt file exported from DESeq2; Fold Change represent relative gene expression levels in layer compared to non-layers

organism: Gallus gallus

source_name: Magnum

extract_protocol:
Magnum tissues were collected and snap frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA library Prep Kit (Cat#RS-122-2101) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hy-line

value: Magnum

value: 35-60 weeks


title: KO_3


title: WT_S2

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the brains of 3 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline with force_counts set to 2000. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: brain

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

value: brain

value: 5 months

tag: gender

value: male


title: KO_1


title: RNAseq_ZFSssI_T3_line2_plus_rep3

description: RNAseq data for ZFSssI_T3_line2_plus_rep3

value: inflorescence

value: Columbia 0


title: Non-Lay rep2 [S5_RNOD27]

description:
S5_RNOD27
domesticated


title: KO_2


title: Non-Lay rep1 [S4_RNOD26]

description:
S4_RNOD26
domesticated


title: SOX2_b_KD

city: Geneva

first: victor

last: YTHIER

state: Geneva

address: Rue Michel-Servet,1

department: GEDEV

country: Switzerland

institute: University of Geneva

description:
Bisulfite-treated DNA
Percentage of methylation per CpG position

data_processing:
Bisulfite-Seq
Filtering base on barcode-motif-barcode sequence using R v3.6.2 and BioString package v2.54.0 (0 missmatch fixed=FALSE)
Alignment on each reference sequence using bismark v0.20.0 (–non_directional -X 1000 -N 0 -q ref/${motif_name})
Filtering on nonCG conversion (ESC and NP only) (filter_non_conversion -p --percentage_cutoff 2)
UMI deduplication using umitools v0.5.5
Methylation extraction (bismark_methylation_extractor -p --no_overlap --bedGraph --cytosine_report --CX  --genome_folder  ref/${motif_name})
Genome_build: fr1 sequence with particular barcode-motif-barcode into beta globuline locus
Supplementary_files_format_and_content: tab-delimited text files include percentage of methylation for each library per Cell type and treatment.
Supplementary_files_format_and_content: *_mincov0.tab: extraction information
Supplementary_files_format_and_content: *_pm_mincov0.tab: methylation percentage summary

source_name: Embryonic Stem Cell

extract_protocol:
cf paper
Bisulfite-Seq – AmpBis-Seq


title: Lay rep3 [S3_RNOD05]

description:
S3_RNOD05
domesticated

value: 35 weeks


title: SOX2_ab_KD


title: OCT4_ab_KD


title: RNAseq_ZFSssI_T3_line2_plus_rep1

description: RNAseq data for ZFSssI_T3_line2_plus_rep1


title: Lay rep2 [S2_RNOD04]

description:
S2_RNOD04
domesticated


title: RNAseq_ZFSssI_T2_line2_plus_rep4

description: RNAseq data for ZFSssI_T2_line2_plus_rep4


title: RNAseq_ZFSssI_T2_line2_plus_rep3

description: RNAseq data for ZFSssI_T2_line2_plus_rep3


title: Lay rep1 [S1_RNOD01]

description:
S1_RNOD01
domesticated


title: All_siRNAs


title: BE2C_siI1_3

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and FPKM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

source_name: neuroblastoma derived cell line

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% FBS. BE(2)-C cells were cultured in EMEM:DMEM/F12 (1:1) medium supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Poly-A RNA was enriched using oligo(dT) beads. RNAs are fragmented randomly by adding fragmentation buffer. cDNA is synthesized by using random hexamers primer followed by second strand synthesis. Strand-specific double-stranded cDNA libraries are completed by size selection (250-300bp) and PCR enrichment.

treatment_protocol: 72 hours upon transfection cells were harvested for RNA extraction.

tag: cell line

tag: sirna

value: siRNA pool against IGF2BP1

tag: passages

value: harvested 72h upon transfection


title: ΔrnhB782::kan-replicate3

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

data_processing:
Library strategy: HydEn-seq
All reads were trimmed for quality and adaptor sequence with cutadapt 1.2.1 (-m 15 -q 10–match-read-wildcards). Pairs with one or both reads shorter than 15 nt were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligonucleotides used in the preparation of these libraries using Bowtie 0.12.8 (DOI: 10.1186/gb-2009-10-3-r25) and the flags -m1 -v2. All pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the sacCer3 S. cerevisiae UCSC reference genome (-m1 -v2 -X10000–best). Single-end alignments were then performed with mate 1 of all unaligned pairs with the flags -m1 -v2.
Genome_build: Escherichia_coli_K_12_DH10B_NCBI_2008-03-17
Supplementary_files_format_and_content: bed: tab-separated bedgraph file format. Column one holds the chromosome name, column two and three hold the nucleotide position, column four holds the read count.

organism: Escherichia coli

source_name: culture

growth_protocol: Cells were streaked out from frozen stocks on LB agar plates containing kanamycin (50μg/ml), spectinomycin (25μg/ml), and zeocin (25μg/ml). 4-6 colonies were diluted in 2-3 ml LB media containing antibiotics and incubated at 37°C overnight. The overnight culture was then diluted 1:X into 25 ml LB media containing antibiotics. Where noted, ciprofloxacin was added to the media to a final concentration of 30 ng/ml. Cells were grown 2-3 hours to reach exponential growth (OD600=0.4-0.6) and then centrifuged to harvest the cell pellet. The saved pellet was used for DNA extraction. For spot survival assays, the bacterial cells were cultured overnight in LB medium containing kanamycin (50μg/ml), spectinomycin (25μg/ml), and zeocin (25μg/ml).  For all strains, a series of serial dilutions were prepared. Then, 10 µl of the suspension was spotted on LB agar plates with overnight incubation at 37°C. For ciprofloxacin experiments, the plates contained 30 ng/ml ciprofloxacin.

extract_protocol:
DNA was extracted using MasterPure™ Complete DNA and RNA Purification Kit (Lucigen, Epicentre, MC85200) and its concentration was measured using Qubit® dsDNA BR Assay Kit (Life technologies, molecular probes, Q32853).
1 µg extracted DNA was mixed with 0.3 M KOH and incubated at 55°C for 2 hours. After ethanol precipitation, the pellet was dissolved in 20 µl elution buffer (Qiagen, 1014609). DNA was denatured by 3 min incubation at 85°C. In the phosphorylation step, 5'-OH end generated after KOH hydrolysis at the ribonucleotide site was phosphorylated using a mix of 10 U 3'-phosphatase minus T4 polynucleotide kinase (BioLabs, M0236L), 2.5 µl of 10X reaction buffer (BioLabs, B0201S), and 2.5 µl of 10 mM adenosine 5'-triphosphate (BioLabs, P0756S) in a total volume of 25 µl. After 30 min incubation at 37°C, the reaction was stopped by 20 min incubation at 65°C. The samples were bead-washed using CleanPCR kit (GC biotech, CPCR-0050). In the ligation step, ARC140 adaptor was ligated to the 5'-OP. Denatured DNA was ligated using a mix of 10 U T4 RNA Ligase 1 (ssRNA Ligase) (BioLabs, M0204S), 5 µl of 10X reaction buffer (BioLabs, B0216S), 0.5 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 25 µl PEG8000(50%), 5 µl of 10 mM [Co(NH3)6]Cl3, and 0.5 µl of 100 µM oligo ARC140 in a total volume of 50 µl. After overnight incubation at the room temperature, the samples were twice beads-washed and dissolved in 14 µl elution buffer. In second strand synthesis step, denatured DNA was polymerized at the room temperature for 5 min using a mix of 4 U T7 DNA polymerase (unmodified) (BioLabs, M0274L), 2 µl of 10X reaction buffer (BioLabs, B0274A), 2 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 0.8 µl of BSA (1 mg/ml) (BioLabs, B9000S), and a heterodimer oligo, ARC76/77 in a total volume of 20 µl. After beads-wash and elution, the libraries were amplified by PCR reactions using KAPA HiFi hotstart readymix (2X) kit (KAPA biosystems, KK2602, 07958935001) with PCR parameters as follows: 95 °C for 45 s, followed by 18 cycles at 95 °C for 15 s, 65 °C for 30 s, and 72 °C for 30 s. The amplified libraries were beads-washed and eluted in 20 µl TE. The library concentration was measured using Qubit® dsDNA HS Assay Kit (Life technologies, molecular probes, Q32854). The library quality was checked by the Agilent 2100 bioanalyzer system (Agilent Technologies). Illumina NextSeq 500 system was used for paired-end sequencing.


title: BE2C_siI1_2


title: RNAseq_ZFSssI_T2_line2_plus_rep2

description: RNAseq data for ZFSssI_T2_line2_plus_rep2


title: Langerhans cell triplicate 3

city: Singapore

first: Christiane

last: Ruedl

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

data_processing:
Illumina bcl2fastq for fastq generation
Sequenced reads were trimmed for adaptor sequence and poor quality reads with Trim_Galore v0.4.5 with parameters -q 20 --stringency 5 --paired
Map trimmed reads to GRCm38 with STAR v2.6.0a using the "multi-sample 2-pass mapping" approach
Gene's read counting with featureCount from the subread package v1.4.6-p5, with parameter -s 0 --primary, on the gene annotation GTF file from GENCODE M19
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression count matrix

source_name: Lymph node antigen presenting cell (sorted cells)

extract_protocol:
Invitrogen Picopure RNA kit
NuGen Ovation® Mouse RNA-Seq System 1-16 protocol

treatment_protocol: Tissue was collected digested by collagenase to single cells, which were sorted into different populations by FACS aria III.

