title: KO CD4 rep 5

description:
counts.txt
sample name in processed data file: 14713X10

source_name: CD3+ CD4+ FACS sorted splenocytes

tag: cell type

value: CD4 T cell


title: MiaPaCa2_KO_rep1

status: Public on Apr 27 2020

type: SRA

city: Beppu,Oita

first: Atsushi

last: Fujii

address: 4546 Tsurumibaru

department: Department of Surgery

country: Japan

institute: Kyushu University Beppu Hospital

library_source: transcriptomic

data_processing:
The in-house pipeline Genomon 2.6.0  (https://genomon-project.github.io/GenomonPagesR)  was used for quality control and mapping.
The sequencing libraries generated from the RNA were analyzed by BGISEQ-500. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the reads were aligned to the human reference sequence and the gene annotations (UCSC hg19) using Tophat2 v2.0.14 with following parameters; --runThreadN 6 --outSAMstrandField intronMotif --outSAMunmapped Within --alignMatesGapMax 500000 --alignIntronMax 500000 --alignSJstitchMismatchNmax -1 -1 -1 -1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12.
STAR v2.5.2a was used to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) values.
Genome_build: UCSC hg19 with Gencode v28 annotations
Supplementary_files_format_and_content: tab-delimited text files of read counts per gene from STAR v2.5.2a

molecule: total RNA

organism: Homo sapiens

source_name: PDAC cell line

extract_protocol:
Total RNA was extracted from the cells using ISOGEN II (Nippon Gene).
Total RNA extracted from ASAP2 knockout or wild-type Panc1 and MiaPaCa2 cells was subjected to RNA-seq analysis. The sequencing libraries generated from the RNA were analyzed by BGISEQ-500.

tag: cell line

value: pancreatic ductal adenocarcinoma (PDAC) cells

tag: cell no

value: RIKEN BRC Cat# RCB2094

tag: genotype

value: ASAP2 knockout


title: 0 h rep3

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

country: China

institute: Shenzhen University

data_processing:
Zebra process software (version 0.5.0.13875) was used for basecalling.
Data was filtered by software SOAPnuke (version v1.5.2, parameters -l 15 -q 0.5 -n 0.1) to remove reads with adaptors, unknown bases (more than 10%), and low quality reads.
HISAT (version v2.0.4) was used to do the genome mapping, and clean reads were mapped to reference genes using Bowtie2 (version v2.2.5).
Gene expression level (FPKM) was calculated with RSEM software (version v1.2.12)
Genome_build: Chromochloris zofingiensis v5.2.3.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Chromochloris zofingiensis

source_name: microalgae

growth_protocol: Chromochloris zofingiensis  were grown in 250 ml columns of photoreactor with 80 μE m-2 s-1 continuous illumination and 1.5% CO2 enriched air.

extract_protocol:
Total RNA was extracted  using the plant RNA extraction kit (TaKaRa, Japan) and poly-A  mRNA was purified using poly-T oligo-attached magnetic beads.
The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, which was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR amplification. The PCR yield was quantified by Qubit, and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.

tag: strain

tag: time point

value: 0 h


title: 0 h rep2


title: KO CD4 rep 4

city: Holl

first: Ryan

last: O'Connell

state: UT

department: Pathology

country: USA

institute: University of Utah

description:
counts.txt
sample name in processed data file: 14713X9

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 87.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using Subread's command featureCounts (version 1.5.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw gene counts (Subread's featureCounts output files combined into a single tab-delimited matrix).

organism: Mus musculus

extract_protocol:
CD4 and CD8 T cells were FACS sorted from homogenized and RBC lysed spleens of 8 week old Male MPC1fl/fl (WT) and Vav Cre MPC1fl/fl (MPC1 KO).
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold

tag: tissue

value: Spleen

value: Vav-Cre MPC1 fl/fl


title: Pig13_border

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

data_processing:
Fastq files were trimmed to remove adapter and loq quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the reference (Sscrofa11) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM and Counts
Genome_build: Sscrofa11
Supplementary_files_format_and_content: tab-delimited text files include TPM and COUNTS for all samples

organism: Sus scrofa

source_name: Left ventricular myocardial tissue

growth_protocol: None- tissue was extracted when pigs were 4-weeks post surgery and rapidly frozen before RNA extracted.

extract_protocol:
Myocardial tissue was harvested 4-weeks following surgery and cut into zonal sections. Tissue was washed in PBS and rapidly frozen in liquid nitrogen, before transfer to a -80C freezer for storage. RNA was then extracted using a commercially available kit (NucleoSpin RNA kit (740955, Macherey-Nagel) and eluted in RNAse free H20 prior to submission to CCHMC DNA Core for processing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol

treatment_protocol: Ischemia/reperfusion= 1-hour occlusion of the left anterior descending artery, just below the second diagonal branch, following by reperfusion. Sham= same procedure but no occlusion of artery.

tag: surgery

value: Sham

tag: zone

value: Border

tag: Sex

value: Male


title: MiaPaCa2_WT_rep3

value: wild-type


title: 6 h rep3

value: 6 h


title: KO CD4 rep 3

description:
counts.txt
sample name in processed data file: 14713X8


title: 0 h rep1


title: KO CD4 rep 2

description:
counts.txt
sample name in processed data file: 14713X7


title: MiaPaCa2_WT_rep2


title: MiaPaCa2_WT_rep1


title: Control_WT_1

city: Hangzhou

first: Dongli

last: Pan

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Control transfected, infected with WT virus

data_processing:
Reads were trimmed to remove adapters, low-quality reads, and reads less than 30 bases long using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic)
The trimmed reads were aligned with the HSV-1 strain KOS (GenBank accession number KT899744.1) using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml).
Counts of reads aligned to each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
Genome_build: Herpes simplex virus 1 strain KOS (GenBank accession number KT899744.1)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral gene

organism:
Mus musculus
Human alphaherpesvirus 1

source_name: HSV-1 infected Neuro-2a cells

extract_protocol:
Total RNAs were purified using an RNeasyPlus Mini Kit following the manufacturer’s instructions (Qiagen)
mRNAs were isolated using a Takara mRNA Isolation Kit. Libraries were prepared using a PrepX RNA-seq Library Preparation Kit

treatment_protocol: Neuro-2a cells were transfected with 40 nM of a miR-138 or scrambled mimic for 24 h, and infected with WT or M138 virus (MOI = 10) for 16 h before performing RNAseq

tag: mouse cell line

tag: transfected with

value: scrambled mimic (control)

tag: virus genotype

value: WT


title: Pig11_border

value: IR


title: Healthy individual 4

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

description: raw.counts.txt.gz [Non-CHD4]

data_processing:
TrimGalore
STAR
featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts

source_name: iPSC-CM

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

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

value: iPSC-CM

tag: cell origin

value: Human


title: Panc1_KO_rep3

value: RIKEN BRC Cat# RCB2095


title: KO CD4 rep 1

description:
counts.txt
sample name in processed data file: 14713X6

value: CD4 T cell


title: Pig11_scar

value: Scar


title: Healthy individual 3

description: raw.counts.txt.gz [Non-CHD3]


