title: SAM23150218 Neut5.4

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description:
SAM23150218 Neut5.4 MEKi, Plus LPS 6 hrs.
PolyA RNA

data_processing:
Processing and analysis of RNA-sequencing data was performed using custom scripts written in the R programming language (http://r-project.org), along with packages from the Bioconductor project (http://bioconductor.org).
Raw RNA-sequencing data were processed using the HTSeqGenie Bioconductor package (version 3.16.1). Reads were aligned to the reference human genome (Genome Reference Consortium release 37) using the GSNAP algorithm.
Uniquely aligned reads that aligned within coding exon boundaries were tallied to estimate individual gene expression levels. Genes with low expression levels were filtered out; only genes that showed >10 reads in at least 3 samples were included.
Differential expression analysis for RNA-sequencing data was performed using the DESeq2 Bioconductor package. The generalized linear model used to determine differential expression included terms for stimulation with LPS, and the small molecule treatment cohorts, and included the cell donor as a covariate. Count level data were subjected to the variance stabilizing transformation implemented in the DESeq2 package for use in visualization using heat maps. P-values were adjusted for multiple testing using the Benjamini-Hochberg method. Genes were considered differentially expressed if they showed a minimum 1.5-fold change with an adjusted p-value <0.01.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: Entrez Gene IDs, gene exonic counts, gene length, and RPKM values.

source_name: Purified neutrophils, MEKi, Plus LPS 6 hrs

growth_protocol: Human neutrophils were isolated from whole blood from healthy donors using a negative selection kit (StemCell Technologies). All neutrophil purifications were conducted at room temperature with minimal pipetting and no braking during centrifugation. Neutrophil purity was consistently ≥99% as assessed by FACS.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions with an on-column DNase I digestion.
Library was prepared using the TruSeq RNA Sample Preparation Kit v2 (Illumina). Concentration was determined by a qPCR-based method using the KAPA library quantification kit. The libraries were multiplexed and then sequenced on Illumina HiSeq 2500 (Illumina) to generate 30M of single-end 50-base-pair reads.

treatment_protocol: Cells were resuspended in low (0.5%) serum RPMI and pretreated with vehicle (0.5% DMSO) or the specified small molecule inhibitors at least 30 min prior to stimulation.

tag: inventory sample name

tag: inventory patient id

tag: patient number

value: Donor 5

tag: disease status

value: Healthy

tag: primary tissue

value: Purified neutrophils

tag: treatment name

value: MEKi, Plus LPS 6 hrs

tag: lps

value: yes

tag: compound

value: MEKi


title: High grade serous ovarian cancer, Patient13

status: Public on Jul 01 2019

type: genomic

city: Iowa City

first: Henry

middle: D

last: Reyes

state: Iowa

address: 200 Hawkins Drive

department: OBGYN

country: USA

institute: University of Iowa

description: Primary

hyb_protocol: According to MethylationEPIC protocols

scan_protocol: Methylation intensity is measured with the Illumina iScan

data_processing: Results were reported as DNA methylation ratios (proportion of methylated/ unmethylated) referred to as Beta and processed using the Minfi R package

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Zymo EZ DNA methylation kit was used with 500 ng of total gDNA for bisulfite conversion. Infinium Illumina methylationEPIC arrays were used with Illumina Iscan to interrogate and measure methylation eintensity patterns.

extract_protocol: Samples and controls were collected and flash frozen. Genomic DNA was collected via Qiagen DNEasy blood and tissue kit.

tag: tissue

value: High grade serous ovarian cancer

tag: clinical outcomes

value: dead

tag: fu (months)


title: PTU_WT_rep1_H3K9Ac

type: SRA

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: WT mice match with L-NCORdeltaID

library_source: genomic

data_processing:
RNA-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression, H3K27Ac and H3K9Ac were analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
H3K27Ac and H3K9Ac domains were indentified using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text file with RPKM

organism: Mus musculus

source_name: liver

extract_protocol:
Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
ChIP-seq were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.

value: liver

tag: genotype

value: WT

tag: treatment

value: PTU

tag: chip antibody

value: H3K9Ac (Milipore, 06-942)


title: SAM23150216 Neut5.2

description:
SAM23150216 Neut5.2 Vehicle, Plus LPS 6 hrs.
PolyA RNA

library_source: transcriptomic

molecule: total RNA

source_name: Purified neutrophils, Vehicle, Plus LPS 6 hrs

value: Vehicle, Plus LPS 6 hrs

value: Vehicle


title: PTU_T3_PV_rep1_Pvexp_H3K27Ac

value: TRbetaPV

value: H3K27Ac (Abcam, ab4729)


title: PTU_T3_WT_rep1_H3K9Ac

description: WT mice match with L-NCORdeltaID


title: OX7X: Old animal 7

city: Cambridge

first: Lee

last: Rubin

state: MA

address: 7 Divinity Ave

institute: Harvard University

description: 10x single cell data

data_processing:
Cell Ranger (version 1.2) (10X Genomics) was used to perform sample de-multiplexing, barcode processing and single cell gene unique molecular identifier (UMI) counting, while a digital expression matrix was obtained for each experiment with default parameters, mapped to the 10x reference for mm10, version 1.2.0.
After the initial sequencing, the samples in each pool were re-pooled based on the actual number of cells detected by Cell Ranger, aiming to sequence each sample to a similar depth (number of reads/cell) (median: 40,007). Multiple NextSeq runs were conducted to achieve over 70% sequencing saturation as determined again by Cell Ranger (median: 75%).
Basic processing and visualization of the scRNA-seq data were performed using the Seurat package (version 2.3) in R (version 3.3.4)
Meta data with cell types, nUMI, nGene, and lineage are in the additional meta data file within the processed data section.
Genome_build: mm9
Supplementary_files_format_and_content: There are 16 processed files that are txt files with matrices for each gene and each cell from that animal.  In addtion, there is a combined additional metadata file that has each cell as a row and meta data including the following parameters nGene, nUMI, cluster (e.g. cell type), animal_type (young or old), cell_class (immune_lin, olg_lin, etc), and a final variable combining cell type and age.

source_name: 10x of dissociated mouse brain - old 14

extract_protocol:
Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul.
For every sample, 17,400 cells were loaded into a Chromium Single Cell 3’ Chip (10x Genomics) and processed following the manufacturer’s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1.

value: brain

tag: age

value: 21-22 months

tag: cells


title: YX4R: Young animal 4

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 4

value: 2-3 months


title: PTU_NCORdeltaID_rep2_H3K27Ac

value: L-NCORdeltaID


title: SAM23150215 Neut5.1

description:
SAM23150215 Neut5.1 Vehicle, No LPS 6 hrs.
PolyA RNA

source_name: Purified neutrophils, Vehicle, No LPS 6 hrs

value: Donor 5

value: Healthy

value: Purified neutrophils

value: Vehicle, No LPS 6 hrs

value: no


title: High grade serous ovarian cancer, Patient91

description: Primary

value: High grade serous ovarian cancer

value: alive


title: YX3R: Young animal 3

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 3


title: SAM23150217 Neut5.3

description:
SAM23150217 Neut5.3 TPLi, Plus LPS 6 hrs.
PolyA RNA

source_name: Purified neutrophils, TPLi, Plus LPS 6 hrs

value: TPLi, Plus LPS 6 hrs

value: yes


title: SAM23150214 Neut4.4

description:
SAM23150214 Neut4.4 MEKi, Plus LPS 6 hrs.
PolyA RNA

value: Donor 4

value: MEKi, Plus LPS 6 hrs

value: MEKi


title: PTU_T3_WT_rep2_H3K27Ac

description: WT mice match with L-NCORdeltaID

value: liver

value: WT

value: H3K27Ac (Abcam, ab4729)


title: High grade serous ovarian cancer, Patient84

description: Primary

value: dead


title: YX2L: Young animal 2

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 2

value: brain

value: 2-3 months


title: YX5R: Young animal 5

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 5


title: YX1L: Young animal 1

description: 10x single cell data

source_name: 10x of dissociated mouse brain - young 1


title: PTU_NCORdeltaID_rep1_H3K27Ac

value: L-NCORdeltaID

value: PTU


title: High grade serous ovarian cancer, Patient82

description: Primary


title: High grade serous ovarian cancer, Patient87

description: Primary


title: PTU_T3_WT_rep1_H3K27Ac

description: WT mice match with L-NCORdeltaID


title: SAM23150213 Neut4.3

description:
SAM23150213 Neut4.3 TPLi, Plus LPS 6 hrs.
PolyA RNA

value: Healthy

value: Purified neutrophils


title: High grade serous ovarian cancer, Patient78

description: Primary

value: High grade serous ovarian cancer


title: PTU_WT_rep1_H3K27Ac

description: WT mice match with L-NCORdeltaID


title: High grade serous ovarian cancer, Patient86

description: Primary


title: SAM23150211 Neut4.1

description:
SAM23150211 Neut4.1 Vehicle, No LPS 6 hrs.
PolyA RNA

value: Vehicle, No LPS 6 hrs

value: no

value: Vehicle


title: SAM23150210 Neut3.4

description:
SAM23150210 Neut3.4 MEKi, Plus LPS 6 hrs.
PolyA RNA

value: Donor 3

value: yes


title: PTU_WT_rep2_H3K27Ac

description: WT mice match with L-NCORdeltaID


title: flG4_RNA

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: RNA library. Second flow cell. Cells from individual mouse.

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation with flag ‘--sjdbOverhang 74’ equivalent to (read length – 1), via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting. Lexogen SIRVome was independently aligned and quantified for qualitative assessment of library concordancy.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average) and subsequent differential-expression analysis comparisons within flow cells (i.e. respective wild-type samples were used). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including gene counts (STAR output) and non-thresholded DESeq2 differential-expression analysis.

source_name: endometrial epithelium

growth_protocol: Mice were housed at the Van Andel Research Institute Animal Facility and the Michigan State University Grand Rapids Research Center in accordance with protocols approved by the Van Andel Research Institute and Michigan State University, under AUF# 01/16-099-00.

extract_protocol:
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Lexogen SIRV-set2 RNAs were spiked into RNA prior to library preparation at a concentration of 1% by mass. RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq Kit from 100 ng of total RNA material.

treatment_protocol: Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec).

tag: strain

value: EPCAM+ endometrial epithelium

tag: phenotype

value: atypical hyperplasia


title: High grade serous ovarian cancer, Patient80

description: Primary


title: High grade serous ovarian cancer, Patient81


title: SAM23150209 Neut3.3

description:
SAM23150209 Neut3.3 TPLi, Plus LPS 6 hrs.
PolyA RNA

tag: inventory sample name

tag: inventory patient id

value: TPLi, Plus LPS 6 hrs


title: High grade serous ovarian cancer, Patient76


title: flG3_RNA


title: A.thaliana_GEMoe_+ABA_rep2

type: RNA

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

hyb_protocol: Material was hybridized to Nimblegen 12x135K array slides, in duplicate, that cover the expression of 39,042 genes of A. Thaliana (4 60mer probes per gene)

scan_protocol: Slides were scanned in a DNA Micorarray Scanner G2505C (Agilent Technologies) at 532 nm and at a 3 um resolution, and TIF images imported into NimbleSan v2.6 for quantification of signal intensity

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleSann v 2.6. (Roche NimbleGen, Inc.)

organism: Arabidopsis thaliana

source_name: Whole seedling, 10 day-old

label_protocol: cDNA amplified from 10 μg of total RNA was labeled with Cy3 fluorophore.