value: Langerhans cell


title: BSPCR_ZFSssI_fwa_nrpd1

description:
PCR amplified DNA
BS-PCR over FWA in ZFSssI_in_fwa_nrpd1_region1to3

data_processing:
Library strategy: BSPCR-seq
BS-PCR-seq analysis was conducted as previously described (Gallego-Bartolome et al., 2019). Briefly, raw sequencing reads with designed BS-PCR primers were first filtered and trimmed based on the primer sequence with customized scripts. Trimmed reads were then mapped to the reference TAIR10 genome with BSMAP (Xi et al., 2009) (v.2.74) by allowing maximal two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described 19. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were excluded for further analysis. To visualize the BS-PCR-seq data, only cytosines within amplified regions were kept and plotted with R (ggplot2 package, https://ggplot2.tidyverse.org/).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
WGBS analysis was performed as previously described (Gallego-Bartolome et al.,2019). Raw reads were first aligned to the reference TAIR10 genome using BSMAP (Xi  et al., 2009) (v2.74) by allowing up to two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described (Cokus  et al.,2008). Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between ZF-SssI and Col-0 were defined similar to before using the R package DMRcaller (Gallego-Bartolome et al.,2019). To increase coverage for DMR analysis, biological replicates were merged for each genotype (ZF-SssI + and ZF-SssI -), each generation (T2 to T5) and each transgenic lines (line 1 and line 2). In general, the whole TAIR10 genome was divided into 200 bp bins, and only bins with at least four cytosines, with each cytosine covered at least four times, more than 10% more methylation in ZF-SssI than Col-0, and a significance level of less than 0.05 were kept. To define hCG DMRs for T2 and T3, the intersect hCG DMRs of two transgenic lines in each generation were first calculated, then the union set of T2 and T3 in the same genotype (either ZF-SssI + or ZF-SssI -) were kept. DMRs overlapping with 200 bp bins in each cluster were considered as DMRs specific for certain clusters. Genomic location for DMRs and mCG equivalent control were annotated using the Homer (Heinz  et al.,2010) ‘annotatePeaks’ function with default parameters. For T4 and T5, two transgenic lines were separated in order to trace the heritable hCG DMRs. To define heritable hCG DMRs, T2 ZF-SssI – were compared with T2 ZF-SssI + and the shared hCG DMRs were considered as heritable hCG DMRs in T2 ZF-SssI –. For T3 ZF-SssI + and ZF-SssI -, hCG DMRs were overlapped with T2 ZF-SssI +. For T4 ZF-SssI – heritable hCG sites, DMRs were first intersected with T3 ZF-SssI + and then intersected with T2 ZF-SssI + while T5 ZF-SssI – heritable hCG sites were further intersected with T4 ZF-SssI – hCG DMRs.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al., 2019, Buenrostro et al., 2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmead et al., 2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al., 2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al., 2014) or deepTools (Ramirez et al., 2014).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
For ChIP-seq data, raw reads were first mapped to the reference TAIR10 genome with Bowtie (Langmead et al.,2009) (v0.12.8) by allowing uniquely mapped reads and maximal two mismatches. PCR-duplicated reads were then filtered with SAMTools (Li  et al.,2009) (v 1.19) . To call ZF-SssI FLAG peaks, the MACS2 calldiff function (Zhang et al.,2008) (v 2.1.2) was used to compare ZF-SssI FLAG ChIP-seq and Col-0 FLAG ChIP-seq data with default parameters. Genomic location and enriched motifs of ZF-SssI FLAG-specific peaks were then annotated with Homer (Heinz et al.,2010) ‘annotatePeaks’ and ‘findMotifGenome’ functions using 100 bp flanking the summit of the peaks. Promoter regions were defined as default in homer (upstream 1kb and downstream 100bp of TSS). ChIP-seq data visualizations were performed using ngs.plot (Shen  et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al.,2019, Buenrostro et al.,2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmeadet al.,2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al.,2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

extract_protocol:
BS-PCR-seq was performed as previously described (GallegoBartolome et al., 2019). Briefly, leaf tissues from adult plants of representative T2 lines containing the ZF-SssI transgene were collected and DNA was extracted following a CTAB-based method. Bisulfite conversion was done using the Epitect Bisulfite Conversion kit (QIAGEN). The following regions of FWA were analyzed: Region 1 (chr4: 13038143-13038272); Region 2 (chr4: 13038356-13038499); Region3 (chr4: 13038568-13038695), which cover fragments of the promoter and 5′ transcribed region of FWA. Pfu Turbo Cx (Agilent) was used to amplify bisulfite-treated DNA using primers containing Illumina adaptors. The primers used are listed in Table S1.
For each sample, individual PCR products from each of the three FWA regions were pooled and purified using AMPure beads (Beckman Coulter) before making the libraries. Libraries were made from purified PCR products using a TruSeq Nano DNA Library Prep kit for Neoprep automated library preparation machine (Illumina), a Kapa DNA hyper kit (Kapa Biosystems) with Illumina TruSeq DNA adapters or an Ovation Ultralow V2 kit (NuGEN). Libraries were sequenced on Illumina HiSeq 2000 or HiSeq 2500.


title: ESC_sssi_sc


title: RNAseq_ZFSssI_T2_line2_plus_rep1

description: RNAseq data for ZFSssI_T2_line2_plus_rep1


title: RNAseq_ZFSssI_T3_line2_plus_rep2

description: RNAseq data for ZFSssI_T3_line2_plus_rep2


title: BE2C_siI1_1


title: BE2C_siC_3

value: Control siRNA


title: ESC_untrt_sc


title: ΔrnhB782::kan-replicate2


title: RNAseq_ZFSssI_T3_line1_minus_rep3

description: RNAseq data for ZFSssI_T3_line1_minus_rep3


title: ΔrnhB782::kan-replicate1


title: DH5alpha-replicate3


title: ESC_untrt_wt


title: RNAseq_ZFSssI_T3_line1_minus_rep2

description: RNAseq data for ZFSssI_T3_line1_minus_rep2


title: MV3_2

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.2) with parameters  -p 6 -N 1 --un-gz
alignments were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -1 -t miRNA -g ID and miRBase annotations (v 21, GRCh 38)
Gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and CPM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file containing CPM values

source_name: melanoma derived cell line

growth_protocol: A549, ES2, MV3, PANC1 and HepG2 cells were cultured in DMEM supplemented with 10% FBS. BE(2)C cells  were cultured in EMEM:DMEM/F12 (1:1) medium supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
For A549, ES2, MV3 and PANC1 cells, 50ng of total RNA served as input using the NEXTflex Small RNA Library Prep Kit v3 (Bioo Scientific). Small RNA-seq libraries for HepG2 and B(E)2C cells were prepared by Novogene (Hong Kong).

treatment_protocol: A549, ES2, MV3, PANC1 and HepG2 cells were harvested for RNA extraction 48 hours upon seeding. BE(2)C cells were harvested 24 hours upon seeding for RNA extraction.

value: parental cell line

value: harvested 48h upon seeding


title: non_targeted


title: RNAseq_ZFSssI_T3_line1_minus_rep4

description: RNAseq data for ZFSssI_T3_line1_minus_rep4


title: DH5alpha-replicate1


title: PANC1_1

source_name: pancreas cancer derived cell line


title: MV3_1


title: RNAseq_ZFSssI_T3_line1_minus_rep1

description: RNAseq data for ZFSssI_T3_line1_minus_rep1


title: RNAseq_ZFSssI_T3_line2_minus_rep4

description: RNAseq data for ZFSssI_T3_line2_minus_rep4


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pJM963-replicate3

value: ciprofloxacin


title: HEPG2_siI1_2

source_name: liver cancer derived cell line


title: ES2_2

source_name: ovarian cancer derived cell line


title: HEPG2_siI1_1


title: RNAseq_ZFSssI_T3_line2_minus_rep3

description: RNAseq data for ZFSssI_T3_line2_minus_rep3


title: HEPG2_siI1_3


title: ES2_1


title: RNAseq_ZFSssI_T3_line2_minus_rep2

description: RNAseq data for ZFSssI_T3_line2_minus_rep2


title: BE2C_siC_2


title: HEPG2_siC_3


title: DH5alpha-replicate2


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pJM963-replicate1


title: BE2C_siC_1


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pJM963-replicate2


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pRW134-replicate3


title: HEPG2_siC_2


title: RNAseq_ZFSssI_T3_line2_minus_rep1

description: RNAseq data for ZFSssI_T3_line2_minus_rep1


title: A549_2

source_name: lung cancer derived cell line


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pRW134-replicate2


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pRW134-replicate1


title: MM.1S_JQKD82_RNAseq, replicate1

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRDA

country: Japan

institute: Kumamoto University

data_processing:
Sequenced reads were aligned to the reference human genome (hg38) using RNA-specific STAR aligner.
Reads were further assigned to respective hg38 refseq of transcripts using the featureCounts tool.
Differential gene expression analysis to compare JQKD82-treated samples with control DMSO-treated samples was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and normalized counts for each sample

source_name: multiple myeloma cell line

growth_protocol: MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

treatment_protocol: MM.1S cells were treated with 1 µM JQKD82 or DMSO for 48h.