title: WT CD4 rep 5

description:
counts.txt
sample name in processed data file: 14713X5

value: MPC1 fl/fl


title: Pig9_border


title: Panc1_KO_rep2

value: pancreatic ductal adenocarcinoma (PDAC) cells

value: ASAP2 knockout


title: WT CD4 rep 4

description:
counts.txt
sample name in processed data file: 14713X4

value: Spleen


title: Panc1_KO_rep1


title: Healthy individual 1

description: raw.counts.txt.gz [Non-CHD1]


title: Pig13_scar

value: Sham


title: Pig2_border

value: Ischemia/reperfusion (IR)

value: Border

value: Female


title: WT CD4 rep 3

description:
counts.txt
sample name in processed data file: 14713X3


title: WT CD4 rep 2

description:
counts.txt
sample name in processed data file: 14713X2


title: Panc1_WT_rep3

value: wild-type


title: Healthy individual 5

description: raw.counts.txt.gz [Non-CHD5]


title: Pig12_border

value: Male


title: Pig2_scar


title: WT CD4 rep 1

description:
counts.txt
sample name in processed data file: 14713X1


title: Tetralogy of Fallot 4

description: raw.counts.txt.gz [TOF4]


title: Panc1_WT_rep2


title: Tetralogy of Fallot 3

description: raw.counts.txt.gz [TOF3]


title: Excitatory neurons, shNUDT21 4

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
Raw reads were trimed using fastp
Trimed reads were aligned to the reference genome using bowtie2
Samtools were used to sort, convert and index alignment files
Deeptools were used to generate bigwig files
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: Excitatory neurons

growth_protocol: We used WA09 (H9; RRID:CVCL_9773) female embryonic stem cells (ESCs) to generate human neurons. We differentiated neural progenitors into human neurons over three weeks, changing the media every 3 d. Afterwards, we passaged the neurons with trypsin. Three days after passaging, we infected the neurons with lentiviruses containing pGIPZ shRNA clones at a multiplicity of infection of 10. We verified the tropism and infectivity of the virus using the tGFP reporter signal. At day 3 after infection, we treated the neurons with puromycin (0.75–1.25 g/ml) for 6 days to select for infected cells. We cultured the cells for 60 days after infection, changing the media three times per week.

extract_protocol:
After 60 days of culturing after infection, we aspirated all the media and washed the cells with PBS before freezing them at -80C for later RNA extraction. We extracted RNA from shRNA-infected, human ESC-derived neurons in a 12-well plate. We lysed the neurons in the tissue-culture plate with TRIzol Reagent (ThermoFisher Scientific) and immediately transferred the lysate to microfuge tubes for trituration. We then isolated the RNA by chloroform phase separation, precipitation with 2-propanol, washing with 75% ethanol, and eluting in water.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

treatment_protocol: We infected the neurons at a multiplicity of infection of 10 with pGIPZ lentiviral shRNA clones: RHS4348 and V2LHS_253272 (Dharmacon).

value: WA09 embryonic stem-cell derived excitatory neurons

tag: culture duration

value: 60 days

tag: shRNA


title: Healthy individual 2

description: raw.counts.txt.gz [Non-CHD2]

value: iPSC-CM


title: Tetralogy of Fallot 2

description: raw.counts.txt.gz [TOF2]

value: Human


title: Excitatory neurons, shNUDT21 3


title: Tetralogy of Fallot 1

description: raw.counts.txt.gz [TOF1]


title: Pig9_scar

value: IR


title: Excitatory neurons, shNUDT21 2


title: Flash freeze harvesting with harringtonine ribosome profiling

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

description: Ribosome profiling

data_processing:
Library strategy: Ribo-seq
All ribosome profiling data was analyzed using previously established methods and python scripts in E. coli (Muhammed, et al. 2019). In brief, reads were trimmed using trim_galore, reads corresponding to rRNA and tRNA were discarded, and the remaining reads were then mapped against the H. volcanii NCBI RefSeq genome (taxonomy identification [taxid] 2246; 1 chromosome, 4 plasmids) (allowing two mismatches) using Bowtie v 0.12.7. These alignments were then used in custom python scripts to: (a) calculate read density (assigned to the 3’-end of reads) across the genome, (b) calculate average ribosome position and read length distributions along ORFs using metagene analysis (3’- or 5’-end of reads as noted) on all transcripts, leadered transcripts, or leaderless transcripts, (c) calculate average amino acid and codon pause scores, (d) asymmetry scores for ORFs, and (e) expression for each gene. Custom bash/awk scripts were used to separate 10-20nt and 27nt footprint reads and these alignments were analyzed in the same manner.
TSS identification using a harringtonine (HHT) ribosome profiling library was done using previously published custom python scripts that were modified for our purposes (Meydan et al, 2019). Identification of novel TSS and smORFs was done as previously published with the following changes: (a) rpkm was calculated for each TSS peak in both the HHT and no challenge library, and (b) the TSS peak rpkm needed to be >=2-fold enriched in HHT compared to no challenge. Identification of known TSS, internal TSS (iTSS), and N-terminal extensions was done as previously published using density files assigned to the 3’-end of reads and adjusted for the P-site (15nt offset) (Meydan et al, 2019).
Genome_build: ASM2568v1 GCF_000025685.1
Supplementary_files_format_and_content: wig, bigwig, gff, txt

organism: Haloferax volcanii DS2

source_name: Cellular culture

growth_protocol: H. volcanii H98 single colonies were picked and grown overnight at 42°C shaking at 220 rpm in Hv-YPC medium supplemented with thymidine (50 μg/mL final concentration) until saturation (OD600 > 1.0).

extract_protocol:
The frozen culture form small pellets which are collected and 50g of pellets were weighed in order to add 1x lysis buffer (3.4 M KCl, 500 mM MgCl2, 50 mM CaCl2, 1 M Tris pH 7.5) and 100 μg/mL anisomycin to prevent ribosome elongation when thawed later on. The pellets were pulverized in a cryomill at 10 cycles due to the larger volume of input (1 minute of grinding at 10 Hz, 1 minute of cooling). The lysates were thawed at room temperature and ribosomes were pelleted over a 60% sucrose cushion (sucrose dissolved in lysis buffer) in an ultracentrifuge with a Ti-70 rotor at 60,000 rpm for 2 hours at 4°C. Ribosome pellets were resuspended in 200 μL lysis buffer. Cell lysates (from cells harvested by centrifugation or direct freezing) were processed by first treating 20 AU of lysate RNA (Nanodrop) with 12,000 units of MNase (Nuclease S7, Roche) for 1 hour at 25°C. After nuclease digestion, samples were loaded onto 10-50% sucrose gradients and RNA was isolated from monosome fractions. Briefly, 250 μL Trizol LS (Lifesciences) was added to gradient fractions, vortexed, and incubated at room temperature for 1 minute. 150 µL chloroform was added to the samples, vortexed, and centrifuged at 14,000 x g for 10 minutes at 4 C. The mixtures separated into a lower red phenol-chloroform, an interphase, and a colorless upper aqueous phase, and the aqueous phase was transferred into a new tube. Glycoblue (NEB) was added and an equal volume of 2-proponal was added to samples and incubated at room temperature. Samples were centrifuged again at 14,000 x g for 30 minutes at 4 C to pellet RNA, supernatant was aspirated, and RNA pellets were washed twice with 75% ethanol. Pellets were air dried for 2 minutes and resuspended in nuclease-free water.
Library preparation was performed as previously described (Muhammed, et al 2019). Briefly, 10 µg of RNA fragments was used to purify 15-45 nt RNA fragments by gel electrophoresis (15% TBE Urea gel); RNA fragments were treated with T4 polynucleotide kinase (NEB), then ligated to the linker (NEB Universal miRNA Cloning Linker) using T4 RNA ligase (NEB), and gel extracted from a 10% TBE Urea gel. Lastly, rRNA fragments were subtracted using the Ribo-Zero rRNA removal kit for bacteria (Illumina), then fragments reverse transcribed with SuperScript III (Invitrogen) using custom primers previously described (Muhammed, et al 2019), template RNA was degraded using NaOH and high heat, gel extracted from a 10% TBE Urea gel, circularized using CircLigase (Epicentre) and PCR amplified (8-12 cycles) with Phusion polymerase (NEB) using custom primers (ref), and PCR products gel extracted from a 10% TBE gels. PCR products were analyzed for size and concentration using a BioAnalyzer high sensitivity DNA kit (standard protocol) before sequencing on an Illumina HiSeq 2500 at the Johns Hopkins Sequencing Core Facility (Baltimore, MD).