growth_protocol: A. thaliana plants (Col-0) were grown on 0.8% agar plates supplemented with MS salts medium and 1% sucrose under a 16h/8h ligth/dark photoperiod, at 22 ºC and 70% relative humidity.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) and purified with RNeasy Plant Kit columns (Qiagen).

treatment_protocol: Treatment with ABA (100 μM) was carried out for two hours.

value: ABA

tag: cultivar

value: 35S overexpressor


title: A.thaliana_GEMoe_-ABA_rep2


title: A.thaliana_GEMoe_+ABA_rep1


title: flG2_RNA


title: SAM23150206 Neut2.4

description:
SAM23150206 Neut2.4 MEKi, Plus LPS 6 hrs.
PolyA RNA

tag: patient number

value: Donor 2

tag: disease status

tag: primary tissue

value: MEKi, Plus LPS 6 hrs

value: MEKi


title: High grade serous ovarian cancer, Patient77

description: Primary

value: dead


title: flG1_RNA


title: A.thaliana_GEMoe_-ABA_rep1


title: SAM23150208 Neut3.2

description:
SAM23150208 Neut3.2 Vehicle, Plus LPS 6 hrs.
PolyA RNA

value: Healthy

tag: treatment name

value: Vehicle, Plus LPS 6 hrs

tag: lps

tag: compound


title: High grade serous ovarian cancer, Patient73

tag: tissue

value: High grade serous ovarian cancer

tag: clinical outcomes

tag: fu (months)


title: High grade serous ovarian cancer, Patient75

description: Primary


title: SAM23150205 Neut2.3

description:
SAM23150205 Neut2.3 TPLi, Plus LPS 6 hrs.
PolyA RNA

value: Purified neutrophils


title: A.thaliana_gem1_+ABA_rep2

tag: treatment

tag: genotype

value: T-DNA insertion


title: A.thaliana_gem1_+ABA_rep1


title: SAM23150203 Neut2.1

description:
SAM23150203 Neut2.1 Vehicle, No LPS 6 hrs.
PolyA RNA

value: Vehicle, No LPS 6 hrs

value: no

value: Vehicle


title: High grade serous ovarian cancer, Patient72

description: Primary


title: SAM23150202 Neut1.4

description:
SAM23150202 Neut1.4 MEKi, Plus LPS 6 hrs.
PolyA RNA

value: Donor 1

value: yes


title: SAM23150212 Neut4.2

description:
SAM23150212 Neut4.2 Vehicle, Plus LPS 6 hrs.
PolyA RNA

value: Donor 4


title: A.thaliana_gem1_-ABA_rep2


title: High grade serous ovarian cancer, Patient71

description: Primary


title: Uhomo4_RNA

description: RNA library. First flow cell. Cells from individual mouse.

value: EPCAM+ endometrial epithelium

value: atypical hyperplasia


title: SAM23150201 Neut1.3

description:
SAM23150201 Neut1.3 TPLi, Plus LPS 6 hrs.
PolyA RNA

value: TPLi, Plus LPS 6 hrs


title: High grade serous ovarian cancer, Patient79

description: Primary


title: A.thaliana_Col0_+ABA_rep2

value: ABA

value: Wild-type


title: SAM23150200 Neut1.2

description:
SAM23150200 Neut1.2 Vehicle, Plus LPS 6 hrs.
PolyA RNA


title: Uhomo3_RNA


title: SAM23150207 Neut3.1

description:
SAM23150207 Neut3.1 Vehicle, No LPS 6 hrs.
PolyA RNA

value: Donor 3


title: A.thaliana_Col0_+ABA_rep1


title: High grade serous ovarian cancer, Patient68

description: Primary

value: dead


title: High grade serous ovarian cancer, Patient66

description: Primary


title: Uhomo2_RNA


title: High grade serous ovarian cancer, Patient70

description: Primary


title: High grade serous ovarian cancer, Patient69

description: Primary


title: SAM23150199 Neut1.1

description:
SAM23150199 Neut1.1 Vehicle, No LPS 6 hrs.
PolyA RNA

value: Healthy


title: High grade serous ovarian cancer, Patient89

description: Primary

value: High grade serous ovarian cancer


title: A.thaliana_Col0_-ABA_rep2


title: Uhomo1_RNA


title: A.thaliana_gem1_-ABA_rep1


title: Uhet4_RNA


title: Ovol2

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome with Tophat.
Mapped reads are provided as input to Cufflinks, which produces one file of assembled transfrags for each replicate. The assembly files are merged with the reference transcriptome annotation into a unified annotation for further analysis. This merged annotation is quantified in each condition by Cuffdiff, which produces expression data in a set of tabular files.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fragments per kilobase of transcript per million fragments mapped (FPKM) values for each sample .
Supplementary_files_format_and_content: expression abundance EV vs Zeb
Supplementary_files_format_and_content: expression abundance EV vs Snail
Supplementary_files_format_and_content: expression abundance EV vs Ovol2

growth_protocol: MCF10A cells were cultured in DMEM/F12(1:1) supplemented with horse serum (5%), epidermal growth factor (10 ng/mL), cholera toxin (100 ng/mL) and insulin (0.023 IU/mL).

extract_protocol:
Total RNA was harvested using RNAeasy column kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library construction was performed according to the Illumina TruSeq RNA v2 protocol.

treatment_protocol: Cells were infected with recombinant lentiviruses expressing Ovol2, Snail and Zeb1 (pHIV-ZsGreen). Six days after transfection, GFP-positive cells were purified by flow cytometry.

value: mammary gland

tag: cell line

tag: lentivirus induction

value: Ovol2 overexpression


title: High grade serous ovarian cancer, Patient64

description: Primary


title: High grade serous ovarian cancer, Patient90

description: Primary


title: Snail

value: Snail overexpression


title: Uhet3_RNA

tag: strain

tag: phenotype


title: High grade serous ovarian cancer, Patient67

description: Primary


title: DHX36-KO RNA-seq 2

city: Würzburg

first: Markus

last: Sauer

address: Am Hubland, Biozentrum - Lehrstuhl für Biochemie

country: Germany

institute: University of Würzburg

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output

growth_protocol: HEK293 cells and DHX36-KO-HEK293 were grown and routinely passaged in DMEM supplemented with 10% FCS and 1% pen/strip.

extract_protocol:
RNA was isolated using Trizol.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion

tag: genotype/variation

value: CRISPR/Cas9-mediated DHX36 Knockout


title: A.thaliana_Col0_-ABA_rep1

tag: cultivar


title: Zeb1

value: Zeb1 overexpression


title: SAM23150204 Neut2.2

description:
SAM23150204 Neut2.2 Vehicle, Plus LPS 6 hrs.
PolyA RNA

tag: inventory sample name

tag: inventory patient id

tag: patient number

value: Donor 2

value: Purified neutrophils

value: Vehicle, Plus LPS 6 hrs

value: Vehicle


title: Uhet2_RNA

value: EPCAM+ endometrial epithelium

value: atypical hyperplasia


title: DHX36-KO RNA-seq 1


title: High grade serous ovarian cancer, Patient63

description: Primary


title: High grade serous ovarian cancer, Patient65

description: Primary


title: High grade serous ovarian cancer, Patient60

description: Primary


title: High grade serous ovarian cancer, Patient62

description: Primary


title: Wildtype RNA-seq 2

source_name: HEK293 cells

value: wild type


title: DEL_spoControl_rep1

city: Rehovot

first: Miguel

middle: A.

last: Garcia-Campos

state: Center District

address: Herzl 234, Meyer Bldg., Room 1410

department: Molecular Genetics

country: Israel

institute: Weizmann Insitute of Science

data_processing:
RNA-seq reads were aligned to the Saccer 3 genome using STAR (V. 2.5.3a) and parameters ‘-- alignIntronMax 300 --alignMatesGapMax 1000’
Single-base coverage was extracted using bedtools (V. 2.26.0)
Genome_build: yeast SK1
Supplementary_files_format_and_content: Tab delimited text file, with single-base resolution normalized cleavage efficiencies by sample

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Diploid yeast cells

growth_protocol: YPD, 30 °C

extract_protocol:
MasterPure RNA extraction kit
Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment

treatment_protocol: Induction of meiosis in yeast

value: MAT a/alpha lys2/lys2 ho::LYS2/ho::LYS2 ndt80::LEU2/ndt80::LEU2 ime4::HIS3/ime4::HIS3

tag: developmental stage

value: 8 hours sporulation


title: EEwt2_ATAC

description: ATAC library. Cells from pooled mice. Note, peak file is from reads subsampled to fl/fl vs. control comparison.

data_processing:
Raw reads from technical replicates were concatenated (forward-forward and reverse-reverse) then trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned to mm10 reference genome via Bowtie2 with flags ‘--very-sensitive’ and ‘-X 1000’ in concordance with the library size-selection step.
Mitochondrial reads were then discarded from BAMs, via Harvard ATACseq module removeChrom, and subsequently filtered for only properly-paired mates by samtools view with flags '-f 3'.
Library complexity was estimated with ATACseqQC and normalized by subsampling to lowest complexity within experimental design based on interpolation estimates calculated from preseqR.
PCR duplicates were removed with Picard MarkDuplicates.
Final BAM files were converted to BEDPE format with bedtools bamtobed with flag ‘-bedpe’, and coordinates were shifted 4 and 5 bp to correct for TN5 transposase integration. BEDPE files were then re-written to minimal BEDPE format as defined by MACS2.
MACS2 was used to call broad peaks from final “minimal” BEDPE fragment coordinates with FDR < 0.05 threshold and no control input, and resulting peaks were repeat-masked by filtering to ENCODE mm10 blacklist.
In csaw, reads were counted in replicate-overlapping regions defined by MACS2, windows greater than 1 kb in width and low count windows were filtered (logCPM < -3), then trended biases were removed by lowess-normalization. Differential-accessibility was calculated by edgeR in csaw, and proximal windows (within 500 bp) were merged.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including blacklist-filtered broadPeaks (MACS2 output) and non-thresholded differential-accessibility results (lowess-normalized csaw output).

extract_protocol:
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. Nuclei were isolated in cold lysis buffer (10mM Tris-HCL [pH 7.4], 10 mM NaCl, 3mM MgCl2, 0.1% NP-40) by centrifugation at 500Xg for 10 min.
ATAC-seq libraries were prepared using the Nextera DNA Library Prep Kit, puified using the Qiagen MinElute Reaction Cleanup Kit, amplified by PCR and purified using Kapa Pure Beads.

value: Control wild-type

value: normal healthy


title: DEL_spoControl_rep2


title: Wildtype RNA-seq 1


title: WT_spoControl_rep2

value: MAT a/alpha lys2/lys2 ho::LYS2/ho::LYS2 ndt80::LEU2/ndt80::LEU2


title: EEwt1_ATAC


title: DHX36-KO Riboseq 3

extract_protocol:
Cells were lysed in extraction buffer and lysate were titruated 6 times through a 26 G needle. After Rnase treatment, ribosomes were purified by ultracentrifugation through a sucrose cushion. Ribosome-bound RNA was isolated with Trizol
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 3 min before harvesting, cells were treated with 100 µg/ml cyclohexamide to freeze translating ribosomes

tag: passages

tag: treated with

value: 100 µg/ml cyclohexamide


title: High grade serous ovarian cancer, Patient54

description: Primary

tag: tissue

value: High grade serous ovarian cancer

value: dead


title: EEflG2_ATAC

description: ATAC library. Cells from individual mouse.