value: multiple myeloma cell line


title: RNAseq_ZFSssI_T2_line1_minus_rep4

description: RNAseq data for ZFSssI_T2_line1_minus_rep4


title: MM.1S_JQKD82_RNAseq, replicate2


title: RNAseq_ZFSssI_T2_line1_minus_rep1

description: RNAseq data for ZFSssI_T2_line1_minus_rep1


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pGB2-replicate2


title: HEPG2_siC_1


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pGB2-replicate3


title: MM.1S_DMSO_RNAseq, replicate1


title: MM.1S_DMSO_RNAseq, replicate2


title: Δ( umuDC)596::ermGT ΔdinB61::ble ΔpolB::ΩSpc ΔrnhB782::kan with pGB2-replicate1


title: RNAseq_ZFSssI_T2_line2_minus_rep3

description: RNAseq data for ZFSssI_T2_line2_minus_rep3


title: RNAseq_ZFSssI_T2_line1_minus_rep3

description: RNAseq data for ZFSssI_T2_line1_minus_rep3


title: RNAseq_ZFSssI_T2_line2_minus_rep4

description: RNAseq data for ZFSssI_T2_line2_minus_rep4


title: A549_1


title: RNAseq_ZFSssI_T2_line2_minus_rep1

description: RNAseq data for ZFSssI_T2_line2_minus_rep1


title: RNAseq_ZFSssI_T2_line2_minus_rep2

description: RNAseq data for ZFSssI_T2_line2_minus_rep2


title: P2 H126D mutant Clone D rep2

first: Adrian

middle: Kee Keong

last: Teo

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

institute: IMCB, A*STAR

description: iP002d 2

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.33, and then mapped to hg19 whole genome using tophat-2.0.14
Raw counts were calculated using HtSeq-count
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human skin fibroblast

growth_protocol: HiPSCs generated from human fibroblast cells and H9 ESCs were cultured at 37°C with 5% CO2 in DMEM/F-12 supplemented with 15 mM HEPES (STEMCELL Technologies), 20% KnockOut™ serum replacement (KOSR), L-glutamine, NEAA (Life Technologies) and 10 ng/ml FGF2 (Miltenyi Biotec). HPSCs were seeded on irradiated CF-1 mouse embryonic fibroblasts (MEFs) and hiPSC media was replaced every 24 hours. HPSCs were split when the cells reached 80% confluency.

extract_protocol:
RNA was harvested from cells using the PrepEase RNA Spin Kit (Affymetrix)  mRNA was first isolated with poly dT beads from 1-10µg of total RNA. RNA-seq libraries were prepared using the NEXTflex Rapid Directional RNA-SEQ Kit (dUTP-Based) v2 as per manufacturer's direction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HiPSCs and H9 cells were differentiated along the pancreatic lineage into endocrine progenitors and β-like cells as described previously (Pagliuca et al., 2014), with some modifications. Cells were dissociated into single cells using TrypLETM Express Enzyme and passed through 40µM cell strainer before being re-plated at 106cells/ml in mTESR medium supplemented with 10μM Y-27632 in suspension culture on non-treated 6 well plates (Eppendorf). Cells were cultured at 37°C with 5% CO2 on a rotating platform. Differentiation was initiated 48h after cell dissociation (designated as “D0”). In general, 2–3 independent hiPSC lines per subject were used in experiments, with biological triplicates analysed for each line.

value: female


title: P2 H126D mutant Clone D rep1

description: iP002d 1


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782 ::kan with pJM963-replica3


title: P2 H126D mutant Clone D rep3

description: iP002d 3


title: RNAseq_col_for_T2_T3_rep4

description: RNAseq data for col_for_T2_T3_rep4


title: P2 H126D mutant Clone B rep2

description: iP002b 2


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pRW134-replicate3


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782 ::kan with pJM963-replica2


title: P2 H126D mutant Clone B rep1

description: iP002b 1


title: RNAseq_col_for_T2_T3_rep3

description: RNAseq data for col_for_T2_T3_rep3


title: RNAseq_col_for_T2_T3_rep2

description: RNAseq data for col_for_T2_T3_rep2


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pGB2-replicate2


title: P2 H126D mutant Clone A rep3

description: iP002a 3


title: P2 H126D mutant Clone A rep2

description: iP002a 2


title: RNAseq_col_for_T2_T3_rep1

description: RNAseq data for col_for_T2_T3_rep1


title: P2 H126D mutant Clone A rep1

description: iP002a 1


title: lexA51(Def)recA730Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pRW134-replicate3


title: lexA51(Def)recA730Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pRW134-replicate2


title: lexA51(Def)recA730Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pRW134-replicate1


title: P2 H126D mutant Clone B rep3

description: iP002b 3


title: WGBS_ZFSssI_T3_line2_minus_rep1

description: WGBS for ZFSssI_T3_line2_minus_rep1

extract_protocol:
For T2 and T3 WGBS, DNA from inflorescences of adult plants was extracted following a CTAB-based method.  For T4 and T5 WGBS, DNA from inflorescences of adult plants was extracted using the DNeasy Plant Mini Kit (QIAGENE).
For T2 and T3 WGBS, 100 ng of DNA was sheared to 200 bp with a Covaris S2 (Covaris) and used for library preparation using the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. For T4 and T5 WGBS, 250 ng of DNA was sheared to 200 bp with a Covaris S2 (Covaris) and used for library preparation using the Epitect Bisulfite Conversion kit (QIAGEN) and the Kapa DNA hyper kit (Kapa Biosystems) with Illumina TruSeq DNA adapters following the manufacturer’s instructions.


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pRW134-replicate2


title: P1 H126D homozygous mutant rep 1

description: iP001c -/-


title: WGBS_ZFSssI_T2_line2_minus_rep2

description: WGBS for ZFSssI_T2_line2_minus_rep2


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pGB2-replicate3


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM964-replicate2


title: WGBS_ZFSssI_T3_line2_plus_rep1

description: WGBS for ZFSssI_T3_line2_plus_rep1


title: P1 H126D mutant Clone C rep3

description: iP001c 3


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM1282-replicate3


title: P1 H126D mutant Clone B rep3

description: iP001b 3


title: P1 H126D mutant Clone C rep2

description: iP001c 2


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM964-replicate3


title: P1 H126D mutant Clone C rep1

description: iP001c 1


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM964-replicate1


title: P1 H126D mutant Clone B rep2

description: iP001b 2


title: WGBS_ZFSssI_T2_line2_plus_rep2

description: WGBS for ZFSssI_T2_line2_plus_rep2


title: WGBS_ZFSssI_T2_line2_minus_rep1

description: WGBS for ZFSssI_T2_line2_minus_rep1


title: WGBS_ZFSssI_T2_line2_plus_rep1

description: WGBS for ZFSssI_T2_line2_plus_rep1


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM1282-replicate1


title: WGBS_ZFSssI_T3_line2_minus_rep2

description: WGBS for ZFSssI_T3_line2_minus_rep2


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM1282-replicate2


title: WGBS_ZFSssI_T3_line1_minus_rep2

description: WGBS for ZFSssI_T3_line1_minus_rep2


title: P1 H126D mutant Clone A rep2

description: iP001a 2


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pGB2-replicate3


title: P1 H126D mutant Clone B rep1

description: iP001b 1


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pGB2-replicate2


title: WGBS_ZFSssI_T3_line2_plus_rep2

description: WGBS for ZFSssI_T3_line2_plus_rep2


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pGB2-replicate1


title: WGBS_ZFSssI_T2_line1_minus_rep2

description: WGBS for ZFSssI_T2_line1_minus_rep2


title: RNAseq_ZFSssI_T2_line1_minus_rep2

description: RNAseq data for ZFSssI_T2_line1_minus_rep2


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM963-replicate3


title: iPSC Control iAG clone B rep3

description: iAgb 3

value: Wild Type


title: P1 H126D mutant Clone A rep1

description: iP001a 1


title: WGBS_ZFSssI_T2_line1_minus_rep1

description: WGBS for ZFSssI_T2_line1_minus_rep1


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM963-replicate2


title: iPSC Control iAG clone B rep1

description: iAgb 1


title: lexA51(Def)recA730 Δ(umuDC)596::ermGT ΔdinB61::bleΔrnhB782::kan with pJM963-replicate1


title: WildType H9 rep3

description: H9 3

source_name: human embryonic stem cell line


title: WGBS_ZFSssI_T3_line1_plus_rep1

description: WGBS for ZFSssI_T3_line1_plus_rep1


title: WGBS_ZFSssI_T2_line1_plus_rep2

description: WGBS for ZFSssI_T2_line1_plus_rep2


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pRW134-replicate1


title: WGBS_ZFSssI_T2_line1_plus_rep1

description: WGBS for ZFSssI_T2_line1_plus_rep1


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782 ::kan with pJM963-replicate3


title: WGBS_ZFSssI_T3_line1_plus_rep2

description: WGBS for ZFSssI_T3_line1_plus_rep2


title: WildType H9 rep2

description: H9 2


title: A9091_Input

status: Public on Mar 21 2021

type: genomic

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

hyb_protocol: Hybridization  to Affymetrix's Human Promoter 1.0R GeneChips at 45 °C for 16 hrs in an Affymetrix GeneChip Hybridization Oven 640 was performed exactly as recommended by the manufacturer's protocol.