treatment_protocol: These cultures were diluted to OD600 0.02 in fresh media, grown to  OD600 0.4 and split evenly into two flasks; one flask was used as a no treatment control and the other was treated with either 1 mg/mL homo-harringtonine (Sigma Catalog #SML1091), 20 mM serine hydroxamate (Sigma Catalog #S4503), or 100 μg/mL anisomycin, final concentrations. Cells were harvested by centrifugation or direct freezing of the culture in liquid nitrogen. For cells harvested by centrifugation, cultures were immediately centrifuged at 9,600 x g for 3 minutes at room temperature, the supernatant removed, and the pellets flashed frozen in liquid nitrogen. For cell lysis, the frozen pellets were resuspended in 1 mL of 1x lysis buffer (3.4 M KCl, 500 mM MgCl2, 50 mM CaCl2, 1 M Tris pH 7.5) with an additional 100 μg/mL anisomycin, transferred to a cryomill, and pulverized with 5 cycles (1 minute of grinding at 5 Hz, 1 minute of cooling). Lysates were then thawed at room temperature, centrifuged at 10,000 x g for 5 minutes, and transferred to a new tube on ice. For direct freezing of cultures in liquid nitrogen, 100 mL of culture sprayed directly into liquid nitrogen using a serological pipette.

tag: strain/background

tag: treatment

value: flash freeze harvesting with harringtonine


title: Single ventricle disease 5

description: raw.counts.txt.gz [SVD5]

tag: cell type


title: Flash freeze harvesting with anisomycin ribosome profiling

description: Ribosome profiling

value: flash freeze harvesting with anisomycin


title: Flash freeze harvesting with serine hydroxamate ribosome profiling

description: Ribosome profiling

value: flash freeze harvesting with serine hydroxamate


title: Tetralogy of Fallot 5

description: raw.counts.txt.gz [TOF5]


title: Excitatory neurons, shNUDT21 1


title: Single ventricle disease 4

description: raw.counts.txt.gz [SVD4]


title: Replicate 2 flash freeze harvesting no drugs ribosome profiling

description: Ribosome profiling

value: flash freeze harvesting no drugs


title: Excitatory neurons, Scramble 4

value: Scramble


title: Total RNA treated with MNase ribosome profiling

description: Ribosome profiling

value: MNase


title: Panc1_WT_rep1

tag: cell line

value: pancreatic ductal adenocarcinoma (PDAC) cells

tag: cell no

value: RIKEN BRC Cat# RCB2095


title: Single ventricle disease 3

description: raw.counts.txt.gz [SVD3]


title: Excitatory neurons, Scramble 3


title: Replicate 1 flash freeze harvesting no drugs ribosome profiling

description: Ribosome profiling


title: Replicate 2 centrifugation harvesting ribosome profiling

description: Ribosome profiling

value: centrifuge harvesting


title: Single ventricle disease 2

description: raw.counts.txt.gz [SVD2]


title: Excitatory neurons, Scramble 2


title: Single ventricle disease 1

description: raw.counts.txt.gz [SVD1]


title: Replicate 1 centrifugation harvesting ribosome profiling

description: Ribosome profiling


title: Excitatory neurons, Scramble 1


title: normal skin-2

type: RNA

city: Beijing

first: Hua

last: Yang

address: Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, 100730, China

institute: Peking Union Medical College Hospital

description: A total of 13247 circRNAs were detected by microarray analysis. By setting a threshold of fold change＞2 and p-value＜0.05, totally 355 significantly differentially expressed circRNA were discriminated in cholesteatoma compared with normal skin tissues.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.
When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes >2 and p-values < 0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: normal skin

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNAs were extracted from cholesteatoma and post-auricular skin tissues by TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel and Agilent 2100 Bioanalyzer.

treatment_protocol: All specimens were stored at -80°C immediately after collection for later RNA extraction.

value: normal skin


title: normal skin-4


title: cholesteatoma-2

source_name: cholesteatoma

value: cholesteatoma


title: normal skin-1


title: cholesteatoma-3


title: cholesteatoma-1


title: blood_POST_Subject_13

status: Public on Apr 26 2020

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole human genome oligonucleotide microarray (Agilent grid ID  072363), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE)  ver 10.7  software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09 for FE ver 10.7 ).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using R, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, which is a statistical method approximately equivalent to discard features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale.  Differentially expressed genes were selected using R-Bioconductor by a combination of different statistical tests: one-way repeated measure ANOVA (factor=time) with Tukey posthoc tests and pairwise comparisons between time points using the R Limma test (FDR<0.05; |Log2 fold-change ratio| >1.0).

source_name: blood

label_protocol: For each sample 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: Few weeks before the beginning of the mission, the 13 crew members were still living in Germany at sea level, when and the first blood samples were collected (PRE time point). Then they moved to the Antarctica Concordia station, which is located at Dome C on the Antarctic Plateau at 3233 m above sea level. They remained there for  12 months: during this period other blood samples were collected at Day 30 and Day 150 after arriving at Concordia (Day30 and Day150 time points). At the end of the mission the crew members came back to Germany and after  some weeks the last blood samples were collected (POST time point).

extract_protocol: Peripheral blood samples (2.5 mL) were collected in PAXgene Blood RNA Tubes (PreAnalytiX, Qiagen, Valencia, CA, USA) and stored at -80°C before RNA extraction. Total RNA was isolated using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s instructions. RNA purity was assessed by using a spectrophotometer (NanoDrop ND-1000 UV-visible spectrophotometer; Labtech International, Ringmer, UK); 260/280 and 260/230 ratios were evaluated and concentrations and integrity were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples were loaded on to the Eukaryote total RNA 6000 nano Kit (Agilent Technologies, Santa Clara, CA, USA). The RNA integrity number (RIN) for all the samples was calculated and samples with a value lower than 8.0 were discarded.