title: Uhet1_RNA


title: WT_sporulation_8


title: High grade serous ovarian cancer, Patient59

description: Primary

tag: clinical outcomes


title: WT_spoControl_rep1


title: EEflG1_ATAC


title: DHX36-KO Riboseq 2

value: CRISPR/Cas9-mediated DHX36 Knockout


title: DHX36-KO Riboseq 1


title: High grade serous ovarian cancer, Patient56

description: Primary

tag: fu (months)


title: Wildtype Riboseq 3


title: EV

value: mammary gland

value: Empty vector control


title: EEhet1_ATAC


title: WT_sporulation_6

value: 6 hours sporulation


title: Wildtype RNA-seq 3


title: High grade serous ovarian cancer, Patient61

description: Primary


title: High grade serous ovarian cancer, Patient52

description: Primary


title: Wildtype Riboseq 2


title: WT_sporulation_5

value: 5 hours sporulation


title: WT_sporulation_7

value: 7 hours sporulation


title: EEflfl1_ATAC

value: EPCAM+ endometrial epithelium


title: WT_sporulation_4

value: 4 hours sporulation


title: High grade serous ovarian cancer, Patient55


title: EEhet2_ATAC

value: atypical hyperplasia


title: DHX36-KO RNA-seq 3


title: EEflfl2a_ATAC


title: 09_038B_00EEGothen_mTN11-sg1_BACH1_mm_i91

city: Stockholm

first: Martin

last: Bergö

address: Hälsovägen 7C (Neo building)

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality > = 25) were used for further analysis. Alignments were extended in silico at their 3′-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff P value = 10-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed
Signal maps and peak locations were used as input data to the Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.

source_name: Lung tumor

growth_protocol: Cells were grown in DMEM medium glutaMAX, glucose 1g/L containing 10% FBS, supplemented with NEAA (1%), penicillin/streptomycin (1%)

extract_protocol:
Lysates were sonicated and the DNA sheared to an average length of 300–500 bp. Genomic DNA (input) was prepared by incubating chromatin aliquots with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 mg) was pre-cleared with protein G agarose beads (Life technologies). Genomic DNA regions of interest were isolated using 4 mg antibody recognizing BACH1 (AF577, R&D
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75-nt reads, single end).

treatment_protocol: no specific treatment was applied

tag: antibody

value: mixed C57BL/6-129/Sv

value: KrasG12D/+, BACH1 KO

value: Lung tumor

tag: agent

value: NAC-Treated


title: WT_sporulation_3.5

tag: genotype

value: MAT a/alpha lys2/lys2 ho::LYS2/ho::LYS2 ndt80::LEU2/ndt80::LEU2

value: 3.5 hours sporulation


title: 05_037H_00EEGothen_mTN13_BACH1_mm_i94

value: NAC-treated (drinking water of mice)


title: WT_sporulation_3

value: 3 hours sporulation


title: High grade serous ovarian cancer, Patient51

description: Primary

value: High grade serous ovarian cancer

value: dead


title: DHX36-KO cPDS-RNA-seq 1

description:
4_KO_cPDS_RNAseq
processed data file:
PDS_WT_vs_KO_gene_exp.diff
PDS_WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_KO_gene_exp.diff

treatment_protocol: 42 h before harvesting, cells were treated with 2 µM cPDS

tag: cell line

value: CRISPR/Cas9-mediated DHX36 Knockout

value: 2 µM carboxyPyridostatin (cPDS)


title: High grade serous ovarian cancer, Patient53

description: Primary


title: WT_sporulation_2

tag: strain

value: 2 hours sporulation


title: High grade serous ovarian cancer, Patient48

description: Primary


title: 06_03E4_00EEGothen_mTN14_BACH1_mm_i94


title: Wildtype cPDS-RNA-seq 3

description:
3_wt_cPDS_RNAseq
processed data file:
PDS_WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_WT_gene_exp.diff

value: wild type


title: 04_037G_00EEGothen_mTN11_BACH1_mm_i93


title: High grade serous ovarian cancer, Patient49

description: Primary


title: Wildtype Riboseq 1

value: 100 µg/ml cyclohexamide


title: 02_037E_00EEGothen_mTC14_BACH1_mm_i87

value: Control


title: WT_sporulation_1

value: 1 hours sporulation


title: High grade serous ovarian cancer, Patient46

description: Primary


title: 01_037D_00EEGothen_mTC11_BACH1_mm_i86

value: mixed C57BL/6-129/Sv


title: DHX36-KO cPDS-RNA-seq 3

description:
6_KO_cPDS_RNAseq
processed data file:
PDS_WT_vs_KO_gene_exp.diff
PDS_WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_KO_gene_exp.diff


title: IME4-KO IP replicate 2

data_processing:
RNA-seq reads were aligned to the Saccer 3 genome using STAR (V. 2.5.3a) and parameters ‘-- alignIntronMax 300 --alignMatesGapMax 1000’
Single-base coverage was extracted using bedtools (V. 2.26.0)
Genome_build: yeast SK1
Supplementary_files_format_and_content: Normalized cleavage efficiency in all samples

value: MAT a/alpha lys2/lys2 ho::LYS2/ho::LYS2 ndt80::LEU2/ndt80::LEU2 ime4::HIS3/ime4::HIS3


title: Wildtype cPDS-RNA-seq 2

description:
2_wt_cPDS_RNAseq
processed data file:
PDS_WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_WT_gene_exp.diff


title: DHX36-KO chrRNA-seq 3

extract_protocol:
After harvesting, subcellular fractionation was performed to isolate the chromatin. RNA was isolated using Trizol.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion


title: IME4-KO input replicate 2

value: input


title: High grade serous ovarian cancer, Patient42

description: Primary


title: High grade serous ovarian cancer, Patient45

description: Primary


title: High grade serous ovarian cancer, Patient50

description: Primary

value: alive


title: DHX36-KO cPDS-RNA-seq 2

description:
5_KO_cPDS_RNAseq
processed data file:
PDS_WT_vs_KO_gene_exp.diff
PDS_WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_KO_gene_exp.diff


title: IME4-KO IP replicate 1


title: DHX36-KO chrRNA-seq 2


title: ESC METTL3 WT replicate 3

data_processing:
RNA-seq reads were aligned to the mm9 genome using STAR (V. 2.5.3a) and default parameters
Single-base coverage was extracted using bedtools (V. 2.26.0)
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file with cleavage efficiencies at single-nucleotide resolution

source_name: Embryonic stem cells

growth_protocol: mESCs expansion was carried out in 500 mL of High-glucose DMEM (ThermoScientific), 15% USDA certified fetal bovine serum (FBS- Biological Industries), 1 mM L-Glutamine (Biological Industries), 1% nonessential amino acids (Biological Industries), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Biological Industries), 1% Sodium-Pyruvate (Biological Industries), 10μg recombinant human LIF (Peprotech). Cells were maintained in 20% O2 conditions on irradiation inactivated mouse embryonic fibroblast (MEF) feeder cells, and were passaged following 0.25% trypsinization.

extract_protocol:
Nucleozol RNA extraction.
Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment

treatment_protocol: mESCs were grown on Gelatin for three passages in FBS free N2B27-based media: 250 mL DMEM:F12 (ThermoScientific), 250 mL Neurobasal (ThermoScientific), 5 mL N2 supplement (Invitrogen; 17502048 or in-house prepared), 5 mL B27 supplement (Invitrogen; 17504044), 1 mM L-Glutamine (Biological Industries), 1% nonessential amino acids (Biological Industries), 0.1 mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Biological Industries), 10μg recombinant human LIF (Peprotech) and small-molecule inhibitors CHIR99021 (CH, 3 μM- Axon Medchem) and PD0325901 (PD, 1 μM - Axon Medchem) termed 2i. For in vitro embryoid bodies (EBs) formation, roughly 5 million mESCs were disaggregated with trypsin and transferred to non-adherent suspension culture dishes, and cultured in MEF medium (DMEM supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin-streptomycin, 1% Sodium-Pyruvate and 15% FBS – does not contain LIF or 2i) for 9 days. Media replacement was carried out every 2 days.

tag: cell type

value: Embryonic stem cells

value: WT


title: ESC METTL3 WT replicate 2


title: WT_sporulation_0

value: MAT a/alpha lys2/lys2 ho::LYS2/ho::LYS2 ndt80::LEU2/ndt80::LEU2

value: 0 hours sporulation


title: DHX36-KO chrRNA-seq 1

tag: genotype/variation


title: IME4-KO input replicate 1


title: High grade serous ovarian cancer, Patient41

description: Primary

value: High grade serous ovarian cancer


title: ESC METTL3 WT replicate 1


title: WT IP replicate 2


title: GC_380_ppm_CO2_rep4

first: Marcus

last: Dittrich

address: Biozentrum, Am Hubland

department: Biozentrum

description: Gene expression in enriched guard cell fraction of Arabidopsis thaliana

hyb_protocol: one-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006)

scan_protocol: Agilent Microarray Scanner,extended dynamic range (XDR) at high resolution (5 µm)

data_processing: The data were normalized using quantile-quantile as normalization method

source_name: enriched guard cells, 4h 380 ppm CO2, replicate4

label_protocol: RNeasy Plant Mini Kit, according to the manufacturers protocol

growth_protocol: Arapidopsis thaliana plants were grown in soil and cultivated in a greenhouse under short-day conditions (8 h light/16 h darkness, 22°C/16°C) with illumination by 100 µmol m-2 sec-1 white light. Samples were collected after 4-5h of illumination or 1h illumination and 4h darkness.

extract_protocol: total RNA

treatment_protocol: CO2 treatment: Single potted 6-7 week old Arabidopsis thaliana (COL-0) plants were subjected to an airstream containing ambient CO2 (380ppm) and 50 ± 5 % rh in climate chambers at 22 ± 2 °C and 100 µmol m-2 sec-1 white light. After 1h half of the plants were treated with 1000 ppm CO2 for 4h. Darkness treatment: Single potted 6-7 week old Arabidopsis thaliana  (COL-0) plants were subjected to an airstream containing ambient CO2 (400ppm) and 50 ± 5 % rh in climate chambers at 22 ± 2 °C and 100 µmol m-2 sec-1 white light. After 1h half of the plants were kept into darkness for 4h.

tag: treatment

value: 4h 380 ppm CO2

tag: ecotype

value: enriched guard cells

tag: age

value: 6 - 7 weeks


title: Wildtype chrRNA-seq 2


title: Wildtype chrRNA-seq 3


title: WT input replicate 2


title: High grade serous ovarian cancer, Patient47

description: Primary

value: dead


title: ESC METTL3 KO replicate 3


title: 03_037F_00EEGothen_mTC31_BACH1_mm_i92

value: Lung tumor


title: High grade serous ovarian cancer, Patient40

description: Primary


title: High grade serous ovarian cancer, Patient38

description: Primary


title: WT IP replicate 1


title: Wildtype cPDS-RNA-seq 1

description:
1_wt_cPDS_RNAseq
processed data file:
PDS_WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_WT_gene_exp.diff

value: wild type

value: 2 µM carboxyPyridostatin (cPDS)


title: ESC METTL3 KO replicate 2


title: Wildtype chrRNA-seq 1


title: ESC METTL3 KO replicate 1


title: GC_380_ppm_CO2_rep2

source_name: enriched guard cells, 4h 380 ppm CO2, replicate2


title: High grade serous ovarian cancer, Patient39

description: Primary


title: High grade serous ovarian cancer, Patient37

description: Primary


title: B3

city: Shanghai

first: Sun

last: Licheng

address: No. 399, wanyuan road

country: China

institute: Fudan University

description: mRNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat 2.0.6.
Fragments Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using cufflink 2.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each Sample .