scan_protocol: The GeneChips were scanned following hybridization on an Affymetric GeneChip Scanner 3000 7G attached to a Dell Precision Computer 670.

data_processing:
CEL files generated by the scanner were imported into Partek Genomics Suite microarray analysis software for analysis using the workflow for tiling arrays.  The default method of normalization for tiling arrays includes: Adjust for probe sequence, RMA background correction, quantile normalization, and log (base 2) transformation.  Additional analyses included ANOVA on IP (antibody to MeC pulldown) and diagnostic status.
Probe intensity data for each enriched region in every sample were imported into MeV software for further analyses to identify potential classifier genes based on differential methylation.  These additional analyses utilized the modules for: Pavlidis Template Matching and Uncorrelated Shrunken Centroids.
results file description: Matrix table showing normalized probe intensities for each sample after subtraction of corresponding intensities from "Input" DNA

label: biotin

source_name: lymphoblastoid cell line

label_protocol: Biotin labeling of the amplified and fragmented DNA was performed following Affymetrix's labeling protocol for the human promoter array.

growth_protocol: LCL obtained from the Autism Genetic Resource Exchange were cultured in DMEM medium supplemented with 15% FBS and 1% penicillin-streptomycin.

extract_protocol: Genomic DNA was extracted from the LCL using Qiagen's DNeasy Blood and Tissue Kit according to the manufacturer's protocol.  Methylation-enriched DNA was obtained from a portion of the DNA extract using Epigentek's Methylamp Methylated DNA Capture Kit, according to the manufacturer's protocol.  The remaining DNA was used as "Input DNA" which was separately hybridized to another Promoter GeneChip.  The isolated DNA was sonicated using 5-10 brief (10-12 sec) pulses at level 2 with a probe tip sonicator.  The sonicated DNA was then treated with RNase before library preparation, amplification and fragmentation of the dsDNA prior to labeling with biotin, all according to Affymetrix's protocols for preparation of DNA samples for hybridization on the human promoter arrays.

treatment_protocol: Cells were not treated with anything prior to DNA extraction

value: DNA isolation, sonication,  5-10 brief (10-12 sec) pulses, no antibody

tag: antibody

tag: disease status

value: Autistic

tag: Sex

value: M

tag: race/ethnicity

value: Asian


title: A9091_MeDIP

value: DNA isolation, sonication, 5-10 brief (10-12 sec) pulses, anti-methylC

value: Anti-MeC


title: C9089_MeDIP

value: Control

value: Not Available


title: A8990_Input

value: F

value: White, Non-Hispanic


title: A8990_MeDIP


title: C9089_Input


title: lexA51(Def) ΔumuDC596::ermGT ΔdinB61::ble ΔrnhB782::kan with pGB2-replicate1


title: WGBS_ZFSssI_T3_line1_minus_rep1

description: WGBS for ZFSssI_T3_line1_minus_rep1

tag: tissue

value: inflorescence

value: Columbia 0


title: C8989_Input


title: C8989_MeDIP


title: C8748_Input


title: C8748_MeDIP


title: A8746_Input


title: iPSC Control iAG clone B rep2

description: iAgb 2

value: male


title: C5803_MeDIP


title: A8746_MeDIP


title: C5803_Input


title: A5620_Input

value: White, Hispanic


title: WildType H9 rep1

description: H9 1


title: C5619_Input


title: A5576_Input


title: C5619_MeDIP


title: C5575_Input


title: A5249_MeDIP

value: Unknown


title: C5248_Input


title: A5576_MeDIP


title: A5229_Input


title: A5229_MeDIP


title: C5034_Input


title: A5035_Input


title: C5248_MeDIP


title: A4912_Input


title: A4912_MeDIP


title: A5035_MeDIP


title: C5034_MeDIP


title: C4910_MeDIP


title: A5620_MeDIP


title: C3839_MeDIP

value: Black, Non-Hispanic


title: A3847_Input


title: C3839_Input


title: A3847_MeDIP


title: A3673_Input


title: A3650_Input


title: A3673_MeDIP


title: C3670_MeDIP


title: C5575_MeDIP


title: A3650_MeDIP


title: A5249_Input


title: C3649_MeDIP


title: C3649_Input


title: C3670_Input


title: A3437_MeDIP


title: C3406_Input


title: C2684_MeDIP


title: C3406_MeDIP


title: A3437_Input


title: C2684_Input


title: A2683_Input


title: A2683_MeDIP


title: C2553_MeDIP

value: Multi, Non-Hispanic


title: C2553_Input

value: DNA isolation, sonication,  5-10 brief (10-12 sec) pulses, no antibody


title: C2482_Input


title: A2555_MeDIP

value: Autistic


title: C4910_Input


title: C2482_MeDIP

value: M


title: A2480_Input


title: A2480_MeDIP


title: C2022_Input


title: A2044_MeDIP


title: A2044_Input


title: A1699_Input


title: A1699_MeDIP


title: C1698_Input


title: C2022_MeDIP


title: C588_MeDIP


title: A589_MeDIP


title: A489_Input


title: C1698_MeDIP


title: C588_Input


title: A489_MeDIP


title: C25_Input


title: C487_Input


title: C487_MeDIP


title: A2555_Input


title: A24_Input


title: A24_MeDIP


title: C25_MeDIP


title: A589_Input


title: 5644876029_I

type: RNA

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized by Bioconductor (3.0) lumi pipeline with loess normalization

label: biotin-SA Cy3

source_name: Pseudomyxoma peritonei

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V3 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

tag: diagnosis

value: Pseudomyxoma peritonei

value: liver

tag: surgery type

value: Debulking

tag: cc score

tag: unique sample barcode (disease type-patient3digit-surgery2digit-sample2digit)


title: 5993427080_L


title: 8508870044_L

source_name: Colorectal cancer

value: Colorectal cancer

value: Debulking CRC


title: 6303256082_H


title: 3998532084_B


title: 3998532084_C

value: Cytoreduction


title: 3998532086_D


title: sputum transcriptome for subject 11630 in time point 6month

city: Collegeville

first: Zhang

last: Wang

state: PA

address: 1250 S Collegeville Rd

institute: GlaxoSmithKline R&D

description:
Gene expression data for COPD subject 11630 in time point 6month
EA13101_373974_HG-U133_PLUS_2_11630V2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The raw microarray data (CEL files) were corrected for background signal, quantile normalized and summarized using robust multiarray average (RMA) normalization to generate probeset-level microarray data using Array Studio v10.0 (OmicSoft, Cary, NC, USA).

source_name: COPD patients sputum_time point 6month

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: subject id

tag: subject status

value: chronic obstructive pulmonary disease (COPD) patient

tag: timepoint

value: sputum


title: sputum transcriptome for subject 10810 in time point Stable

description:
Gene expression data for COPD subject 10810 in time point Stable
EA13101_373969_HG-U133_PLUS_2_10810V1

source_name: COPD patients sputum_time point Stable

value: Stable


title: sputum transcriptome for subject 3235 in time point E0

description:
Gene expression data for COPD subject 3235 in time point E0
EA13101_373972_HG-U133_PLUS_2_3235E0

source_name: COPD patients sputum_time point E0


title: 3998532086_C


title: 3998532084_D


title: 3998532075_C


title: 3998532075_G


title: 3998532086_E


title: 3998532086_B


title: sputum transcriptome for subject 14440 in time point E0

description:
Gene expression data for COPD subject 14440 in time point E0
EA13101_373975_HG-U133_PLUS_2_14440E0


title: sputum transcriptome for subject 11630 in time point E6

description:
Gene expression data for COPD subject 11630 in time point E6
EA13101_373968_HG-U133_PLUS_2_11630E6

source_name: COPD patients sputum_time point E6


title: 3998532084_E


title: 3998532081_H


title: sputum transcriptome for subject 12577 in time point E6

description:
Gene expression data for COPD subject 12577 in time point E6
EA13101_373973_HG-U133_PLUS_2_12577E6


title: sputum transcriptome for subject 6036 in time point E0

description:
Gene expression data for COPD subject 6036 in time point E0
EA13101_373966_HG-U133_PLUS_2_6036E0


title: 5552277092_K


title: 8508870044_K


title: sputum transcriptome for subject 14412 in time point E0

description:
Gene expression data for COPD subject 14412 in time point E0
EA13101_373967_HG-U133_PLUS_2_14412E0


title: sputum transcriptome for subject 9910 in time point 6month

description:
Gene expression data for COPD subject 9910 in time point 6month
EA13101_373976_HG-U133_PLUS_2_9910V2