treatment_protocol: The peripheral blood samples were extracted from healthy human subjects, who did not undergo any pharmacological or medical treatment.

tag: attachment style

value: whole peripheral blood

tag: individual

value: subject 13

value: male

tag: age

value: POST mission time point


title: normal skin-3

tag: tissue


title: blood_POST_Subject_5

value: subject 5

tag: time point


title: blood_POST_Subject_8

value: subject 8

tag: Sex


title: cholesteatoma-4


title: blood_POST_Subject_12

value: subject 12


title: blood_POST_Subject_9

value: subject 9


title: blood_POST_Subject_3

value: subject 3


title: blood_POST_Subject_11

value: subject 11


title: blood_Day150_Subject_9

value: Day150 mission time point


title: blood_POST_Subject_10

value: subject 10

value: female


title: blood_POST_Subject_4

value: subject 4


title: blood_Day150_Subject_11


title: blood_POST_Subject_6

value: subject 6


title: blood_POST_Subject_2

value: subject 2


title: blood_Day150_Subject_6


title: blood_Day150_Subject_5


title: blood_Day150_Subject_7

value: subject 7


title: blood_Day150_Subject_13

value: whole peripheral blood


title: blood_Day150_Subject_12


title: blood_Day150_Subject_8


title: blood_POST_Subject_1

value: subject 1


title: blood_Day150_Subject_4

value: male


title: blood_Day150_Subject_3


title: blood_Day150_Subject_1


title: blood_Day150_Subject_2


title: blood_Day30_Subject_11

value: Day30 mission time point


title: blood_Day30_Subject_1


title: blood_Day30_Subject_13

value: subject 13


title: blood_Day30_Subject_6


title: ChIP-seq_H3K27ac_Bic/4AP

city: Fukuoka

first: TOMONORI

last: KAMEDA

address: 3-1-1, Maidashi, Higashi-ku, Fukuoka-shi

institute: Kyushu-University

library_source: genomic

data_processing:
Bisulfite-Seq;  Bisulfite-seq was performed with 100-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short and low quality reads, followed by trimming of the adaptor sequence. Processed reads were mapped to the mouse mm10 reference genome using BMap software with default parameter settings. We utilized WGBS data composed of more than 0.98 billion reads, with 75% of CpG sites in the mouse genome covered by at least five reads.
RNA-seq; RNA-seq was performed with 36-bp single-end sequencing by an Illumina Hiseq 3000. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence. Processed reads were mapped to the mouse genome mm10 genome using TopHat/Bowtie2.
ChIP-seq; ChIP-seq was performed with 66-bp single-end sequencing by an Illumina Hiseq 3000. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.  Processed reads were aligned to the mouse genome (UCSC mm10) using Bowtie v2.2.4. All redundant reads were removed from further analysis. SAM files were converted to the BAM format using SAMtools (v0.1.19).  Peak calling for H3K27ac was performed using MACS version 1.4.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bisulfite-Seq; tab-delimited text files include each CpG methylation level for each sample. RNA-seq; tab-delimited text files include RPKM values for each Sample. ChIP-seq; tab-delimited text files include peak region for each samples.

molecule: genomic DNA

extract_protocol:
Bisulfite-Seq; Genomic DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Nacalai Tesque). RNA-seq; Total RNAs were isolated with Sepasol-RNA I Super G (Nacalai Tesque), Total RNAs were purified using Poly (A) mRNA Magnetic Isolation Module (New England Biolabs). ChIP-seq; Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Bisulfite-Seq; Genomic DNA was subjected to bisulfite treatment with the EZ DNA Methylation-Gold Kit (ZYMO Research) according to the manufacturer’s instructions. In this study, we adopted a strategy termed post-bisulfite adaptor tagging (PBAT), which provides an unbiased methylome analysis (Miura et al. 2012). The multiplex PBAT method is described in detail on the CREST/IHEC Japan webpage (http://crest-ihec.jp/english/epigenome/index.html) (Miura et al. 2012). RNA-seq; Purified mRNAs by polyA beads were used for library construction with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). ChIP-seq; Sequencing libraries were made using the NEBNext ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: strain

value: ICR

value: E17 hippocampus

value: Cultured hippocampal neurons (10DIV)

tag: chip antibody

value: mouse monoclonal anti-H3K27ac; MBL


title: ChIP-seq_H3K27ac_non_treat

source_name: Treatment: non


title: Bisulfite-seq_PBAT_TTX

source_name: Treatment: tetrodotoxin


title: blood_Day30_Subject_4


title: blood_Day30_Subject_10


title: blood_Day30_Subject_9

value: subject 9


title: blood_PRE_Subject_12

value: subject 12

value: PRE mission time point


title: blood_Day30_Subject_5

value: subject 5


title: Bisulfite-seq_PBAT_Bic_4AP_3hrs


title: blood_Day30_Subject_3

value: subject 3


title: blood_PRE_Subject_13


title: blood_PRE_Subject_11

value: subject 11


title: blood_Day30_Subject_12


title: blood_Day30_Subject_2

value: subject 2


title: blood_POST_Subject_7

value: subject 7

value: POST mission time point


title: blood_Day30_Subject_8

value: whole peripheral blood

value: subject 8


title: blood_Day30_Subject_7

value: male

value: Day30 mission time point


title: blood_PRE_Subject_8


title: blood_PRE_Subject_9


title: blood_PRE_Subject_6

value: subject 6

value: female


title: RNA-seq_Bic_4AP_rep3

value: ICR

value: E17 hippocampus

value: Cultured hippocampal neurons (10DIV)


title: HepG2_rep2

city: Berlin

first: Lorenzo

last: Calviello

address: Robert-Rössle-Straße 10, MDC, Haus 89

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

description:
Ribosome profiling of HepG2_rep2
Footprinted RNA
processed data file: HepG2_P_sites_minus.bw
processed data file: HepG2_P_sites_plus.bw
processed data file: HepG2_junctions.tsv

data_processing:
Library strategy: Ribo-seq
Adapter sequence TGGAATTCTCGGGTGCCAAGG was removed from the 3’ using cutadapt; reads were collapsed and 4nt UMIs were removed from each end of the reads.
Reads were mapped to rRNA, snoRNA, miRNA and tRNA using Bowtie2; unmapped reads were retained.
Splice-aware mapping was performed with STAR 2.6.0 using GENCODE 25 annotation, allowing a maximum of 2 mismatches and retaining only 1 alignment per read.
ORF finding and quantification were performed using ORFquant with a cutoff of 2 for minimum percentage of gene translation and using unique reads only.
hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig files for P-sites position on each genomic strand, using all reads from two pooled replicate for each cell line.
Supplementary_files_format_and_content: tsv files containing reads mapping to each annotated splice junction are provided for two pooled replicates for each cell line.

extract_protocol: Cell lysis was performed in lysis buffer supplemented with 100μg/ml CHX. RNA fragments around 29nt were isolated and subjected to rRNA depletion using RiboZero.