source_name: CD4 T cells (PM2.5 treated)

growth_protocol: CD4 naïve T cells were isolated from spleen C57BL/6 mice (6 weeks old female mice were used unless specified) of by CD4+ T Cell Isolation Kit (130-104-453, Miltenyi). About 4×10^5 cells were seeded into the plates which were pre-coated with Anti-CD28 (BD,553295) and Anti-CD3e(BD,553058) in Invitrogen RPMI 1640 (#12633) with 10% FBS and 55 μM 2-mercaptoethanol. The differentiation conditions are as followed: Th17 Differentiation: 5ug/ml Anti-IFNγ(BD,557530), 5 ug/ml Anti-IL4 (BD,554432), 20ng/ml IL-6 (R&D, 7666-MB-005), 10ng/ml IL-23 (R&D,1686-MR-050), 2ng/ml TGFβ (R&D,406-ML-025) and 5ng/ml IL-2（R&D,402-ML-020）.

extract_protocol:
Cells were cultrued for 4 days, and washed by PBS for 2 times. The total RNA was extracted using the TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina Xten at Shanghai Biotechnology Corporation)

treatment_protocol: For PM2.5 group, 100ug/ml of PM2.5 suspensions were added to culture medium 6 hours after stimulation. Otherwise, PBS was used as mock in control group.

tag: strain background

tag: mouse age

value: 6 weeks

tag: mouse sex

value: female

value: spleen

tag: cell type source

value: CD4 naïve T cells

tag: stimulation

value: CD3/CD28 antibodies and TH17 polarization for 4 days

value: 100ug/ml of PM2.5 suspensions


title: WT input replicate 1

value: input


title: EBS METTL3 WT replicate 2

source_name: Embryoid bodies

value: Embryoid bodies

value: WT


title: B2

description: mRNA-seq

tag: tissue


title: EBS METTL3 WT replicate 1


title: GC_1000_ppm_CO2_rep4

source_name: enriched guard cells, 4h 1000 ppm CO2, replicate4

value: 4h 1000 ppm CO2


title: GC_380_ppm_CO2_rep1

source_name: enriched guard cells, 4h 380 ppm CO2, replicate1

value: 4h 380 ppm CO2


title: CEM Input MeDIP/hMeDIP

city: Augusta

first: Jan

last: van Riggelen

state: GA

address: 1410 Laney Walker Blvd.

institute: Augusta University

description: Input for MeDIP-Seq and hMeDIP-Seq.

data_processing:
MeDIP-seq and hMeDIP-seq: Raw sequencing data generated from Illumina HiSeq 4000 that pass the Illumina chastity filter are used for following analysis. The fragments were 5’, 3’-adaptor trimmed and filtered ≤16 bp reads with cutadapt software. Trimmed reads (trimmed 5’, 3’-adaptor bases) are mapped to reference genome (hg19 or mm10) with Hisat2 software. The mapped reads were used for statistically significant unbiased methylation/hydroxymethylation region detection. LncRNA, mRNA and Small ncRNA associated DMRs and hDMRs enriched regions (peaks) with statistically significant were identified by diffReps (Cut-off: log2FC ≥ 1, P-value ≤ 10-4). LncRNA, mRNA and Small ncRNA associated hDMRs within promoter were annotated by the nearest gene using the UCSC RefSeq database. Promoter peaks were defined as 2,000 bp upstream and downstream from the transcription start site (TSS); Gene Body Peaks were defined as +2,000 bp downstream of the transcription start site (TSS) to the transcription termination site (TTS); and, Intergenic Peaks were defined as the other genomic regions not included in either promoters or gene body. MeDIP and hMeDIP analysis was performed by Arraystar Inc. (Rockville, MD).
RNA-seq: After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software. The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group ≥ 0.5. RNA-sequencing data analysis was performed by Arraystar Inc. (Rockville, MD).
Genome_build: mm10 (GRCm38), hg19 (GRCh37)
Supplementary_files_format_and_content: wig, txt

source_name: CCRF-CEM T-ALL

growth_protocol: Medium (RPMI1640, 10%FBS, 1%PenStrep, 1% L-glut, 50uM 2-mercaptoethanol) incubated at 37C with 5% CO2.

extract_protocol:
Nucleospin RNA and Nucleospin Tissue-gDNA (Macherey Nagel).
MeDIP and hMeDIP: Genomic DNA Sample Kit (FC-102-1002, Illumina).
RNA-seq: KAPA stranded RNA-seq library prep kit (Illumina).

value: Patient-derived T-ALL cell line


title: High grade serous ovarian cancer, Patient32

description: Primary

value: High grade serous ovarian cancer

tag: clinical outcomes

tag: fu (months)


title: CEM TET1sh1 RNA-seq

description:
Purified total RNA
processed data file: RNA-seq_CEM_SCR_and_TET1sh1_gene_expression.txt


title: High grade serous ovarian cancer, Patient34

description: Primary

value: dead


title: GC_1000_ppm_CO2_rep2

source_name: enriched guard cells, 4h 1000 ppm CO2, replicate2

value: enriched guard cells

value: 6 - 7 weeks


title: EBS METTL3 KO replicate 2


title: GC_1000_ppm_CO2_rep3

source_name: enriched guard cells, 4h 1000 ppm CO2, replicate3


title: B1

description: mRNA-seq


title: A3

description: mRNA-seq

source_name: CD4 T cells

value: PBS (untreated control)


title: CEM TET1sh1 hMeDIP

data_processing:
Library strategy: hMeDIP-Seq
MeDIP-seq and hMeDIP-seq: Raw sequencing data generated from Illumina HiSeq 4000 that pass the Illumina chastity filter are used for following analysis. The fragments were 5’, 3’-adaptor trimmed and filtered ≤16 bp reads with cutadapt software. Trimmed reads (trimmed 5’, 3’-adaptor bases) are mapped to reference genome (hg19 or mm10) with Hisat2 software. The mapped reads were used for statistically significant unbiased methylation/hydroxymethylation region detection. LncRNA, mRNA and Small ncRNA associated DMRs and hDMRs enriched regions (peaks) with statistically significant were identified by diffReps (Cut-off: log2FC ≥ 1, P-value ≤ 10-4). LncRNA, mRNA and Small ncRNA associated hDMRs within promoter were annotated by the nearest gene using the UCSC RefSeq database. Promoter peaks were defined as 2,000 bp upstream and downstream from the transcription start site (TSS); Gene Body Peaks were defined as +2,000 bp downstream of the transcription start site (TSS) to the transcription termination site (TTS); and, Intergenic Peaks were defined as the other genomic regions not included in either promoters or gene body. MeDIP and hMeDIP analysis was performed by Arraystar Inc. (Rockville, MD).
RNA-seq: After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software. The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group ≥ 0.5. RNA-sequencing data analysis was performed by Arraystar Inc. (Rockville, MD).
Genome_build: mm10 (GRCm38), hg19 (GRCh37)
Supplementary_files_format_and_content: wig, txt


title: EBS METTL3 KO replicate 1


title: GC_1000_ppm_CO2_rep1

source_name: enriched guard cells, 4h 1000 ppm CO2, replicate1


title: A2

description: mRNA-seq

value: 6 weeks


title: RNA-Seq NF-YA KD CHX-treated, Rep 2

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description:
RNA from ESCs transfected with NF-YA siRNA and treated with CHX (Cyclohexamide)
NFY-KD-totalRNA-Seq_both_normalized_coverage_plus.bw
NFY-KD-totalRNA-Seq_both_normalized_coverage_minus.bw

data_processing:
MNase-Seq reads were aligned to the mouse genome (mm9) using the Bowtie algorithm. Those reads that mapped to unique locations were retained for further analysis.
Ribo-Seq read pairs were trimmed with cutadapt tool and fragments shorter than 23nt were discarded. The remaining pairs were aligned to the mouse genome (mm9) using CRAC and only read pairs that mapped to unique locations were retained for further analysis.
RNA-Seq reads were mapped to mouse (mm9) genome using TopHat v2.1.0. and only those reads that mapped to unique locations were retained for further analysis.
Start-Seq reads were trimmed for adapter sequence using cutadapt 1.2.1 and read pairs with either of the paired-end-read trimmed to less than 20nt were discarded.  A single additional nucleotide was removed from the 3’ end of each read to facilitate mapping of fully overlapping pairs. Remaining pairs were filtered for rRNA and tRNA by aligning to indices containing each using bowtie 0.12.8, with unmapped read pairs retained. Following this, a similar alignment was performed to an index containing the sequence of spike-in RNAs only, and finally, the remaining unmapped reads were aligned to mm9 utilizing the same parameters, retaining read pairs mapping to unique locations.
RNA-Seq: Paired end reads were mapped to the mouse genome (mm9) using STAR aligner and htseq-count was used to count reads per gene which were utilized in edgeR for differential expression analysis.
ATAC-Seq: Paired end reads were aligned to the mouse genome (mm9) using Bowtie algorithm after removal of low quality reads (mean Phred quality score < 20). Those reads that mapped to unique locations were retained for further analysis.
Genome_build: mm9

source_name: mouse Embryonic Stem Cells (ESCs)

growth_protocol: Mouse ES cells were routinely maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). For experiments,  passage 20-35 cells were cultured on gelatin-coated plates in M15 medium: DMEM (Invitrogen) supplemented with 15% FBS (vol/vol), 10 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Invitrogen), 1× EmbryoMax nucleosides (Millipore), and 1U per ml of ESGRO mLIF (Millipore)

extract_protocol:
Mnase-Seq: DNA was extracted by phenol/chloroform extraction and mono/di-nucleosome fragments were gel-purified.
RNA-Seq: Total RNA was extracted from nuclei using Trizol (Invitrogen). Ribosomal RNA was removed prior to library construction by hybridizing to ribo-depletion beads that contain biotinylated capture probes (Ribo-Zero, Epicentre). RNA was then fragmented and libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming.
Start-Seq: Total RNA was extracted from nuclei using Trizol (Invitrogen). Start-RNA libraries were prepared as described in (PMID:20007866) and size-selected (20-80 nt) to exclude full length snRNA species.
Ribo-Seq: Total RNA and ribosome-protected RNA from Cyclohexamide (CHX)-treated cells were isolated using the TruSeq Ribo Profile Mammalian Kit (Illumina) following the manufacturer’s intructions.
ATAC-Seq:  DNA fragments were purified with 2 successive rounds of AMPure XP beads (1:3 ratio of sample to beads).
MNase-Seq libraries were prepared using NuGen's Ovation Ultralow Library System V2.
RNA-Seq libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming.
Ribo-Seq libraries were prepared according to TruSeq Ribo Profile Mammalian Library Prep Kit (Illumina)
Start-Seq libraries were prepared according to the TruSeq Small RNA Kit (Illumina). Illumina Spike-ins were used for normalization.
ATAC-Seq libraries were prepared according to NuGen's Ovation Ultralow Library System V2.

treatment_protocol: For transfections, ESCs (~25x103) were cultured in M15 medium and transfected with 50nM siRNA using Lipofectamine 2000 (Invitrogen) at day 0 and collected after 48h. Gene-specific siRNAs used: NF-YA (Invitrogen, MSS247473), non-targeting control (Dharmacon, D- 001810-02-50).

value: NF-YA siRNA (Invitrogen, MSS247473)

tag: passages


title: A1

description: mRNA-seq

value: female

value: spleen


title: CEM TET1sh1 MeDIP


title: GC_dark_rep3

source_name: enriched guard cells, 2h light, 2h darkness, replicate3

value: 2h darkness


title: High grade serous ovarian cancer, Patient36

description: Primary

data_processing: Results were reported as DNA methylation ratios (proportion of methylated/ unmethylated) referred to as Beta and processed using the Minfi R package

extract_protocol: Samples and controls were collected and flash frozen. Genomic DNA was collected via Qiagen DNEasy blood and tissue kit.