title: 3998532081_G


title: sputum transcriptome for subject 4542 in time point Stable

description:
Gene expression data for COPD subject 4542 in time point Stable
EA13101_373971_HG-U133_PLUS_2_4542V1


title: sputum transcriptome for subject 12173 in time point Stable

description:
Gene expression data for COPD subject 12173 in time point Stable
EA13101_373964_HG-U133_PLUS_2_12173V1


title: 3998532081_F


title: sputum transcriptome for subject 16534 in time point Stable

description:
Gene expression data for COPD subject 16534 in time point Stable
EA13101_373965_HG-U133_PLUS_2_16534V1


title: 3998532081_D


title: 5644876029_L


title: 3998532081_C


title: 3999305039_B


title: 3998532081_E


title: sputum transcriptome for subject 1584 in time point 6month

description:
Gene expression data for COPD subject 1584 in time point 6month
EA13101_373962_HG-U133_PLUS_2_1584V2


title: sputum transcriptome for subject 7984 in time point Stable

description:
Gene expression data for COPD subject 7984 in time point Stable
EA13101_373961_HG-U133_PLUS_2_7984V1


title: 5552277094_G


title: sputum transcriptome for subject 13943 in time point 6month

description:
Gene expression data for COPD subject 13943 in time point 6month
EA13101_373970_HG-U133_PLUS_2_13943V2


title: sputum transcriptome for subject 12707 in time point Stable

description:
Gene expression data for COPD subject 12707 in time point Stable
EA13101_373958_HG-U133_PLUS_2_12707V1


title: 3999305039_A


title: 9992580074_L


title: sputum transcriptome for subject 7087 in time point E2

description:
Gene expression data for COPD subject 7087 in time point E2
EA13101_373954_HG-U133_PLUS_2_7087E2

source_name: COPD patients sputum_time point E2


title: 5552277088_L


title: sputum transcriptome for subject 7087 in time point E6

description:
Gene expression data for COPD subject 7087 in time point E6
EA13101_373959_HG-U133_PLUS_2_7087E6


title: 5552277092_J


title: sputum transcriptome for subject 16389 in time point Stable

description:
Gene expression data for COPD subject 16389 in time point Stable
EA13101_373956_HG-U133_PLUS_2_16389V1


title: 3998532075_E


title: sputum transcriptome for subject 9910 in time point E0 series 1

description:
Gene expression data for COPD subject 9910 in time point E0 series 1
EA13101_373957_HG-U133_PLUS_2_9910E0181113


title: sputum transcriptome for subject 15116 in time point Stable

description:
Gene expression data for COPD subject 15116 in time point Stable
EA13101_373955_HG-U133_PLUS_2_15116V1


title: sputum transcriptome for subject 11630 in time point E0

description:
Gene expression data for COPD subject 11630 in time point E0
EA13101_373952_HG-U133_PLUS_2_11630E0


title: 3998532086_A


title: sputum transcriptome for subject 4542 in time point E2

description:
Gene expression data for COPD subject 4542 in time point E2
EA13101_373960_HG-U133_PLUS_2_4542E2


title: Aorta , Chow1

city: Socorro

first: Rebecca

last: Reiss

state: NM

address: 801 Leroy Place

department: Biology

institute: New Mexico Institute of Mining and Technology

data_processing:
Base calling software Casava
FASTQC quality control
Genomic Mapping and Alignment Program (GMP) and Tophat with  splice site junction mapping (SJM)
Quantitated using HTSeq count
Statistical Analyais with EdgeR
Data Filtered using Ziph's Law
Genome_build: ENSEMBL release 79 of the rat genome (Rnor_5.0; GCA_000001895.3)
Supplementary_files_format_and_content: Rat_DIet.dat: Joined output of edgeR for GMP and SJM. 9,573 rows. Column (C) 1: Ensembl Gene ID, C2: Position in genome, C3: Gene symbol, C4: Gene Title, C5: Log2 fold-change (FC) GMP, C6: Log2 FC SJM, C7: Log10 Counts per million (CPM) GMP, C8: log10 CPM SJM, C9: PValue GMP, C10: PValue SJM, C11: p(adj) GMP, C12:  p(adj) SJM, C13: Sum raw reads GMP, C14: Sum raw reads SJM
GMAP_Gene_Matrix_Counts.dat: Htseq count from GMAP Column (C) 1: Ensembl Gene ID, C2: Chow 1, C3: Chow2, C4: HFD1, C5:HDF2
TopHat_Gene_Matrix_Counts.dat: Htseq count from Tophat Htseq count from GMAP Column (C) 1: Ensembl Gene ID, C2: Chow 1, C3: Chow2, C4: HFD1, C5:HDF2

organism: Rattus norvegicus

source_name: Aorta

growth_protocol: Rats were maintained on the respective diets for 6 weeks and the food was replaced every 3-4 days to prevent spoiling. All animals had access to food and water ad libitum and were housed in identical cages in the same animal facility and exposed to a 12:12 hour light dark cycle.

extract_protocol:
Total RNA extracted with Qiagen RNeasy kit
Illumina mRNA-SeqPrep Kit RS-100-0801: Two round polyA selection using polyT beads, random fragmentation of RNA, random priming to make cDNA, ligation of bar coded sequencing primers, size selection by electrophoresis
Sequenced on Illumina Genome Analyzer Iix Platform, single read cluster generation kit, GD-203-2001, Standard sequencing kit, 36 cycle, FC-104-3001

treatment_protocol: Four rats per diet dissected, two aorta pooled per sample, frozen at -80°C

tag: strain

value: Sprague-Dawley

value: male

value: Aorta

tag: age

value: 5-6 weeks

tag: treatment

value: Chow diet:18.9% protein, 57.33% carbohydrates, 5% fat


title: Aorta , HFD1

value: High fat diet:20% protein, 20% carbohydrates, 60% fat


title: Aorta , HFD2


title: Aorta , Chow2


title: NR5_pre

city: Palo Alto

first: Haiyu

last: Zhang

state: CA

address: 300 Pasteur Dr.

institute: Stanford University

data_processing:
Sequence reads, after filtering for read quality, were re-filtered by fastx (fastx_artifacts_filter) (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Reads that passed the filter were mapped to the human transcriptome hg19 (refMrna, downloaded from the UCSC genome browser, http://www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches (Guo X, 2013, https://doi.org/10.1186/bcr3586).
Total numbers of sequence reads (read counts) for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix (Guo X, 2013, https://doi.org/10.1186/bcr3586).
Genome_build: Human transcriptome hg19
Supplementary_files_format_and_content: The processed data files are text files. These files can be opened in Microsoft Excel using Text Import Wizard (select: Delimited, Tab, Text for each step to open the file). It contains gene symbol in column A and raw read counts of each gene in column B.

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated using EZNA PX blood RNA kit (Omega bio-tek), and then concentrated using RNA clean & concentrator-5 (ZYMO research).
Alpha- and beta-globin mRNAs were depleted from total RNA samples using GLOBINclear-human globin mRNA removal kit (Life Technologies) according to manufacturer’s instruction. 3SEQ libraries were constructed based on previously published method (Beck AH, 2010, https://doi.org/10.1371/journal.pone.0008768) with modifications. Briefly, after globin mRNA reduction, remaining mRNAs were enriched by poly-A selection using Dynabeads mRNA purification kit (Life Technologies), and heat-fragmented to 100-200 bases. First-strand cDNAs were synthesized using Superscript III reverse transcriptase with Rd2SP-oligodT primer, followed by second-strand cDNA synthesis. Adenine was added to the 3’-end of the double-stranded cDNA and then ligated to the P5-R1SP adapter. The ligated product was amplified by PCR for 15 cycles using primers P5-Rd1SP and P7-index-Rd2SP. Six Illumina indexes, each with six bases, were introduced in the P7 primer. Quality of the library was examined using Agilent DNA 1000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were quantified by Qubit 2.0 fluorometer using Qubit dsDNA BR assay kit (Life technologies). Six samples with different indexes were pooled together and submitted for sequencing at Stanford Center for Genomics and Personalized Medicine. Index associated 36 bp sequences from the P5 primer end, providing the 5’-end sequences of the polyA-containing mRNA fragments, were generated using Illumina HiSeq 2000 system (Illumina, San Diego, CA).
RNA-Seq, specifically, 3’-end sequencing for expression quantification (3SEQ)

treatment_protocol: With informed consent, patients enrolled in this study had been receiving eltrombopag monotherapy (75 mg daily via oral administration) for the management of chronic ITP during the period of blood sample collections.