title: Bisulfite-seq_PBAT_non_treat


title: RNA-seq_Bic_4AP_rep1


title: RNA-seq_Bic_4AP_rep2


title: blood_PRE_Subject_5


title: HepG2_rep1

description:
Ribosome profiling of HepG2_rep1
Footprinted RNA
processed data file: HepG2_P_sites_minus.bw
processed data file: HepG2_P_sites_plus.bw
processed data file: HepG2_junctions.tsv


title: RNA-seq_non_treat_rep3


title: RNA-seq_non_treat_rep2


title: K562_rep2

description:
Ribosome profiling of K562_rep2
Footprinted RNA
processed data file: K562_P_sites_minus.bw
processed data file: K562_P_sites_plus.bw
processed data file: K562_junctions.tsv


title: RNA-seq_non_treat_rep1


title: RNA-seq_TTX_rep1


title: RNA-seq_TTX_rep2


title: RNA-seq_TTX_rep3


title: blood_PRE_Subject_4

value: subject 4


title: R_18_01684_RT_WTS

status: Public on Apr 25 2020

city: Seoul

first: Yeon Hee

last: Park

address: 81 Ilwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: paired-end sequence reads

data_processing:
After trimming poor-quality bases from the FASTQ files obtained from the sequencing, we aligned the reads to the human reference genome (hg19) with TopHat (v 2.0.6) and performed a reference-guided assembly of transcripts with Cufflinks (v 2.1.1).
Alignment quality was verified with SAMTOOLS (v 0.1.19).
Gene expression was  138 estimated from the RNA-Seq data of the patients using a count-based method with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include HTSeq count values for each sample.

source_name: breast tissue of breast cancer patients who have germline BRCA mutations

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
Seqeuncing libraries were prepared using the TruSeq RNA Sample Preparation kit v2 (Illumina) using standard Illumina protocols.

tag: disease

value: breast cancer

value: 32 years

value: breast


title: R_17_00107_RT_WTS

description: paired-end sequence reads

value: 30 years


title: R_17_00114_RT_WTS

description: paired-end sequence reads

value: 35 years


title: R_17_00111_RT_WTS

description: paired-end sequence reads

value: 29 years


title: R_18_01687_RT_WTS

description: paired-end sequence reads

value: 38 years


title: R_15_00889_RT_WTS

description: paired-end sequence reads

value: 41 years


title: R_18_01641_RT_WTS

description: paired-end sequence reads


title: R_18_01640_RT_WTS

description: paired-end sequence reads

value: 33 years


title: K562_rep1

description:
Ribosome profiling of K562_rep1
Footprinted RNA
processed data file: K562_P_sites_minus.bw
processed data file: K562_P_sites_plus.bw
processed data file: K562_junctions.tsv


title: R_17_00843_RT_WTS

description: paired-end sequence reads


title: R_16_00349_RT_WTS

description: paired-end sequence reads

value: 34 years


title: R_16_00353_RT_WTS

description: paired-end sequence reads


title: R_16_00066_RT_WTS

description: paired-end sequence reads

value: 36 years


title: R_16_00340_RT_WTS

description: paired-end sequence reads

value: 46 years


title: blood_PRE_Subject_1

value: whole peripheral blood

value: subject 1

value: female

value: PRE mission time point


title: R_16_00024_RT_WTS

description: paired-end sequence reads


title: R_16_00011_RT_WTS

description: paired-end sequence reads

value: 39 years


title: blood_PRE_Subject_3

value: subject 3

value: male


title: R_17_00655_RT_WTS

description: paired-end sequence reads

value: breast cancer

value: breast


title: R_15_01778_RT_WTS

description: paired-end sequence reads


title: R_17_00459_RT_WTS

description: paired-end sequence reads


title: R_15_01260_RT_WTS

description: paired-end sequence reads

value: 28 years


title: R_15_01755_RT_WTS

description: paired-end sequence reads

value: 49 years


title: R_15_01196_RT_WTS

description: paired-end sequence reads


title: R_15_01353_RT_WTS

description: paired-end sequence reads

value: 35 years


title: R_15_01015_RT_WTS

description: paired-end sequence reads

value: 31 years


title: R_15_01769_RT_WTS

description: paired-end sequence reads


title: R_16_00043_RT_WTS

description: paired-end sequence reads

value: 38 years


title: R_14_00681_TS_WTS

description: paired-end sequence reads

value: 47 years


title: R_14_00027_TS_WTS

description: paired-end sequence reads

value: 25 years


title: R_13_00137_TS_WTS

description: paired-end sequence reads


title: R_14_00544_TS_WTS

description: paired-end sequence reads


title: R_14_00370_TS_WTS

description: paired-end sequence reads

value: 34 years


title: R_14_00211_TS_WTS

description: paired-end sequence reads

value: 36 years


title: R_14_00345_TS_WTS

description: paired-end sequence reads


title: blood_PRE_Subject_2

value: whole peripheral blood

value: subject 2


title: R_13_00160_TS_WTS

description: paired-end sequence reads

value: 33 years


title: chip-22gw_H3K9me3_CP

city: San Francisco

first: John

last: Rubenstein

address: 401 Parnassus Ave

department: Department of Psychiatry

institute: University of California, San Francisco

data_processing:
Data was processed using the ENCODE ATAC-seq and ChIP-seq pipelines.
Predicted regulatory elements were generated using custom Python code.
Genome_build: hg19, hg38
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq signal (fold change over control) in bigWig format, ATAC-seq and ChIP-seq peaks (optimal IDR threshold) in narrowPeak format, OCR and pRE annotations in bed format