title: CEM SCR RNA-seq


title: CEM SCR hMeDIP


title: GC_dark_rep4

source_name: enriched guard cells, 2h light, 2h darkness, replicate4


title: RNA-Seq Control KD CHX-treated, Rep 2

description:
RNA from ESCs transfected with control siRNA and treated with CHX (Cyclohexamide)
Control-KD-totalRNA-Seq_both_normalized_coverage_plus.bw
Control-KD-totalRNA-Seq_both_normalized_coverage_minus.bw

value: non-targeting control siRNA (Dharmacon, D- 001810-02-50)


title: CEM SCR MeDIP


title: RNA-Seq Control KD CHX-treated, Rep 1


title: CEM TET2 RNA-seq

description:
Purified total RNA
processed data file: RNA-seq_CEM_EV_and_TET2_gene_expression.txt


title: Ribo-Seq NF-YA KD, Rep 2

description:
Ribosome-protected RNA from ESCs transfected with NF-YA siRNA
NFY-KD-Ribo-Seq_both_normalized_coverage_plus.bw
NFY-KD-Ribo-Seq_both_normalized_coverage_minus.bw


title: CEM TET2 hMeDIP


title: Ribo-Seq NF-YA KD, Rep 1


title: CEM TET2 MeDIP


title: High grade serous ovarian cancer, Patient30

description: Primary


title: GC_dark_rep1

source_name: enriched guard cells, 2h light, 2h darkness, replicate1


title: High grade serous ovarian cancer, Patient28

value: alive


title: CEM EV RNA-seq


title: GC_light_rep4

source_name: enriched guard cells, 4h light, replicate4

value: 4h light


title: RNA-Seq NF-YA KD CHX-treated, Rep 1


title: Ribo-Seq Control KD, Rep 1

description:
Ribosome-protected RNA from ESCs transfected with control siRNA
Control-KD-Ribo-Seq_both_normalized_coverage_plus.bw
Control-KD-Ribo-Seq_both_normalized_coverage_minus.bw


title: High grade serous ovarian cancer, Patient33

description: Primary


title: GC_light_rep3

source_name: enriched guard cells, 4h light, replicate3


title: Ribo-Seq Control KD, Rep 2


title: GC_light_rep1

source_name: enriched guard cells, 4h light, replicate1


title: GC_380_ppm_CO2_rep3

source_name: enriched guard cells, 4h 380 ppm CO2, replicate3


title: RPE-rd6-2

city: Cleveland

first: Joseph

last: Fogerty

state: OH

address: 9500 Euclid Ave, i3-179

department: Ophthalmic Research

institute: Cleveland Clinic - Cole Eye Institute

hyb_protocol: Affymetrix wash and stain kit.

scan_protocol: Arrays were scanned using the standard Affymetrix protocol, on a GCS3000HR scanner.

data_processing: Analyzed in Affymetrix Expression Console using RMA.

label: biotin

source_name: RPE

label_protocol: cDNA was prepared using the Ambion WT expression kit, and then fragmented and labeled with the GeneChip WT Terminal Labeling kit.

growth_protocol: Animals were 8 weeks old, with the exception of RPE-rd6-1, which were 12 weeks.

extract_protocol: RNA was extracted with Qiagen MinElute columns according to the manufacturer's instructions.

treatment_protocol: Animals were killed with CO2, and the eyes were immediately dissected. The cornea and lens were removed, and eyecups were transferred to RNAProtect (Qiagen) and gently agitated until the RPE detached. RPE cells were then pelleted.

tag: strain/background

value: Mfrp rd6

value: retinal pigment epithelium (RPE)

value: 12 weeks


title: High grade serous ovarian cancer, Patient26

description: Primary


title: RPE-rd6-3


title: CEM EV hMeDIP

value: Patient-derived T-ALL cell line


title: CEM EV MeDIP


title: RPE-rd6-1


title: Pbld8

city: Chengdu

first: xiaomeng

last: liu

address: No.55,Section 4,South Renmin Road

country: Colombia

institute: Sichuan Cancer Hospital & Institute, Sichuan Cancer Center

description:
ccfDNA
protocol: MCTA-Seq
all_samples_sumT_mepm.txt.gz

data_processing:
(1) Illumina CASAVA version 1.8 were used to the basecalling.
(2) Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
(3) Whole or any subsets of adaptor sequences were trimmed at 3'- end of the reads.
(4) The MCTA-Seq primer sequences including 6 bp at the 5'- end and 12 bp at the 3'- end of reads were trimmed.
(5) Low-quality reads, as > 10% bases being N, or Phred quality of > 50% bases being <5 or having  > 3 unmethylated CHs, were discarded.
(6) Cytosines in a read were computationally replaced with thymines and then mapped to computationally converted hg19 references using the Bismark and Bowtie programs.
(7) The reads were discarded if there was < 2 genomic CpG sites ± 3 bp surrounding the position corresponding to the 5'- end of the aligned reads.
(8) For a certain CpG site following a certain CGCGCGG, the methylation value is calculated as the number of fully methylated reads, i.e., all CpGs from the CGCGCGG site to the CpG site on the read were methylated, normalized by the total number of reads uniquely mapped to the whole human genome and expressed as methylated alleles per million mapped reads (MePM).
(9) For all of the amplicons from the 9,513 CGIs with no CGCGCGGs, the duplication rates were calculated by dividing the reads by the "HHHHH" unique molecule identifiers (UMIs) on primer A.
(10) When duplication rate of plasma sample was larger than that of paired white blood cell (WBC) samples, then plasma sample data were normalized to a duplication rate which similar to WBC by random extraction.
Genome_build: hg19
Supplementary_files_format_and_content:  All_samples_sumT_mepm.txt.gz file include the MePM (methylated alleles per million mapped reads) value of each CGCGCGG sites which was processed by step 1-8.
Supplementary_files_format_and_content:  nor_samples.txt.gz file include the MePM (methylated alleles per million mapped reads) value of each CGCGCGG sites which was processed by step 1-10.

source_name: plasma

extract_protocol:
Genomic DNAs were extracted using the Dneasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol.
The plasma cell-free DNAs were extracted using the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer's protocol.
Library were constructed following the MCTA-Seq library preparation protocol in PMID:26620315.

value: plasma

tag: disease state

value: benign liver disease patient


title: Start-Seq NF-YA KD, Rep 1

description:
Cap-protected RNA from ESCs transfected with NF-YA siRNA
NFY-KD_mean_5pr_startRNA_spikeNorm_plus.bedgraph.gz
NFY-KD_mean_5pr_startRNA_spikeNorm_minus.bedgraph.gz

tag: cell line


title: Start-Seq Control KD, Rep 3

description:
Cap-protected RNA from ESCs transfected with control siRNA
Control-KD_mean_5pr_startRNA_spikeNorm_plus.bedgraph.gz
Control-KD_mean_5pr_startRNA_spikeNorm_minus.bedgraph.gz


title: Start-Seq NF-YA KD, Rep 2


title: RPE-174delG-3

value: Mfrp 174delG

value: 8 weeks


title: Start-Seq Control KD, Rep 2


title: Pbld7


title: Pbld6


title: Start-Seq Control KD, Rep 1


title: RPE-174delG-1


title: High grade serous ovarian cancer, Patient27

description: Primary

value: High grade serous ovarian cancer

value: dead


title: Pbld5


title: Ppa8

value: acute pancreatitis patient


title: RNA-Seq NF-YA KD, Rep 2

description:
RNA from ESCs transfected with NF-YA siRNA
NFY-KD-merge_plus.bw
NFY-KD-merge_minus.bw

value: NF-YA siRNA (Invitrogen, MSS247473)


title: RPE-WT-3

value: WT


title: RPE-174delG-2


title: Ppa7


title: Lu-ty4 Typical Carcinoids (TCs)

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

description: DNA CpG Methylation profile for Human LCs

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: All IDAT files were processed in R using ChAMP package with QC ,  normalization (FunctionNormalization) and Differentially methylated probes

label: Cy3, Cy5

source_name: Lung Carcinoids

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from LCs samples using Qiagen DNeasy Kit according to standard instructions

tag: diagnosis

value: Typical Carcinoids (TCs)

tag: tumor in specimen

value: Lung

tag: gender

value: F

tag: age (years)

tag: tumor location

value: Central

tag: phenotype

value: Well Differentiated Lung Carcinoids

tag: cell type

value: Pulmonary neuroendocrine cells

tag: lcs subtype

value: LC3 Subtype of Lung Carcinoids


title: RPE-WT-4

tag: genotype/variation

value: retinal pigment epithelium (RPE)

tag: age


title: GC_light_rep2

source_name: enriched guard cells, 4h light, replicate2

tag: treatment

value: 4h light

tag: ecotype

value: enriched guard cells

value: 6 - 7 weeks


title: High grade serous ovarian cancer, Patient29

tag: tissue

tag: clinical outcomes

tag: fu (months)


title: Lu-Aty11 Atypical Carcinoids (ACs)

value: Atypical Carcinoids (ACs)

value: M

value: Peripheral

value: LC2 Subtype of Lung Carcinoids


title: Lu-ty11 Typical Carcinoids (TCs)


title: RNA-Seq NF-YA KD, Rep 1

value: NF-YA siRNA (Invitrogen, MSS247473)

tag: passages


title: Lu-ty17 Typical Carcinoids (TCs)


title: Ppa6

value: plasma

tag: disease state

value: acute pancreatitis patient


title: RNA-Seq Control KD, Rep 3

description:
RNA from ESCs transfected with control siRNA
Control-KD-merge_plus.bw
Control-KD-merge_minus.bw

value: non-targeting control siRNA (Dharmacon, D- 001810-02-50)

tag: cell line


title: RPE-WT-1

tag: strain/background

value: WT

value: 8 weeks


title: RPE-WT-2


title: Ppa5


title: Lu-ty16 Typical Carcinoids (TCs)

tag: diagnosis

value: Typical Carcinoids (TCs)

tag: tumor in specimen

value: Lung

tag: gender

value: F

value: Central

value: Well Differentiated Lung Carcinoids


title: RNA-Seq Control KD, Rep 2


title: Ppa4

extract_protocol:
Genomic DNAs were extracted using the Dneasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol.
The plasma cell-free DNAs were extracted using the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer's protocol.
Library were constructed following the MCTA-Seq library preparation protocol in PMID:26620315


title: Lu-ty2 Typical Carcinoids (TCs)

tag: age (years)

tag: tumor location

tag: phenotype

value: Pulmonary neuroendocrine cells

value: LC3 Subtype of Lung Carcinoids


title: Lu-ty13 Typical Carcinoids (TCs)

tag: cell type

tag: lcs subtype


title: RNA-Seq Control KD, Rep 1

tag: treatment


title: Lu-Aty9 Atypical Carcinoids (ACs)

value: Atypical Carcinoids (ACs)


title: MNase-Seq NF-YA KD, Rep 2

description:
Mnase digested DNA from ESCs transfected with NF-YA siRNA
NFY-KD_N3_MNase-seq_coverage_norm10m.bw


title: Ppa3


title: Ppa2


title: Ppa1


title: Peritoneal fluid-moderate endometriosis-rep2

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

hyb_protocol: 10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.  The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and once in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner using GenePix Pro 4.1 to align and acquire the microarray image.  CodeLink Expression Analysis 4.1.0.4163 was used to apply the background correction.

data_processing: Data in the matrix table were prepared by global median normalization applied by CodeLink Expression Analysis 4.1.0.4163.