tag: disease

value: Immune thrombocytopenia, chronic

value: Eltrombopag

tag: treatment time point

value: Pretreatment

tag: response to treatment

value: Nonresponse


title: NR5_1mon

value: 1 month into treatment


title: NR4_1mon


title: sputum transcriptome for subject 4542 in time point E6

description:
Gene expression data for COPD subject 4542 in time point E6
EA13101_373950_HG-U133_PLUS_2_4542E6


title: sputum transcriptome for subject 9910 in time point Stable

description:
Gene expression data for COPD subject 9910 in time point Stable
EA13101_373951_HG-U133_PLUS_2_9910V1


title: sputum transcriptome for subject 12386 in time point Stable

description:
Gene expression data for COPD subject 12386 in time point Stable
EA13101_373946_HG-U133_PLUS_2_12386V1


title: NR4_1wk

value: 1 week into treatment


title: 3998532081_A

value: Pseudomyxoma peritonei

value: liver

value: cytoHipec

tag: ronnet histology

value: DPAM


title: 3998532075_J

value: Colorectal cancer

value: Debulking CRC


title: 5552277094_A


title: sputum transcriptome for subject 6629 in time point 6month

description:
Gene expression data for COPD subject 6629 in time point 6month
EA13101_373947_HG-U133_PLUS_2_6629V2

value: chronic obstructive pulmonary disease (COPD) patient

value: sputum


title: sputum transcriptome for subject 3742 in time point E2

description:
Gene expression data for COPD subject 3742 in time point E2
EA13101_373948_HG-U133_PLUS_2_3742E2


title: 3998532084_L

value: PMCA


title: sputum transcriptome for subject 6036 in time point 6month

description:
Gene expression data for COPD subject 6036 in time point 6month
EA13101_373943_HG-U133_PLUS_2_6036V2


title: 5552277026_L

value: cytoreduction


title: 3998532084_A


title: 9992580074_F


title: 5552277092_L


title: 8508870021_L


title: 9992580074_I


title: 9992580074_H


title: sputum transcriptome for subject 13955 in time point Stable

description:
Gene expression data for COPD subject 13955 in time point Stable
EA13101_373945_HG-U133_PLUS_2_13955V1

value: Stable


title: sputum transcriptome for subject 9910 in time point E2

description:
Gene expression data for COPD subject 9910 in time point E2
EA13101_373942_HG-U133_PLUS_2_9910E2


title: 6303256082_K


title: sputum transcriptome for subject 11364 in time point Stable

description:
Gene expression data for COPD subject 11364 in time point Stable
EA13101_373941_HG-U133_PLUS_2_11364V1


title: NR3_1mon

value: Immune thrombocytopenia, chronic


title: NR4_pre

value: Eltrombopag


title: NR3_1wk


title: 6303256082_L


title: 3998532075_B


title: 6303256082_I


title: NR2_1mon


title: NR3_pre

value: Pretreatment


title: NR2_1wk

value: Nonresponse


title: sputum transcriptome for subject 3742 in time point Stable

description:
Gene expression data for COPD subject 3742 in time point Stable
EA13101_373940_HG-U133_PLUS_2_3742V1


title: 9992580074_E


title: 9992580074_B


title: NR2_pre


title: 9992580074_D


title: 9992580074_K


title: sputum transcriptome for subject 14412 in time point Stable

description:
Gene expression data for COPD subject 14412 in time point Stable
EA13101_373939_HG-U133_PLUS_2_14412V1


title: 3998532086_L


title: 3998532086_K


title: sputum transcriptome for subject 4541 in time point Stable

description:
Gene expression data for COPD subject 4541 in time point Stable
EA13101_373938_HG-U133_PLUS_2_4541V1


title: UMUC3-c31, Stimulated, Biological Replicate 5

city: Los Angeles

first: Dan

last: Theodorescu

address: 8700 Beverly Blvd., Davis Building, Rm 3057

institute: Cedars Sinai Medical Center

description: AR ChIP

data_processing:
Alignment: Novoalign, Human genome (hg38), duplicate reads removed
Peak identification: Narrow peak detection, MACS2; negative input per sample used for background peak estimation
Motif Analysis: RSAT oligo-analysis; binomial significance >10
Genome_build: hg38
Supplementary_files_format_and_content: BED

growth_protocol: Cells were serum starved for 24 hours prior to treatment using charcoal stripped serum (CSS).  After steroid washout, cells were treated with the described compounds for 24 hours prior to total DNA isolation.

extract_protocol: 1% PFA fixation, DNA shearing, treatment with IgG or AR specific antibody and immunoprecipitation. Anti-Androgen Receptor: Santa Cruz Biotechnology; SC-816X (rabbit polyclonal). Normal Rabbit Serum: Jackson ImmunoResearch; 011-000-001.  1x50 sequencing

treatment_protocol: 24 hour treatment with above specified reagents.

tag: cell line

tag: sample type

value: AR ChIP

tag: stimulation

tag: chip antibody

value: anti-AR


title: 9992580074_C

tag: diagnosis

value: Pseudomyxoma peritonei

tag: tissue

tag: surgery type


title: sputum transcriptome for subject 3742 in time point E0

description:
Gene expression data for COPD subject 3742 in time point E0
EA13101_373936_HG-U133_PLUS_2_3742E0_4

tag: subject id


title: 9992580074_A

value: liver

tag: cc score

tag: unique sample barcode (disease type-patient3digit-surgery2digit-sample2digit)


title: 3998532086_J

value: cytoHipec


title: 3998532086_H

value: DPAM


title: sputum transcriptome for subject 4541 in time point 6month

description:
Gene expression data for COPD subject 4541 in time point 6month
EA13101_373934_HG-U133_PLUS_2_4541V2

tag: subject status

tag: timepoint


title: sputum transcriptome for subject 10611 in time point Stable

description:
Gene expression data for COPD subject 10611 in time point Stable
EA13101_373935_HG-U133_PLUS_2_10611V1


title: sputum transcriptome for subject 9910 in time point E0 series 2

description:
Gene expression data for COPD subject 9910 in time point E0 series 2
EA13101_373933_HG-U133_PLUS_2_9910E0220114


title: 3998532086_F


title: 6303256082_J


title: 3998532086_G


title: NR1_1wk

tag: treatment

value: 1 week into treatment


title: NR1_1mon

tag: disease

value: 1 month into treatment


title: UMUC3-c31, Stimulated, Biological Replicate 4

description: AR ChIP


title: UMUC3-c31, Stimulated, Biological Replicate 3

description: AR ChIP


title: NR1_pre

tag: treatment time point


title: R12_1mon

tag: response to treatment

value: Response


title: UMUC3-c31, Stimulated, Biological Replicate 1

description: AR ChIP


title: UMUC3-c31, Stimulated, Biological Replicate 2

description: AR ChIP


title: R11_1mon


title: R12_pre


title: UMUC3-c31, Stimulated, Input sample

description: Input-ChIP

source_name: R1881 Stimulated-input.R1.fq.gz

value: Input-control (Stimulated)

value: none (input)


title: 9553572040_L

tag: ronnet histology

value: PMCA


title: sputum transcriptome for subject 13943 in time point Stable

description:
Gene expression data for COPD subject 13943 in time point Stable
EA13101_373963_HG-U133_PLUS_2_13943V1

value: chronic obstructive pulmonary disease (COPD) patient

value: Stable

value: sputum


title: 9992580074_G

value: Debulking


title: 9553572040_K


title: UMUC3-c31, Unstimulated, Biological Replicate 5

description: Control

tag: cell line

value: Control

value: unstimulated

value: anti-IgG


title: R11_1wk

value: Immune thrombocytopenia, chronic

value: Eltrombopag


title: UMUC3-c31, Unstimulated, Biological Replicate 4

description: Control

tag: sample type


title: 5552277094_H

value: Pseudomyxoma peritonei

value: liver

value: cytoHipec


title: R10_1mon

value: 1 month into treatment


title: R11_pre

value: Pretreatment

value: Response


title: 3998532086_I

value: DPAM


title: 3998532075_D

value: cytoreduction


title: sputum transcriptome for subject 4542 in time point E0

description:
Gene expression data for COPD subject 4542 in time point E0
EA13101_373932_HG-U133_PLUS_2_4542E0

value: chronic obstructive pulmonary disease (COPD) patient


title: 3998532084_H


title: 9534190125_J


title: 9534190125_L


title: 9534190125_K


title: 3998532084_G

value: PMCA


title: 3998532075_A


title: 9534190124_K


title: R10_1wk

value: 1 week into treatment


title: 9534190124_L


title: 3998532081_B


title: 3998532081_I


title: 9992580074_J


title: 3998532081_L


title: R10_pre


title: 3999305039_I


title: UMUC3-c31, Unstimulated, Biological Replicate 1

description: Control

tag: stimulation


title: UMUC3-c31, Unstimulated, Biological Replicate 3

description: Control

tag: chip antibody


title: UMUC3-c31, Unstimulated, Input sample

description: Input-Control

value: Input-control (Unstimulated)

value: none (input)


title: 3998532081_K

tag: diagnosis


title: UMUC3-c31, Unstimulated, Biological Replicate 2

description: Control

value: Control

value: unstimulated


title: R9_pre

value: Immune thrombocytopenia, chronic


title: R8_1mon

value: Eltrombopag


title: R9_1wk


title: R8_1wk


title: RNA_mouse_NK_WT_UNSTIM_3

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36).
Transcript quantification was performed by salmon (v0.10.2) using arguments '-l IU --gcBias' and tximport (v1.8.0 or v1.10.1) using the UCSC mm10 known gene transcript assembly (v9).
Supplementary_files_format_and_content: Text files are raw estimated gene-level counts (1 count = 1 read pair) as quantified by salmon (v0.10.2) and imported by tximport (v1.8.0). Also provided are gene IDs (Entrez and Ensembl), gene names, and gene descriptions.