source_name: Prefrontal cortex, cortical plate

growth_protocol: none, fresh intact samples from human specimens were used

extract_protocol:
For ATAC-seq samples, from each dissection intact nuclei were isolated by manually douncing the tissue twenty times in 1mL Buffer 1 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 1mM DTT, 1.1mM PMSF, Protease inhibitors) on ice using a loose pestle douncer, and then lysed on ice for 10 minutes after adding 1mL Buffer 2 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 0.1% NP-40, 1mM DTT, 1.1mM PMSF, Protease inhibitors). During this ten minutes, nuclei were counted using trypan blue and 50,000 nuclei were spun down at 7,000rpm for ten minutes at 4C. Nuclei were resuspended in 25uL Tagmentation buffer, 22.5 uL Nuclease Free H20, and 2.5 uL Tagmentation Enzyme from Illumina DNA Kit (number), gently mixed, and placed in 37C water bath for thirty minutes. The tagmentation reaction was stopped by MinElute PCR purification and DNA was eluted in 10uL Nuclease Free water. For ChIP-seq samples, intact nuclei were isolated by manually douncing the tissue twenty times in 1mL Buffer 1 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 1mM DTT, 1.1mM PMSF, 50mM Sodium Butyrate, EDTA-free Protease inhibitors) on ice using a loose pestle douncer, and then lysed on ice for 10 minutes after adding 1mL Buffer 2 (300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, pH 7.5, 5mM MgCl2, 0.1mM EGTA, 0.1% NP-40, 1mM DTT, 1.1mM PMSF, 50mM Sodium Butyrate,  EDTA-free Protease inhibitors). During this ten minutes, nuclei were counted using trypan blue and 500,000 nuclei were spun down at 7,000rpm for ten minutes at 4C.  Nuclei were resuspended in 0.250mL MNase buffer  (320mM sucrose, 50mM Tris-HCl, pH 7.5, 4mM MgCl2, 1mM CaCl2, 1.1mM PMSF, 50mM Sodium Butyrate) and incubated in a 37C water bath with 2 microliters MNase enzyme (NEB) for eight minutes.  MNase digestion was stopped by adding 10 microliters 0.5M EDTA, and chromatin was spun down for 10 minutes 10,000rpm 4C.  Soluble fraction S1 supernatant was saved at 4C overnight, and S2 fraction was dialyzed overnight in 250uL dialysis buffer at 4C (1mm Tris-HCl pH 7.5, 0.2mM EDTA, 0.1mM PMSF, 50mM Sodium Butyrate, Protease Inhibitors).  S1 and S2 fractions were combined, 50 microliters were saved as input, and Chromatin immunoprecipitation was set up in 50mM Tris, pH 7.5, 10mM EDTA, 125 mM NaCl1, 0.1% Tween. 250m M Sodium Butyrate was supplemented for H3K27ac ChIPs.  The following antibodies were used for ChIP: H3K27ac (Millipore, cma309), H3K4me1 (Abcam, ab8895), H3K27me3 (Millipore, 07-449), H4K20me3 (Abcam, ab9053), and H3K9me3 (Abcan, ab8898).  1 microliter of antibody was added to 1mL chromatin in ChIP buffer and incubated overnight with chromatin at 4C rotating.  Protein A and Protein G beads (10 microliters each) were blocked overnight in 700uL ChIP buffer, 20 uL yeast tRNA (20mg/mL), and 300uL BSA (10mg/mL). Beads were washed three times on ice in Wash buffer 1 (50 mM Tris, pH 7.5 , 10mM EDTA , 125mM NaCl, 0.1% Tween-20, with protease inhibitors and 5mM sodium butyrate) and three times in Wash buffer 2 ((50 mM Tris, pH 7.5 , 10mM EDTA , 175mM NaCl, 0.1% NP-40, with protease inhibitors and 5mM sodium butyrate), and ChIP DNA was eluted in elution buffer at 37C and purified by phenol chloroform extraction and ethanol precipitation.
ATAC-seq library generation was performed using Illumina barcode oligos as described (Buenrostro et al 2015), for 8-11 cycles PCR. The number of cycles was empirically determined for each library.   ChIP-seq sequencing lIbraries were made using Nugen Ovation Ultralow kit and quantified by bioanalyzer.
Libraries were bioanalyzed using Agilent High Sensitivity DNA Kit, pooled together and sequenced on Hiseq 2500 using paired end sequencing.

tag: gestational weeks

tag: antibody


title: chip-22gw_H3K27me3


title: chip-18gw_H4K20me3

source_name: Prefrontal cortex


title: chip-22gw_H3K20me3_CP


title: chip-18gw_H3K27ac


title: chip-17gw_H3K27ac


title: chip-17gw_H3K27me3


title: chip-17gw_H3K4me1


title: chip-15gw_H3K4me1


title: chip-15gw_H4K20me3


title: CR_E10_5_H3K27ac

city: Lausanne

first: Ana Rita

middle: Amandio

last: Lhopitallier

address: SV2842, Station 19

department: SV-ISREC-EPFL

country: Switzerland

institute: EPFL

data_processing:
ChIP-seq reads processing was done on the Duboule lab local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011) (options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), with standard settings. The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008). Peak calling in Figure 5 was done using MACS2 (v2.1.0.20160309) callpeak (--gsize 1870000000) using the corresponding input data as control BAM (-c).
Genome_build: mm10

source_name: cloaca region

extract_protocol:
Micro-dissected GT (35 to 40) or CR (70) were crosslinked in 1% formaldehyde/PBS for 20 min and stored at -80oC until further processing. Chromatin was sheared using a water-bath sonicator (Covaris E220 evolution ultra-sonicator). Immunoprecipitation was done using the following antibodies, anti-CTCF (Active Motif, 61311), anti- H3K27ac (Abcam, ab4729), and H3K27me3 (Merck Millipore, 07-449)
Libraries were prepared using the TruSeq protocol, and sequenced on the Illumina HiSeq system (100bp single-end reads) according to manufactures instructions.

value: Cloaca

tag: genotype

value: wild type

tag: developmental stage

value: CBA / C57BL/6 mix


title: chip-15gw_H3K27ac


title: GT_E13_5_WT_CTCF

source_name: genital tubercule

value: genital tubercle

value: CTCF


title: R_14_00096_TS_WTS

description: paired-end sequence reads

value: breast cancer

value: breast


title: CR_E10_5_H3K27me3


title: GT_E13_5_delV_CTCF

value: delV


title: atac-19gw_temporal

source_name: Temporal cortex


title: atac-19gw_s1

source_name: Somatosensory cortex


title: atac-19gw_pfc_ul

source_name: Prefrontal cortex, upper layer


title: atac-19gw_pfc


title: atac-19gw_parietal

source_name: Parietal cortex


title: atac-19gw_motor

source_name: Motor cortex


title: atac-18gw_pfc_dl

source_name: Prefrontal cortex, deep layer


title: atac-18gw_pfc_ul


title: atac-19gw_mge

source_name: Medial ganglionic eminence


title: atac-19gw_cge

source_name: Caudal ganglionic eminence


title: atac-18gw_pfc


title: atac-19gw_lge

source_name: Lateral ganglionic eminence


title: atac-18gw_lge


title: atac-18gw_mge


title: atac-18gw_cge


title: atac-17gw_v1

source_name: Visual cortex


title: atac-19gw_v1


title: atac-19gw_pfc_dl


title: atac-17gw_pfc


title: atac-17gw_cge


title: atac-17gw_motor


title: atac-14gw_v1


title: atac-14gw_s1


title: atac-14gw_pfc


title: atac-14gw_motor


title: atac-14gw_mge


title: atac-14gw_cge


title: 1633

type: genomic

city: Lubbock

first: Caleb

last: Phillips

state: Texas

address: 2901 Main Ave.

department: Department of Biological Sciences

institute: Texas Tech University

hyb_protocol: Followed Illumina procedures.

scan_protocol: Samples were genotyped according to the manufacturer’s protocol using the Infinium™ Global Screening Array -24 v2.0 microarray (Illumina, San Diego, CA, USA), which includes 665,608 markers focused on genome-wide tag-SNP variant coverage and clinically relevant research loci. Data were collected using the iScan System (Illumina), and preliminary processing/analysis (i.e., normalization, SNP clustering, genotype calling, call rate calculations, array-based QC) were conducted using GenomeStudio v.2.0 (Illumina).