label: streptavidin Alexa Fluor 647

source_name: T-HESC cells treated with peritoneal fluid from human subjects with moderate endometriosis

label_protocol: Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  1.0 microgram of total RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on columns.  The double-stranded cDNA was mixed with T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA.  The concentration of cRNA was determined by spectrophotometry. Streptavidin Alexa fluor 647 was incubated with the slides after hybridization to complete the labeling reaction.  One sample was hybridized with each slide so no dye swaps were necessary.

extract_protocol: Treated cultured T-HESC cells were lysed in 1 ml TRI reagent. Bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen) and the purified RNA was eluted.  The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

treatment_protocol: Telomerase – immortalized human endometrial stromal cells (T-HESC; ATCC CRL-4003) were maintained in Dulbecco’s Modified Eagle’s medium (DMEM) with charcoal stripped 10% FBS, insulin, selenious acid, transferrin, BSA, and linoleic acid (ITS+Premix), puromycin and pen/strep.  Cells were plated for experiments at 80% confluence followed by starvation for 6 hours.  Peritoneal fluid was aspirated from human subjects without and with endometriosis who were undergoing pelvic surgery.  This study was approved by the University of South Dakota Institutional Review Board and informed consent was obtained from all subjects.  The stage of endometriosis of each patient was classified using the American Society for Reproductive Medicine paradigm (minimal, mild, moderate or severe).  The fluid was centrifuged and filtered through a 0.22 micron filter to remove cells and debris.  The filtered peritoneal fluid was combined with T-HESC growth medium (DMEM, 4:1) with growth supplements (ITS) and antibiotics (penicillin/streptomycin).  The peritoneal fluid/growth medium was added to T-HESC cells that had been starved for 6 hours, and incubation was continued for 48 hours. After 48 hours of treatment, T-HESC were harvested for RNA isolation.

value: female

tag: disease severity

value: moderate endometriosis

tag: cell treatment

value: peritoneal fluid

tag: cell line treated

value: telomerase-immortalized human endometrial stromal cells


title: Peritoneal fluid-severe endometriosis-rep3

source_name: T-HESC cells treated with peritoneal fluid from human subjects with severe endometriosis

value: severe endometriosis


title: Lu-Aty8 Atypical Carcinoids (ACs)

value: Peripheral

value: LC1 Subtype of Lung Carcinoids


title: Lu-ty10 Typical Carcinoids (TCs)


title: MNase-Seq NF-YA KD, Rep 1

value: NF-YA siRNA (Invitrogen, MSS247473)


title: MNase-Seq NF-YA KD, Rep 3


title: Lu-Aty12 Atypical Carcinoids (ACs)


title: Skin2

description:
genomic DNA
protocol: MCTA-Seq
all_samples_sumT_mepm.txt.gz

source_name: skin

tag: tissue

value: skin

value: healthy individual


title: Peritoneal fluid-moderate endometriosis-rep3


title: MNase-Seq Control KD, Rep 2

description:
Mnase digested DNA from ESCs transfected with control siRNA
Control-KD_N3_MNase-seq_coverage_norm10m.bw

value: non-targeting control siRNA (Dharmacon, D- 001810-02-50)

tag: passages


title: MNase-Seq Control KD, Rep 3


title: Skin1

tag: disease state


title: Peritoneal fluid-severe endometriosis-rep1


title: Peritoneal fluid-severe endometriosis-rep2


title: Peritoneal fluid-moderate endometriosis-rep1


title: Muscle2

source_name: muscle

value: muscle


title: Peritoneal fluid-minimal endometriosis-rep2

source_name: T-HESC cells treated with peritoneal fluid from human subjects with minimal endometriosis

value: minimal endometriosis


title: Lu-ty5 Typical Carcinoids (TCs)

value: Typical Carcinoids (TCs)

value: Lung

value: F

value: Well Differentiated Lung Carcinoids


title: Lu-ty15 Typical Carcinoids (TCs)

value: Pulmonary neuroendocrine cells


title: Muscle1


title: MNase-Seq Control KD, Rep 1

source_name: mouse Embryonic Stem Cells (ESCs)

tag: cell line


title: Peritoneal fluid-minimal endometriosis-rep3

value: female


title: Poly(A) RNA w/o Enrichment (-ADPRC)

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 12

data_processing:
Library strategy: NAD tagSeq
All the reads were aligned to the reference genome and transcriptome of A. thaliana Ensemble 41 separately using minimap 2
For those reads with multiple alignments, only alignments with best mapping quality scores were kept. Reads with or without the tagRNA sequence were separated from the total reads
Native RNAs with a sequence similar to the tagRNA sequence were filtered.
Counts of reads from each gene were normalized in TPM (Transcripts Per Million Reads)
Genome_build: A. thaliana Ensemble 41
Supplementary_files_format_and_content: tab-delimited text files include TPM for each Sample.

source_name: seedling

growth_protocol: Sterile Arabidopsis Col-0 seeds were germinated on solid ½ MS medium with 1% sucrose. Seedlings were grown on plates in a growth room at 23°C under a 16-hr light/8-hr darkness cycle using 100 μmol photons m-2s-1 provided by cool white fluorescent lights.

extract_protocol:
Total RNA was extracted from 12-day-old seedlings using the TransZol reagent (Transgen Biotech) following the manufacturer's suggestion.
Library was prepared using the Nanopore direct RNA sequencing kit following the protocol provided by Oxford Nanopore Technologies.

treatment_protocol: In this study, Arabidposis seedlings were grown under standard condition without special treatment.

tag: cultivar

value: seedling

tag: age

tag: tagrna enrichment

value: NO


title: BW25113_Ribo-seq_rep2

city: guangzhou

first: zhang

last: hong

state: guangdong province

address: Huangpu Boulavard West Jinan uinversity

institute: zhanghong

data_processing:
Library strategy: Ribo-seq
BGI zebra software used for basecalling.
Sequenced reads were trimmed for adaptor sequence(BGI:AGTCGGAGGCCAAGCGGTCTTAG), and masked for low-complexity or low-quality sequence
mapped to GCF_000005845.2_ASM584v2_cds_from_genomic using FANse3g
Genome_build: GCF_000005845.2_ASM584v2

organism: Escherichia coli BW25113

source_name: E. coli strain BW25113 in M9 minimal medium

growth_protocol: Cultures were grown aerobically at 37 °C in 50 mL volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (4 g/L) in vigorously shaken (200 rpm) Fernbach flasks.

extract_protocol:
Trizol method
RNA-seq libraries were prepared for sequencing using standard MGIEasy mRNA Library Prep Kit V2 , Ribo-seq libraries were prepared for sequencing using standard MGIEasy Small RNA Library Prep Kit V1

treatment_protocol: Exponentially growing cells were poured over crushed ice containing 100 μg/ml chloramphenicol and  harvested by centrifugation at 5000g for 10min at 4℃,followed by 3 washed with pre-chilled phosphate buffered saline (PBS). the cell pellect was resuspended in 6ml pre-chilled sucrose-buffer solution[16mM Tris pH 8.1 supplemented with 0.5M RNase-free sucrose,50mM KCL,8.75mM EDTA,100 μg/ml chloramphenicol,12.5mg/ml lysozyme] and gently stirred for 5min on ice.0.3ml of 1M MgCl2 was a`dded to inhibit lysozome and the suspension was spun at 6000g for 10min at 4℃. The pellet was resuspended in 0.6ml freshly prepared lysis buffer (10mM Tris pH 7.8 containting 50mM NH4Cl,0.01M MgCl2,0.2% tritonX-100,100μg/ml chloramphenicol and 10U DNaseⅠ(RNase-free,Thermo)).the lysate was clasrified by centrifugation at 12000g for 10min at 4℃.Up to 0.6ml of clarified lysate was layered onto 35%(w/v) sucrose buffer(10mM Tris pH7.8 containting 50mM NH4Cl,10mM MgCl2,0.2% triton X-100,100μg/ml chloramphenicol) and centrifuged for 5h at 42500 r.p.m in type 70Ti rotor(Beckman) at 4℃. the pellet was slowly resuspended in  0.2ml Micorcocol buffer(50mM Tris pH7.9 containting 5mM CaCl2 and 12mM MgCl2).An aliquot of 1 A260 units of ribosome-bound mRNA fraction was subjected to nucleolytic digestion with 800 units micrococal nuclease(NEB) for 20min at 25℃.The total RNA extraction was performed by Trizol method

tag: strain


title: Poly(A) RNA w/o Enrichment (+ADPRC) Replicate 3

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 11


title: BW25113_Ribo-seq_rep1


title: Pancreas1

source_name: pancreas

value: pancreas


title: Lu-ty3 Typical Carcinoids (TCs)

tag: diagnosis

tag: tumor in specimen

tag: gender

value: M

tag: age (years)

value: Peripheral


title: RNA-Seq NF-YA KD, Rep 3

value: NF-YA siRNA (Invitrogen, MSS247473)


title: Pancreas2


title: Peritoneal fluid-control-no endometriosis-rep2

source_name: T-HESC cells treated with peritoneal fluid from human subjects without endometriosis

value: no disease

value: peritoneal fluid

value: telomerase-immortalized human endometrial stromal cells


title: Peritoneal fluid-control-no endometriosis-rep3


title: Poly(A) RNA w/o Enrichment (+ADPRC) Replicate 2

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 10


title: BW25113_RNA-seq_rep2

data_processing:
BGI zebra software used for basecalling.
Sequenced reads were trimmed for adaptor sequence(BGI:AGTCGGAGGCCAAGCGGTCTTAG), and masked for low-complexity or low-quality sequence
mapped to GCF_000005845.2_ASM584v2_cds_from_genomic using FANse3g
Genome_build: GCF_000005845.2_ASM584v2


title: Peritoneal fluid-minimal endometriosis-rep1


title: Kidney2

source_name: kidney

value: kidney

value: healthy individual


title: Poly(A) RNA w/o Enrichment (+ADPRC) Replicate 1

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 9


title: Lu-ty14 Typical Carcinoids (TCs)

value: Typical Carcinoids (TCs)

tag: tumor location

tag: phenotype

tag: cell type

tag: lcs subtype

value: LC1 Subtype of Lung Carcinoids


title: Lu-Aty4 Atypical Carcinoids (ACs)

value: Atypical Carcinoids (ACs)

value: Lung

value: F


title: BW25113_RNA-seq_rep1


title: U251 glioblastoma monolayer cells genomic DNA biological replicate 3- control

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

country: France

institute: INSERM

description: adherent cells

hyb_protocol: illumina infinium HD assay methylation protocol

scan_protocol: illumina iScan Methylation NXT Scan Setting

data_processing: DNA methylation raw data was extracted from Illumina idat files with Minfi, then normalized according to the FuncNorm procedure

source_name: U251 glioblastoma cell line

extract_protocol: DNA was extracted from tumor spheres and adherent cells using Machery Nagel kit. Then, 1 ug DNA was treated with Zymo kit for bisulfite conversion and 600 ng of treated DNA were processed following the 450k Human methylation Illumina assay protocol

tag: passage

value: monolayer cells


title: Poly(A) RNA (-ADPRC) Replicate3

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 8
Sample treated with TagRNA enrichment.

tag: tissue

value: seedling

value: YES


title: Poly(A) RNA (+ADPRC) Replicate3

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 7
Sample treated with TagRNA enrichment.


title: Kidney1


title: pol3LG_rnh202_24hr_RII

city: Durham

first: Zhi-Xiong

last: Zhou

address: 111 TW Alexander Dr.