source_name: splenic NK cells

extract_protocol:
RNA was isolated from sorted and stimulated cell populations using TRIzol (Invitrogen) or the PicoPure RNA Isolation Kit (Thermo Fisher)
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.705-2ng total RNA with RNA integrity numbers ranging from 6.5 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech catalog # 63488), with 12 cycles of amplification. Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or HiSeq 2500 in Rapid mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2, respectively (Illumina).  An average of 37 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 42% to 70%.

treatment_protocol: Mouse NK cells were stimulated for 3 hr with 20 ng/ml recombinant mouse IL-12, 10 ng/ml recombinant mouse IL-18, or both.

tag: cell type

value: NK cells

tag: genotype

value: WT

tag: condition

value: UNSTIM

tag: replicate


title: R8_pre


title: RNA_mouse_NK_WT_IL18_3


title: RNA_mouse_NK_WT_UNSTIM_2


title: RNA_mouse_NK_WT_UNSTIM_1


title: 5993427080_K

value: Pseudomyxoma peritonei

tag: tissue

value: liver

tag: surgery type

value: cytoHipec

tag: cc score

tag: unique sample barcode (disease type-patient3digit-surgery2digit-sample2digit)


title: Stem RNA-seq

city: Wageningen

first: Esmer

last: Jongedijk

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

data_processing:
De-multiplexing of obtained sequences was done using CASAVA 1.8.1. software.
Reads were mapped on gene models from Salvia dorisiana with CLC Genomics Workbench 8.0 (Qiagen), using the following settings: One reference sequence per transcript; Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.9; Similarity fraction = 0.9; Global alignment = No; Strand specific = Both; Maximum number of hits for a read = 10; Count paired reads as two = No; Expression value = RPKM.
Supplementary_files_format_and_content: Selected genes with characteristics in this study (Excel), Gene models from Salvia dorisiana on which expression data have been mapped (MultiFasta)

organism: Salvia dorisiana

source_name: Stem

growth_protocol: Salvia dorisiana plants were grown in the greenhouse under a 16h photoperiod, 19-21°C, 60% humidity. Plants were multiplied by cutting.

extract_protocol:
Plant tissues were grinded and RNA was isolated with the RNeasy Plant Mini kit (Qiagen) according to the manufacturer protocol. Trichomes were grinded with a pestle and mortar while still frozen in N2, and transferred to a precooled Eppendorf-tube in liquid N2. Buffer RLT was added to the frozen trichomes and RNA was isolated further with the kit. RNA was treated with DNAse1 (Invitrogen).
Of each isolation, one microgram total RNA was used for mRNA isolation and subsequent RNAseq library preparation following TruSeq Stranded mRNA Sample Preparation Protocol (Illumina). In short, mRNA was isolated using oligo dT beads and chemically fragmentized prior to first strand cDNA synthesis using random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis and the addition of Actinomycin D to the first strand master mix. Obtained double stranded cDNA fragments were used for 3’Adenylation and adapter ligation using different barcoded adapters. Adapter ligated cDNA was finally amplified using 15 PCR cycles. Quality control of final libraries was done using an Agilent Tapestation High Sensitivity D1000 Screen Tape assay. Final library quantification was performed using Qubit (Invitrogen). Equimolar amounts of libraries were pooled and diluted towards 6pM concentrations for paired end clustering on one lane of a flow cell V4 (Illumina).
Final sequencing was performed on a HiSeq2500 instrument using a 126,7,126 flow cycle pattern. De-multiplexing of obtained sequences was done using CASAVA 1.8.1. software.

treatment_protocol: No treatment

value: Stem


title: R7_1mon

tag: disease

tag: treatment

value: 1 month into treatment

value: Response


title: 3999305039_G

value: PMCA


title: RNA_mouse_NK_WT_IL18_2


title: Roots RNA-seq

source_name: Roots

value: Roots


title: 3999305039_H


title: 3999305039_F


title: R7_1wk

tag: treatment time point

value: 1 week into treatment

tag: response to treatment


title: Leaves10cm RNA-seq

source_name: Leaves > 10 cm

value: Leaves


title: 3999305039_C

tag: ronnet histology


title: 9534190125_I

value: DPAM


title: 3999305039_E


title: 6303256082_F


title: 3998532075_K


title: 3998532084_J


title: RNA_mouse_NK_WT_IL18_1


title: 3999305039_D


title: 3998532081_J


title: 3998532075_F


title: 6303256082_E


title: RNA_mouse_NK_WT_IL12IL18_3


title: Leaves3cm RNA-seq

source_name: Leaves < 3 cm


title: R7_pre

value: Pretreatment


title: R6_pre

value: Immune thrombocytopenia, chronic


title: Trichomes RNA-seq

source_name: Trichomes

value: Trichomes


title: 6303256082_D


title: 6303256082_C


title: RNA_mouse_NK_WT_IL12IL18_1

value: NK cells


title: RNA_mouse_NK_WT_IL12IL18_2

value: WT


title: R6_1wk

value: Eltrombopag


title: 6303256082_B

value: Pseudomyxoma peritonei


title: Wild type mice at postnatal day 2 library_6 in lane_3

city: Guangzhou

first: Cui

last: Guizhong

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

department: Center of Cell Lineage and Atlas

institute: Guangzhou Laboratory

data_processing:
Custom marker genes of GFP and CRE were added to the reference genome with cellranger mkref
Gene expression matrices were generated using the CellRanger software (version 3.1.0, 10X Genomics)
Seurat package (version 3.1.5) (Stuart et al., 2019) was used to perform quality control steps
Genome_build: Mus_musculus.GRCm38.99
Supplementary_files_format_and_content: Tab-delimited text file includes counts values of testes tissue cells in Ddx5 wild type (barcode-3) and conditional knockout mice (barcode-4).

source_name: Mouse whole testes tissue

extract_protocol:
Single testicular cells of P2 testes were isolated with TrypLE (ThermoFisher). Cell viability was assessed by trypan blue staining and cell capturing
Library preparation used a Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X Genomics) according to the manufacturer’s instructions

tag: age

value: postnatal day 2

value: Wild type

value: testes


title: RNA_mouse_NK_WT_IL12_3


title: Wild type mice at postnatal day 2 library_8 in lane_3


title: Wild type mice at postnatal day 2 library_7 in lane_3


title: 3998532084_F

source_name: Pseudomyxoma peritonei

value: liver

value: cytoHipec


title: Wild type mice at postnatal day 2 library_5 in lane_3


title: R5_1wk

value: Response


title: RNA_mouse_NK_WT_IL12_1


title: RNA_mouse_NK_WT_IL12_2


title: R5_1mon

value: 1 month into treatment


title: R4_1mon


title: R5_pre


title: ATAC_mouse_NK_WT_ATAC_UNSTIM_3

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
ATAC-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on Tn5-shifted, concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated from BAM files using the bamCoverage function from deepTools (v3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled pileups of reads aligned to the genome.

extract_protocol:
Fresh cells were prepared as previously described (Buenrostro et al., 2013). Briefly, sorted, stimulated cells were washed in cold PBS and lysed. The transposition reaction was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004).
DNA was amplified for 5 cycles. After evaluation by real-time PCR, 8-11 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 36 million paired reads were generated per sample.

treatment_protocol: NK cells were stimulated for 3 hr with 20 ng/ml recombinant mouse IL-12, 10 ng/ml recombinant mouse IL-18, or both.

value: UNSTIM


title: Wild type mice at postnatal day 2 library_4 in lane_2


title: ATAC_mouse_NK_WT_ATAC_UNSTIM_2


title: R4_1wk

value: 1 week into treatment


title: R4_pre


title: Wild type mice at postnatal day 2 library_3 in lane_2


title: 5552277088_J

value: PMCA


title: ATAC_mouse_NK_WT_ATAC_UNSTIM_1


title: Wild type mice at postnatal day 2 library_2 in lane_2


title: 5552277088_K


title: F5

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

data_processing:
Quality reads were trimmed with TrimGalore  (version 0.6.5)
Mapped using STAR (version 2.6.1c)
Overlapping Ensembl annotations (version 99)
Analysis was performed using edgeR-robust
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with the raw cout per gene

source_name: fibroid tissue

extract_protocol:
Total RNA was isolated using trizol reagent
Libraries were prepared using a Kapa RNA HyperPrep kit with ribosomal reduction