data_processing:
Plink file sets were exported using the PLINK Input Report Plug-in v.2.1.4 within GenomeStudio. Quality control (QC) filtering was performed in accordance with Anderson et al., 2010. Briefly, individual level QC was performed to remove individuals (1) based on missingness (>0.09) and observed heterozygosity deviations (±3 SD from mean); (2) who exhibited a high degree of allele sharing/relatedness using an Identity-by-Descent threshold of 0.1875; and (3) with a high degree of ancestral divergence assessed via principal component analysis using SNPRelate. Marker-level filtering was performed to remove markers with low genotyping rates <0.05; and minor allele frequency <0.05. Principal component analysis via SNPRelate was performed again on the post-quality control dataset to generate correct eigenvectors for population structure correction in subsequent analyses. Additional information and data processing scripts may be found on corresponding author's github (https://github.com/genotyper/mbGWAS_wounds).
TX_micro.bim - Binary file format output of Illumina Infinium Global Array for human genotyping. Required file for downstream processing in PLINK. Contains raw genotyping information for Cohort 1.
ttgwas_p2.bim - Binary file format output of Illumina Infinium Global Array for human genotyping. Required file for downstream processing in PLINK. Contains raw genotyping information for Cohort 2.
TX_micro.bed - Binary file format output of Illumina Infinium Global Array for human genotyping. Required file for downstream processing in PLINK. Contains raw genotyping information for Cohort 1.
ttgwas_p2.bed - Binary file format output of Illumina Infinium Global Array for human genotyping. Required file for downstream processing in PLINK. Contains raw genotyping information for Cohort 2.
p2_cov2.txt - Contains metadata for cohort 2 in PLINK-friendly format.
cov2.txt - Contains metadata for cohort 1 in PLINK-friendly format.
update_p2_ids_clean.txt - Contains sample mapping for cohort 2 to link arbitrary generated names to sample names in PLINK-friendly format.
ttgwas_p2.fam - Binary file format output of Illumina Infinium Global Array for human genotyping. Required file for downstream processing in PLINK. Contains raw genotyping information for Cohort 2.
pheno_final.txt - Host phenotype file for cohort 1 in PLINK-friendly format.
pheno_p2.txt - Host phenotype file for cohort 2 in PLINK-friendly format.
TX_micro.fam - Binary file format output of Illumina Infinium Global Array for human genotyping. Required file for downstream processing in PLINK. Contains raw genotyping information for Cohort 1.
update_ids.txt - Contains sample mapping for cohort 2 to link arbitrary generated names to sample names in PLINK-friendly format.

label: biotin

source_name: Buccal swab

label_protocol: Followed Illumina procedures.

extract_protocol: Buccal swabs were transferred to the laboratory in liquid nitrogen, briefly thawed and 500 µL of Sterile Longmire’s Solution (100 mM Tris, 100 mM EDTA, 10 mM NaCl, 0.5 % SDS) was added to each sample vial. Extraction of genomic DNA was accomplished using Gentra PureGene Buccal Cell Kits (Qiagen, Gaithersburg, MD, USA) incorporating 65ºC lysis for 1 hour, RNase A treatment at 37 ºC for 30 minutes, and a final elution in HyClone HyPure Molecular Biology Grade Water (GE Healthcare Life Sciences MA, USA). All DNA samples were concentrated, if necessary, and normalized to the range of 10-50 ng/µL.

tag: chart number

tag: patient diagnosis

value: patient with wound

value: buccal swab

value: M

tag: birthdate

tag: racialcategory

value: White

tag: smoker

value: No

tag: cohort

value: Cohort 2


title: 2076


title: 2107

value: F


title: 1620


title: 1732


title: 1434


title: 1404


title: 1374


title: 1828


title: 1737

value: Black


title: 1665


title: 1077


title: atac-17gw_s1


title: 1082

value: Hispanic

value: Yes


title: 1151


title: 1792


title: 1555


title: 1660


title: 1590


title: 1677


title: 1432


title: 1372


title: 1423


title: 1583


title: 1408


title: 1505


title: 1727


title: 1286


title: 1560


title: 1428


title: 1960


title: 1968


title: 1281


title: 1531


title: 1578


title: 1800


title: 1559


title: atac-14gw_lge


title: 32


title: 1341


title: 1326


title: 1294


title: 1461


title: 1320


title: 1798


title: 1550


title: 1457


title: 1299


title: 1712


title: 1448


title: 1007


title: 2132


title: 1651


title: 1654


title: 1567


title: 1751


title: 1908


title: 2078


title: 1588


title: 1914


title: 1379


title: 1754


title: 1395


title: 1343


title: 1331


title: 1468


title: 1687


title: 1592


title: 1734


title: 2099


title: 1453


title: 1044


title: 1130


title: 1231


title: 1363


title: 1906


title: 1479


title: 1356


title: 1546


title: 1389


title: 2063


title: 1327


title: 1118


title: 2106


title: 1621


title: 1450


title: 1587


title: 1565


title: 38

value: Cohort 1


title: 1008


title: 1346


title: 77


title: 53


title: 1182


title: 1011


title: 1107


title: 25


title: 1232


title: 1150


title: 1016


title: 85


title: 59


title: 58


title: 1139


title: 1057


title: 1010


title: 76


title: 1093


title: 48


title: 47


title: 71


title: 9


title: 40


title: 1186


title: 3


title: 30


title: 66


title: 19


title: 1198


title: 1041


title: 28


title: 1064


title: 45


title: 74


title: 1035


title: 1270


title: 21


title: 67


title: 60


title: 49


title: 20


title: 46


title: 52


title: 57


title: 1196


title: 24


title: 7


title: 23


title: 68


title: 5


title: 55


title: 62


title: 41


title: 1125


title: 2


title: 14


title: 35


title: 65


title: 13


title: 6


title: 36


title: 26


title: 1054


title: 1099


title: 43


title: 29


title: 27


title: 42


title: 15


title: 31


title: 12


title: 1267


title: 56


title: 17


title: 63


title: 1043


title: 1179


title: 1145


title: 1038


title: Elm_GL_ml_rep2

first: kucsbl

last: submitter

state: Seoul

address: Anamdong 5-ga, Seongbuk-gu

department: Department of Biotechnology

institute: Korea University

data_processing:
Read data were aligned on the reference genome sequence.
DESeq and edgeR package in the Bioconductor/R packages were used for making RPKM values.
Base-calling by the MiSeq platform
Alignment by Bowtie software
Using R packages for DEG analysis
Genome_build: Eubacterium limosum KIST612 (GenBank ID: GCA_000152245.2)
Supplementary_files_format_and_content: TSV file of normalized RPKM value from edgeR for every samples.

organism: Eubacterium limosum

source_name: cultivated cell colony

growth_protocol: E. limosum KIST612 was cultivated separately supplemented with 20 mM glucose or 101 kPa of gaseous CO or H2/CO2 (80:20, v/v) as a substrate.