institute: National Institute of Envinromental Health Sciences

description:
TAK_1342
TAK_1342-pol3LG_rnh202_24hr_RII

data_processing:
library strategy: HydEn-seq
Base calling and generation of FASTQ files performed by Illumina Hiseq standard pipeline
Reads trimmed for adapter sequence using cutadapt 1.12, discarding pairs with one or both reads shorter than 15 nt
Align end 1 to index of oligos used during library prep, exclude successful pairs from further analysis (bowtie 1.2 -k1 -v2, see supplementary file oligos.fa)
Align remaining pairs to reference sequence (Ch_10_before_BIR.fa/Ch_10_after.fa), trim single nt from 3' end of reads to allow mapping of 100% overlapping pairs (bowtie 1.2 -m1 -v2 -X10000 -3 1)
Align end 1 of unmapped pairs to reference (bowtie 1.2 -m1 -v2)
Retain 5' end only for all single- and paired-end unique alignments, combine
Determine counts of ends mapped to PmeI restriction sites, calculate size factors using method applied in DESeq, Anders et al., 2010
Filter ends mapping within 2 nt of an PmeI restrition site or site with 1 bp mismatch relative to PmeI motif, divide by previously determined size factors
Genome_build: Ch_10_before_BIR.fa, Ch_10_after_BIR.fa
Supplementary_files_format_and_content: bigWig, count of HydEn-seq 5' ends per position

growth_protocol: Yeast strains were grown to log phase at 30°C in YPR medium before treated with 0.1 μg/ml doxycycline, 20 μg/ml nocodazole for 2 hours, followed by 50 μg/ml doxycycline and 2.5 mM IAA for 1 hours before HO induction. Samples were taken at various time points.

extract_protocol:
DNA was isolated using the MasterPure™ Yeast DNA Purification Kit (Epicentre) without RNase A treatment.
HydEn-seq libraries are constructed as previously described (Clausen, et al. 2015 NSMB) with modifications by the following steps. Briefly, extract yeast genomic DNA (gDNA) using Epicenter MasterPure Yeast DNA Purification Kit. Treat 200 ng gDNA with Shrimp Alkaline Phosphatase (rSAP, New England Biolabs). Denature rSAP and restriction digest with PmeI at 37 °C for 1 hour. Split the DNA into two fractions. Treat one fraction with RNase HII (NEB) at 37 °C for 2 hours and designate the other fraction as non-treatment control. Denature the DNA by incubation at 90 °C for 2 min and ligate to adaptor ARC140 by T4 RNA ligase 1 (NEB) overnight at 25 °C. Denature DNA and anneal to the duplex adaptor ARC76/77. Synthesize the second strand using T7 DNA polymerase (NEB). Amplify the library for 20 cycles by primer ARC49 and an indexing primer using KAPA HiFi HotStart Ready Mix (KAPA Biosystems). 0.8 volumes of MagBio HighPrep PCR beads were used to purify DNA between steps that require changing buffers and/or removal of oligo adaptors and in the final library cleanup. The library was sequenced on an Illumina HiSeq 4000 machine for paired end 50 bp reads. The rSAP, SfbI-HF and RNase HII treatments are the main modifications to the original protocol to improve on signal-to-noise ratio, quantitation and specificity.

tag: genotype/variation

value: pol3-L612G rnh202{delta}

tag: growth phase

value: Log phase cell culture


title: Colon1

source_name: colon

value: colon

tag: disease state


title: U251 glioblastoma tumor spheres genomic DNA biological replicate 3

description: cells in suspension

label_protocol: illumina infinium HD assay methylation protocol

value: tumor spheres


title: HOP-62_expressing HDAC5 CDS

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from HOP-62 ectopically transfected with Flag-vector

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw signal data were normalized by GenoStudio v2011.1 software

source_name: Lung cancer cells, was purchased from NCI-60

label_protocol: cRNA were prepared with TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip

growth_protocol: All human lung adenocarcinoma cell lines were grown in RPMI-1640 media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HOP-62 cells were transiently introduced with the Pre-miR-10a* and Pre-NC mimics. HOP-62 cells were ectopically transfected with HDAC5-flag and empty vector.

tag: tumor type

value: lung adenocacinoma


title: U251 glioblastoma monolayer cells genomic DNA biological replicate 1- control

description: adherent cells


title: HOP-62_expressing an empty vector


title: Poly(A) RNA (-ADPRC) Replicate2

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 6
Sample treated with TagRNA enrichment.

tag: cultivar

tag: age


title: Lu-Aty3 Atypical Carcinoids (ACs)

value: Peripheral

value: Well Differentiated Lung Carcinoids

value: Pulmonary neuroendocrine cells


title: Colon2

value: healthy individual


title: U251 glioblastoma tumor spheres genomic DNA biological replicate 2

description: cells in suspension


title: CapEP_KO_13M_transcriptome

city: Boston

first: Chen

last: Chu

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description:
transcriptome
11.CapEP_WTvsKO_13M_transcriptome_RPKM.txt

data_processing:
For transcriptome sequencing, one hundred-base pair (bp) single-ended reads were mapped to mouse genome (mm9) using the TopHat2 short read mapper version 2.1.0 and differential gene expression analysis was quantified using the ‘generalized fold change (GFOLD)’ differential expression analysis program version 1.1.4.
Small RNA sequence tags from the Solexa sequencing were subjected to data cleaning, which filtered low quality tags and contaminants. The small RNA clean reads were mapped to the mouse mm9 genome using bowtie (version 0.12.7) with settings -k 1 -v 2.Small RNA reads with 100% match to the genome were used for further analysis. Small RNA annotation was performed by alignment to GenBank (http://www.ncbi.nlm.nih.gov/genbank/), mirBase (http://mirbase.org/) , Rfam (http://rfam.sanger.ac.uk/)  and piRNABank (http://pirnabank.ibab.ac.in/) .
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are in 'txt' format and contain small RNA reads information as well as the transcriptome RPKM comparison of WT and KO.

source_name: Epididymal Caput tissue

growth_protocol: Normal growth

extract_protocol:
Pooled biological samples instead of biological replicates were used for deep sequencing experiments. Total RNA isolation was performed using Trizol reagent (Invitrogen). Total RNA concentration was measured by Nanodrop ND-2000 (Thermo Scientific), and quality was assessed using an Agilent 2100 Bioanalyzer.
For transcriptome sequencing, cDNAs were prepared from full-length mRNA transcripts using a reverse transcriptase with terminal transferase activity. A total of 2.7 μg cDNA for each sample was sonicated to 200 - 400 bp and used for library preparation with the Illumina Nextera DNA Sample Prep Kit following the standard protocol.The libraries were sequenced by Illumina Hiseq 2000. Small RNA sequencing libraries were created following the Illumina TruSeq Small RNA Sample Preparation protocol. In brief, 5’ and 3’ RNA adapters that were specifically modified to target the ends of small RNA molecules were ligated to 1 μg of high quality total RNA. Reverse transcription was performed to generate cDNA libraries and PCR was used to amplify and add unique index sequences to each library. The amplified cDNA constructs were loaded and separated by polyacrylamide gel electrophoresis (PAGE), and the fraction corresponding to 18 - 40 nt small RNAs was excised, purified and sequenced by Illumina GAIIx orHiseq 2000.

treatment_protocol: Tissue samples were prepared from seven 13-month-old WT mice and seven 13-month-old Gpx5-/- mice that were sacrificed by cervical dislocation. Epididymides were removed and freed of connective, especially fat tissues. Epididymides were then divided into caput, corpus and cauda regions. Testes and corpus epididymides were directly collected for RNA extraction. Caput and cauda epididymides were transferred to a small glass dish containing 1 ml PBS. Repeated punctures with a 26-gauge needle and a 15-min incubation at 37℃ were performed to remove spermatozoa. After sperm cell dispersion, the tissues were collected for RNA extraction.

tag: strain

value: KO

value: Caput

value: 13 month old


title: U251 glioblastoma monolayer cells genomic DNA biological replicate 2- control

description: adherent cells


title: pol3LG_rnh202_12hr_RII

description:
TAK_1341
TAK_1341-pol3LG_rnh202_12hr_RII


title: Poly(A) RNA (+ADPRC) Replicate2

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 5
Sample treated with TagRNA enrichment.

tag: tagrna enrichment


title: Stomach1

source_name: stomach

value: stomach


title: pol3LG_rnh202_0hr_RII

description:
TAK_1339
TAK_1339-pol3LG_rnh202_0hr_RII


title: pol3LG_rnh202_6hr_RII

description:
TAK_1340
TAK_1340-pol3LG_rnh202_6hr_RII


title: Lung2

source_name: lung

value: lung


title: CapEP_WT_13M_transcriptome

value: WT


title: Stomach2


title: U251 glioblastoma tumor spheres genomic DNA biological replicate 1

description: cells in suspension


title: pol3LM_rnh202_24hr_RII

description:
TAK_1338
TAK_1338-pol3LM_rnh202_24hr_RII

value: pol3-L612M rnh202{delta}


title: CapEP_KO_2M_sRNA

description: 18 -40 nt

value: 2 month old


title: HOP-62_expressing the NC mimics

description: Gene expression data from HOP-62 transiently introduced with Pre-NC mimics

value: Lung


title: HOP-62_expressing the miR-10a* mimics

description: Gene expression data from HOP-62 transiently introduced with Pre-miR-10a* mimics


title: Poly(A) RNA (+ADPRC) Replicate1

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 3
Sample treated with TagRNA enrichment.

value: seedling

value: YES


title: Lung1

description:
genomic DNA
protocol: MCTA-Seq
all_samples_sumT_mepm.txt.gz


title: pol3LM_rnh202_12hr_RII

description:
TAK_1337
TAK_1337-pol3LM_rnh202_12hr_RII

value: Log phase cell culture


title: Total RNA (-ADPRC)

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 2


title: CapEP_WT_2M_sRNA

description: 18 -40 nt


title: Poly(A) RNA (-ADPRC) Replicate1

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 4
Sample treated with TagRNA enrichment.


title: HI.3965.007.RPI10.29-2_R1

city: Grafton

first: FARHA

last: RAMZAN

state: AUCKLAND

address: 85 Park road

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: miRNA

data_processing:
Cutadapt - 3’ adapter sequences removed, aligning the reads to miRBase (version21), reads are tallied to generate total counts for each miRNA, statistical significance (p-value) between 2 or more samples is calculated to generate differential expression profiles
Genome_build: miRBase (version21)
Supplementary_files_format_and_content: 58_samples_Readcount.tab- Readcounts of all samples for differential expression

source_name: Plasma

extract_protocol:
Plasma/Serum RNA Purification Kit using  Norgen Biotek (Cat#55000)
a standard library preparation workflow using Norgen's Small RNA Library Prep Kit for Illumina (Cat# 63600). Six microliter of each RNA sample was used as input. The workflow includes the following steps in sequence -  3' adapter ligation, 5' adapter ligation, reverse transcription/cDNA synthesis and then the indexing PCR. The final library is then subjected to column clean-up before resolving on a 6% TBE PAGE gel for size selection. The target band (~141-144 bp) is then excised from PAGE gel and purified

tag: subject id

tag: time

tag: diet

value: protein diet-RDA; 0.8 g/kg/day)

value: plasma

value: >70 years

tag: Sex

value: male


title: pol3LM_rnh202_6hr_RII

description:
TAK_1336
TAK_1336-pol3LM_rnh202_6hr_RII


title: Lu-Aty7 Atypical Carcinoids (ACs)

description: DNA CpG Methylation profile for Human LCs

source_name: Lung Carcinoids

tag: diagnosis

value: Atypical Carcinoids (ACs)

tag: tumor in specimen

tag: gender

value: F

tag: age (years)

tag: tumor location

value: Central

tag: phenotype

value: Well Differentiated Lung Carcinoids

value: Pulmonary neuroendocrine cells

value: LC1 Subtype of Lung Carcinoids


title: HI.3965.007.RPI9.29-1_R1

description: miRNA

value: Baseline

tag: tissue


title: Total RNA (+ADPRC)

description:
processed data files:
NADtagSeq.NAD-RNA.tpm.txt
NADtagSeq.all-RNA.tpm.txt
Sample 1


title: pol3LM_rnh202_0hr_RII

description:
TAK_1335
TAK_1335-pol3LM_rnh202_0hr_RII

tag: genotype/variation

value: pol3-L612M rnh202{delta}

tag: growth phase


title: nicd_d_chip

city: Madison

first: Elena

last: Sorokin

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: UW-Madison

description: chip antibody: 9E10 Myc antibody (Sigma M4439)

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the ce10 genome assembly using bowtie with the following configurations: -q -m 1 -v 3 -sam -best -strata
Peak density, scaled to a total library size of 10 million reads, was visualized using IGV
We specified the minimum fold change of IP to input of four-fold minimum and FDR < 0.01 for the peak call in Homer, for at least two biological replicates.
Genome_build: ce10
Supplementary_files_format_and_content: bedgraph files were generated using Homer where tag densities were scaled to 10 million tags.
Supplementary_files_format_and_content: Peak calling was performed using Homer and MACS, and tag density under each peak was assessed using Homer.