value: fibroid patient

value: fibroid


title: F6


title: 5552277026_K

value: DPAM


title: R3_1mon

value: Immune thrombocytopenia, chronic


title: 6303256082_A


title: F4


title: Wild type mice at postnatal day 2 library_1 in lane_2


title: Ddx5 conditional knockout mice at postnatal day 2 library_8 in lane_3

value: Ddx5 conditional knockout


title: Ddx5 conditional knockout mice at postnatal day 2 library_7 in lane_3


title: ATAC_mouse_NK_WT_ATAC_IL18_1

value: NK cells

value: WT


title: F3


title: Ddx5 conditional knockout mice at postnatal day 2 library_6 in lane_3

value: postnatal day 2


title: F1


title: ATAC_mouse_NK_WT_ATAC_IL18_3


title: ATAC_mouse_NK_WT_ATAC_IL12IL18_2


title: R3_1wk

value: Eltrombopag


title: MF6

source_name: normal tissue from a fibroid patient

value: myometrium


title: R1_1mon


title: Ddx5 conditional knockout mice at postnatal day 2 library_5 in lane_3

value: testes


title: R2_pre

value: Pretreatment


title: R2_1wk

value: Response


title: ATAC_mouse_NK_WT_ATAC_IL12IL18_1


title: Ddx5 conditional knockout mice at postnatal day 2 library_4 in lane_4


title: R1_1wk


title: 5552277092_I

value: Pseudomyxoma peritonei

value: liver

value: cytoHipec


title: F2


title: ATAC_mouse_NK_WT_ATAC_IL12IL18_3


title: MF5


title: ATAC_mouse_NK_WT_ATAC_IL12_3


title: Ddx5 conditional knockout mice at postnatal day 2 library_3 in lane_4


title: R1_pre


title: MF4


title: ATAC_mouse_NK_WT_ATAC_IL12_2


title: MF3


title: Ddx5 conditional knockout mice at postnatal day 2 library_1 in lane_4


title: MF1


title: M6

source_name: normal tissue from a non-fibroid patient

value: non-fibroid patient


title: Card19_KO_LPS_3

city: Philadelphia

first: Rina

last: Matsuda

address: 3800 Spruce Street

institute: University of Pennsylvania

description:
Card19_norm.txt
Card19_non_norm.txt

data_processing:
fastq files were aligned to mouse reference genome GRCm38 using Kallisto version 0.46.2
expression data was normalized by TMM method using edgeR package in R
data were variance-stabilized using VOOM function in the Limma package in R
differentially expressed genes (³2-fold and £10% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each sample, with or without normalization

source_name: bone marrow-derived macrophages

growth_protocol: 1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: BMDMs were either left unstimulated, or stimulated with LPS (100 ng/mL) for 3 hrs.

tag: background strain

value: LPS stimulation for 6hr


title: Card19_KO_LPS_2

description:
Card19_norm.txt
Card19_non_norm.txt


title: Card19_KO_3

description:
Card19_norm.txt
Card19_non_norm.txt

value: untreated


title: Card19_KO_LPS_1

description:
Card19_norm.txt
Card19_non_norm.txt


title: Card19_KO_2

description:
Card19_norm.txt
Card19_non_norm.txt


title: M5


title: Ddx5 conditional knockout mice at postnatal day 2 library_2 in lane_4


title: B6_LPS_3

description:
Card19_norm.txt
Card19_non_norm.txt

value: wild-type


title: ATAC_mouse_NK_WT_ATAC_IL12_1


title: M4


title: B6_LPS_2

description:
Card19_norm.txt
Card19_non_norm.txt


title: M3


title: MF2

value: fibroid patient


title: B6_LPS_1

description:
Card19_norm.txt
Card19_non_norm.txt


title: M2


title: B6_3

description:
Card19_norm.txt
Card19_non_norm.txt


title: M1


title: Leaves3_10cm RNA-seq

source_name: Leaves 3 - 10 cm

value: Leaves


title: B6_2

description:
Card19_norm.txt
Card19_non_norm.txt


title: 256740610715_1_3

city: Fuzhou

first: Yi

last: Sun

state: Fujian Province

address: Minhou County, Fuzhou, 350122, China Minhou County, Fuzhou, 350122, China

institute: Fujian Medical University

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Peripheral blood leukocyte, Control

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: Peripheral blood leukocyte

tag: gender

value: Female

tag: disease state

value: healthy subject


title: siCtrl- sample-2

city: Hyderabad

first: Bramanandam

last: Manavathi

state: Telangana

address: Dept. of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad

department: Department of Biochemistry

country: India

institute: University of Hyderabad

description: Gene expression data from siCtrl

hyb_protocol: Hybridization cocktail is prepared  including fragmented targets and probe assay comtrol . Nybridized to the probe array during 16 hours incubation period

scan_protocol: Probe array scan controlled by Affymetrix microarray suite or GCOS . Scanning can be processed using Gene chip scanner 2500

data_processing:
The analysis was performed using R/Bioconductor (v 3.12, R 4.0.2). The ReadAffy function of the affy package was used to store the expression values from CEL files. The quality control was done on the log2 transformed expression data. Background correction, quantile normalization, and the RMA (Robust Multichip Average) algorithm were performed using the rma function of the affy package.
The file normalized_data_with_all_controls.txt includes the normalized data for the ERCC controls.

source_name: BeWo Cell line

label_protocol: Invitro Transcription reaction biotin labeled cRNA from the cDNA.One cycle and two cycle labeling assay

growth_protocol: Cell lines were mainitained in DMEM/F12 complete medium containing 10% FBS and 100 µg/mL penicillin and 100 µg/mL streptomycin at 37 ºC in 5% humidified CO2.

extract_protocol: Trizol reagent was used to extract the total RNA from the cells.

treatment_protocol: Cell lines were transfected with either siCtrl and siHPIP using Lipofectamine 2000, and then grown for 48 hr using complete medium.

tag: cell line

value: BeWo

tag: cell type

value: Choriocarcinoma

tag: knockdown

value: siCtrl


title: 256740610714_1_3


title: B6_1

description:
Card19_norm.txt
Card19_non_norm.txt

tag: genotype


title: UMUC3-c31, 10nM R1881, 24hrs_2

description: 10nM R1881

hyb_protocol: These Affymetrix samples were processed and analyzed at the University of Colorado-Anschutz Medical Campus Genomics and Microarray Core Facility.

data_processing: Expression values were normalized and summarized into probesets using robust multichip analysis (RMA) using AffymetrixPowerTools.

source_name: UMUC3-c31 cell line

growth_protocol: Cells were serum starved for 24 hours prior to treatment using charcoal stripped serum (CSS).  After steroid washout, cells were treated with the described compounds for 24 hours prior to total RNA isolation.

extract_protocol: Qiagen RNeasy kit

tag: group

value: 1881 treated


title: 256740610713_1_4

tag: tissue

value: Male


title: siHPIP-sample-2

description: Gene expression data from siHPIP

value: siHPIP


title: siHPIP-sample-1

description: Gene expression data from siHPIP


title: UMUC3-c31, 10nM R1881, 24hrs_1

description: 10nM R1881

scan_protocol: These Affymetrix samples were processed and analyzed at the University of Colorado-Anschutz Medical Campus Genomics and Microarray Core Facility.


title: 256740610715_1_1

source_name: Peripheral blood leukocyte, Case

value: patient with coronary heart disease


title: T24RTHZ1_6h

city: Taipei

first: Po-Ming

last: Chow

address: No. 7, Zhongshan S. Rd., Zhongzheng Dist.

department: Department of Urology

country: Taiwan

institute: National Taiwan University Hospital

description: epithelial, adherent

data_processing:
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads.
Trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Read pairs from each sample were aligned to the reference genome (H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes.
Genome_build: H. sapiens GRCh38
Supplementary_files_format_and_content: FeatureCounts_T24R_Ctrl.txt: The featurecounts of each gene mapped to the reference genome (GRCh38) by the HISAT2.
Supplementary_files_format_and_content: FeatureCounts_T24RTHZ1_6h.txt: The featurecounts of each gene mapped to the reference genome (GRCh38) by the HISAT2.
Supplementary_files_format_and_content: Map_Summary.xlsx: The percentage of read counts from each sample mapped to the reference genome (GRCh38) by the HISAT2.
Supplementary_files_format_and_content: T24RTHZ1_6h.T24R_Ctrl_DO_Summary.xlsx: Data analyzed by disease ontology.
Supplementary_files_format_and_content: T24RTHZ1_6h.T24R_Ctrl_GO_Summary.xlsx: Data analyzed by gene ontology.
Supplementary_files_format_and_content: T24RTHZ1_6h.T24R_Ctrl_GSEA_Summary.xlsx: Data analyzed by GSEA C2.all.v7.0.

source_name: urinary bladder

growth_protocol: T24/R cells were cultured in RPMI 1640 medium supplemented with 10% FBS. The media were supplemented with 2 mM L-glutamine, and 100 µg/ml streptomycin-100 units/ml penicillin. We cultured the cells at 37°C with 5% CO2 atmosphere.

extract_protocol:
RNA was extracted from the cells with TRIzol Reagent (#15596018, Invitrogen).
Sequencing libraries were produced using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) underlying the manufacturer’s instructions.

treatment_protocol: DMSO or THZ1 6 hours.

tag: treatment time


title: UMUC3-c31, Vehicle control_2

description: Vehicle control

label_protocol: These Affymetrix samples were processed and analyzed at the University of Colorado-Anschutz Medical Campus Genomics and Microarray Core Facility.

value: control


title: T24R_Ctrl

description: epithelial, adherent

value: DMSO control