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: ~104 L4 stage worms were crosslinked and used for chromatin immunoprecipitation (ChIP) of DNAs preferentially bound to LAG-1(N-tag), GLP-1 (C-tag) or Control worms using established protocols.  Modifications include: using 4 mg/mL extract, omission of the wash with FA buffer containing 1 M NaCl.

extract_protocol:
Immunocomplexes, from each sample, were collected using 10 µg of M2 Flag antibody (F1804 Sigma) or 10 µg of 9E10 Myc antibody (Sigma M4439) overnight at 4 °C.  Then each sample was incubated for 1-2hr at 4 °C with 75 µL Dynabeads-Protein G (Novex 10003D).  Lysate samples and immunoprecipated protein samples were analyzed by immunoblot analysis using standard protocols.
ChIP-Seq DNA libraries were prepared using standard protocols and assessed for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  DNA sequencing was performed on four lanes of an Illumina HiSeq2000 at the University of Wisconsin-Madison Biotechnology Center (Madison, WI).

tag: developmental stage

value: L4 larva

tag: growth temperature ('c)


title: nicd_c_input

tag: strain


title: pol2MG_rnh202_24hr_RII

description:
TAK_1334
TAK_1334-pol2MG_rnh202_24hr_RII

value: pol2-M644G rnh202{delta}


title: HIV 293T N2-CLIP Neg

first: Bryan

middle: R

last: Cullen

address: 213 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

description:
Aligned to the HIV genome
NSUN2-CLIP

data_processing:
CASAVA 1.8.2
fastx toolkit
Bowtie (1)
Aligned to hg19 genome to remove human reads
Aligned remainder of the reads to the HIV genome
Genome_build: HIV genome from Genbank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to the HIV genome. Column 4 includes the read abundance normalised to the total number of reads.

organism: Human immunodeficiency virus

source_name: Negative control NSUN2-CLIP from HIV infected 293T cells

extract_protocol:
PAR-CLIP protocol
All samples were processed with the Illumina Tru-seq small RNA-seq kit

tag: human cell line

tag: virus

value: HIV

tag: technique

tag: transfection

value: CLIP RNA


title: HI.3965.007.RPI8.28-2_R1

description: miRNA

tag: subject id

tag: time

tag: diet

value: Protein diet-2xRDA; 1.6g/kg/day

tag: age

tag: Sex


title: HI.3965.007.RPI7.28-1_R1

description: miRNA


title: nicd_c_chip


title: HIV 293T N2-CLIP Pos

description:
Aligned to the HIV genome
NSUN2-CLIP

source_name: NSUN2-CLIP from HIV infected 293T cells


title: pol2MG_rnh202_12hr_RII

description:
TAK_1333
TAK_1333-pol2MG_rnh202_12hr_RII

value: Log phase cell culture


title: HIV CEM virions PA-m6A-seq

description: Aligned to the HIV genome

data_processing:
Library strategy: PA-m6A-seq
CASAVA 1.8.2
fastx toolkit
Bowtie (1)
Aligned to hg19 genome to remove human reads
Aligned remainder of the reads to the HIV genome
Genome_build: HIV genome from Genbank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to the HIV genome. Column 4 includes the read abundance normalised to the total number of reads.

source_name: PA-m6A-seq of virion RNA from HIV infected CEM cells

value: CEM

tag: par-clip antibody

value: anti-m6A, Synaptic Systems, Cat No 202111, Lot No, 202111/4

value: virion RNA


title: nicd_b_input


title: pol2MG_rnh202_6hr_RII

description:
TAK_1332
TAK_1332-pol2MG_rnh202_6hr_RII


title: HI.3965.007.RPI4.26-2_R1

description: miRNA

value: protein diet-RDA; 0.8 g/kg/day)

value: plasma

value: >70 years

value: male


title: HIV CEM cells PA-m6A-seq

description: Aligned to the HIV genome

source_name: PA-m6A-seq of cellular RNA from HIV infected CEM cells

value: polyA RNA


title: HI.3965.007.RPI3.26-1_R1

description: miRNA


title: pol2MG_rnh202_0hr_RII

description:
TAK_1331
TAK_1331-pol2MG_rnh202_0hr_RII


title: pol1YA_rnh202_24hr_RII

description:
TAK_1330
TAK_1330-pol1YA_rnh202_24hr_RII

value: pol1-Y869A rnh202{delta}


title: nicd_b_chip


title: HIV PBMC virions PA-m5C-seq

description: Aligned to the HIV genome

data_processing:
Library strategy: PA-m5C-seq
CASAVA 1.8.2
fastx toolkit
Bowtie (1)
Aligned to hg19 genome to remove human reads
Aligned remainder of the reads to the HIV genome
Genome_build: HIV genome from Genbank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to the HIV genome. Column 4 includes the read abundance normalised to the total number of reads.

source_name: PA-m5C-seq of virion RNA from HIV infected PBMC cells

value: PBMC

value: anti-m5C, Diagenode, Cat No C15200081, Lot No, RD-004


title: HI.3965.007.RPI6.27-2_R1

description: miRNA


title: HIV 293T cells PA-m5C-seq

description: Aligned to the HIV genome

source_name: PA-m5C-seq of cellular RNA from HIV infected 293T cells


title: nicd_a_input

value: L4 larva


title: HI.3965.007.RPI5.27-1_R1

description: miRNA

value: Baseline


title: nicd_a_chip


title: pol1YA_rnh202_12hr_RII

description:
TAK_1329
TAK_1329-pol1YA_rnh202_12hr_RII


title: pol1YA_rnh202_6hr_RII

description:
TAK_1328
TAK_1328-pol1YA_rnh202_6hr_RII


title: HIV N2KO cells PA-m5C-seq

description: Aligned to the HIV genome

source_name: PA-m5C-seq of cellular RNA from HIV infected 293T-N2 cells

value: HIV


title: HI.3965.007.RPI22.23-2_R1

description: miRNA


title: HIV CEM virions PA-m5C-seq

description: Aligned to the HIV genome

source_name: PA-m5C-seq of virion RNA from HIV infected CEM cells


title: HI.3965.007.RPI21.23-1_R1

description: miRNA


title: myc_d_chip

description: chip antibody: M2 Flag antibody (F1804 Sigma)


title: HIV CEM cells PA-m5C-seq

description: Aligned to the HIV genome

source_name: PA-m5C-seq of cellular RNA from HIV infected CEM cells


title: pol1YA_rnh202_0hr_RII

description:
TAK_1327
TAK_1327-pol1YA_rnh202_0hr_RII


title: myc_c_input


title: myc_d_input


title: HI.3965.007.RPI2.25-2_R1

description: miRNA


title: rnh202_24hr_RII

description:
TAK_1326
TAK_1326-rnh202_24hr_RII


title: HI.3965.007.RPI1.25-1_R1

description: miRNA


title: HIV CEM gRNA RNA-seq

description: Aligned to the HIV genome

source_name: RNA-seq of purified gRNA from virions isolated from HIV infected CEM cells

value: RNA-seq

value: virion gRNA


title: HIV 293T gRNA RNA-seq

description: Aligned to the HIV genome

source_name: RNA-seq of purified gRNA from virions isolated from HIV transfected 293T cells


title: myc_c_chip


title: rnh202_12hr_RII

description:
TAK_1325
TAK_1325-rnh202_12hr_RII

value: Log phase cell culture


title: rnh202_0hr_RII

description:
TAK_1323
TAK_1323-rnh202_0hr_RII


title: rnh202_6hr_RII

description:
TAK_1324
TAK_1324-rnh202_6hr_RII


title: HI.3965.007.RPI23.24-1_R1

description: miRNA


title: HI.3965.007.RPI24.24-2_R1

description: miRNA


title: myc_a_chip


title: lag_e_input


title: pol3LG_rnh202_24hr_NT

description:
TAK_1322
TAK_1322-pol3LG_rnh202_24hr_NT

value: pol3-L612G rnh202{delta}


title: HI.3965.007.RPI19.22-1_R1

description: miRNA


title: myc_a_input


title: pol3LG_rnh202_6hr_NT

description:
TAK_1320
TAK_1320-pol3LG_rnh202_6hr_NT


title: pol3LG_rnh202_12hr_NT

description:
TAK_1321
TAK_1321-pol3LG_rnh202_12hr_NT


title: lag_c_input


title: HI.3965.007.RPI18.21-2_R1

description: miRNA


title: pol3LG_rnh202_0hr_NT

description:
TAK_1319
TAK_1319-pol3LG_rnh202_0hr_NT


title: lag_c_chip


title: HI.3965.007.RPI17.21-1_R1

description: miRNA


title: HI.3965.006.RPI16.20-2_R1

description: miRNA

value: Protein diet-2xRDA; 1.6g/kg/day


title: nicd_d_input


title: pol3LM_rnh202_24hr_NT

description:
TAK_1318
TAK_1318-pol3LM_rnh202_24hr_NT

value: pol3-L612M rnh202{delta}


title: lag_b_chip


title: HI.3965.006.RPI15.20-1_R1

description: miRNA


title: pol3LM_rnh202_12hr_NT

description:
TAK_1317
TAK_1317-pol3LM_rnh202_12hr_NT


title: lag_e_chip


title: Peritoneal fluid-control-no endometriosis-rep1

source_name: T-HESC cells treated with peritoneal fluid from human subjects without endometriosis

tag: gender

value: female

tag: disease severity

value: no disease

tag: cell treatment

value: peritoneal fluid

tag: cell line treated

value: telomerase-immortalized human endometrial stromal cells


title: pol3LM_rnh202_6hr_NT

description:
TAK_1316
TAK_1316-pol3LM_rnh202_6hr_NT

tag: genotype/variation

tag: growth phase


title: lag_a_input

tag: developmental stage

tag: growth temperature ('c)

tag: strain


title: pol3LM_rnh202_0hr_NT

description:
TAK_1315
TAK_1315-pol3LM_rnh202_0hr_NT


title: lag_b_input


title: HI.3965.006.RPI11.18-1_R1

description: miRNA

tag: tissue

value: plasma

value: >70 years

value: male


title: lag_a_chip