extract_protocol:
Total RNA was isolated from E. limosum KIST612 at the mid-log and early-stationary phases. The RNAprotect Bacterial Reagent and an RNeasy Mini Kit (Qiagen, Germany) were used for RNA isolation and a Ribo-zero rRNA Removal Kit (Epicentre, USA) was used for ribosomal RNA removal.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: substrate

value: Glucose

tag: growth phase

value: mid-log phase


title: Elm_GL_ml_rep1


title: 81

tag: tissue


title: Elm_GL_es_rep2

value: early-stationary phase


title: Elm_GL_es_rep3


title: Elm_HC_ml_rep2


title: Elm_GL_es_rep1


title: 50

tag: Sex


title: Elm_HC_es_rep3

tag: strain


title: 10


title: Elm_HC_es_rep2


title: Elm_CO_ml_rep1

value: CO


title: Elm_HC_es_rep1


title: Elm_CO_ml_rep2


title: Elm_CO_es_rep3


title: Elm_CO_es_rep2


title: Elm_GL_ml_rep3


title: Elm_CO_es_rep1


title: Elm_HC_ml_rep3


title: Elm_HC_ml_rep1


title: MH63_young_leaf_H3K4me1_H3K9me2

city: Wuhan

first: Liang

last: Xie

state: Hubei

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MSU.7.0/MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with --nomodel -B  -q 0.01 --fe-cutoff 1.2 -g 3.6e+8
Genome_build: MH63
Supplementary_files_format_and_content: bigWig file by deepTools bamCoverage

organism: Oryza sativa

source_name: MH63 young leaf

growth_protocol: Germinating seeds were obtained by soaking dry seeds in water for 72 h at 37 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °C. Roots were obtained 7 d after planting on moist filter paper, and young leaves were obtained from 2-week-old plants cultured hydroponically as described34. Approximately 20-d-old seedlings were transplanted to the field and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. Mature leaves at the floral induction phase and young panicles were harvested.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody twice.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10–15 min and quenched with 0.2 M glycine at room temperature.

value: young leaf

tag: development stage

value: two-week old seedlings

tag: cultivar

value: Minghui 63

tag: chip antibody

value: H3K4me1 H3K9me2


title: MH63_young_leaf_H3K4me3_H3K27ac

value: H3K4me3 H3K27ac


title: MH63_young_leaf_H3K9me2_H3K4me1


title: MH63_young_leaf_H3K27ac_H3K4me3


title: ZS97_mature_leaf_DNAmeth

data_processing:
The sequence quality of the whole-genome bisulfite sequencing (WGBS) libraries was evaluated using FastQC, and the adapter sequences and low-quality reads were filtered using Trimmomatic
The cleaned reads were then mapped to the MH63/ZS97 reference genome using BatMeth
The uniquely mapped reads were used for further analysis. Individual cytosines with coverage of at least 3 were considered for methylation-level calling.
The DNA methylation level of each cytosine was obtained by dividing the depth of methylated reads by the total coverage of individual cytosines
Genome_build: MH63,MSU7.0

source_name: ZS97 mature leaf

extract_protocol:
Genomic DNA was extracted using a DNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 69104).
Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-GoldTM kit (ZYMO, D5005), and the bisulfite-treated DNA libraries were constructed using the Illumina TruSeq DNA sample prep kit, following the manufacturers’ instructions.

treatment_protocol: Fresh samples are frozen using liquid nitrogen.

tag: tissues

value: mature leaf


title: Nip_mature_leaf_DNAmeth

source_name: NIP mature leaf

value: Nipponare


title: C051_young_leaf_DNAmeth

tag: age

value: young leaves from two-week old seedlings


title: C019_young_leaf_DNAmeth

value: Aijiaonante


title: C135_young_leaf_DNAmeth

value: Xibaizhan


title: ZS97_panicle_DNAmeth_P1.additional

source_name: ZS97 panicle

value: panicle

value: panicle (1.5–4.6 cm)


title: ZS97_panicle_DNAmeth_P2.additional

value: panicle (1.5–4.7 cm)


title: Nip_young_leaf_DNAmeth_1

source_name: NIP young leaf


title: Nip_panicle_DNAmeth_1

source_name: NIP panicle

value: panicle (1.5–4.5 cm)


title: ZS97_root_DNAmeth_P1.additional

source_name: ZS97 root

value: root

value: one-week old root after planting


title: ZS97_root_DNAmeth_1


title: ZS97_panicle_DNAmeth_P3.additional

value: panicle (1.5–4.8 cm)


title: Nip_root_DNAmeth

source_name: NIP root


title: Elm_CO_ml_rep3

value: CO

value: mid-log phase


title: ZS97_young_leaf_DNAmeth_P1.additional

source_name: ZS97 young leaf

value: young leaf


title: ZS97_panicle_DNAmeth_1


title: ZS97_young_leaf_DNAmeth_1


title: MH63_matrue_leaf_DNAmeth_P1.additional

source_name: MH63 mature leaf

value: mature leaves were flag leaf at floral induction phase

value: Minghui 63


title: MH63_young_leaf_DNAmeth_1


title: MH63_matrue_leaf_DNAmeth_1

value: mature leaf


title: MH63_young_leaf_DNAmeth_P1.additional


title: MH63_panicle_DNAmeth_P1.additional

source_name: MH63 panicle


title: W306_young_leaf_FAIRE_rep2

data_processing:
Library strategy: FAIRE-seq
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MSU.7.0/MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
Peak was calling using MACS2 with callpeak -t <input file> --nomodel --shift -100 --extsize 200 -f BAM –n <output peak file> -B -q 0.05 -g 3.6e+8
Genome_build: MH63,MSU7.0
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
The isolated nuclei pellet was resuspended in 400 ml of Sonic-FAIRE buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5% SDS, and protease inhibitor cocktail) and fragmented into 200–400-bp pieces by sonication in a Bioruptor (Diagenode). Lysates were centrifuged at 20,000 × g for 10 min at 4 °C, and the supernatant was transferred to a new tube. To prepare FAIRE DNA, 1 volume of phenol:chloroform:isoamyl alcohol was added to the supernatant; the mixture was vortex-mixed and centrifuged at 20,000 × g for 10 min; and the supernatant was transferred to a new tube. These steps were repeated at least twice to remove nucleosome-coated DNA. After ethanol precipitation, FAIRE DNA was resuspended in TE buffer.
DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645).

value: BASMATI 385


title: MH63_root_DNAmethy_1

source_name: MH63 root


title: MH63_panicle_DNAmeth_1


title: W081_young_leaf_FAIRE_rep2

value: young leaves from two-week old seedlings

value: Gasym Hany


title: W257_young_leaf_FAIRE_rep2


title: W257_young_leaf_FAIRE_rep1


title: W128_young_leaf_FAIRE_rep2

value: TAINO 38


title: W294_young_leaf_FAIRE_rep2

value: LABELLE


title: W169_young_leaf_FAIRE_rep2


title: W125_young_leaf_FAIRE_rep2

value: Yong Chal Byo


title: W128_young_leaf_FAIRE_rep1


title: W169_young_leaf_FAIRE_rep1


title: W261_young_leaf_FAIRE_rep1

value: Ginga


title: C148_young_leaf_FAIRE_rep1


title: C148_young_leaf_FAIRE_rep2


title: W161_young_leaf_FAIRE_rep1


title: W294_young_leaf_FAIRE_rep1


title: W161_young_leaf_FAIRE_rep2


title: C151_young_leaf_FAIRE_rep1


title: MH63_root_DNAmethy_P1.additional


title: W261_young_leaf_FAIRE_rep2


title: W125_young_leaf_FAIRE_rep1


title: C151_young_leaf_FAIRE_rep2


title: W081_young_leaf_FAIRE_rep1


title: W306_young_leaf_FAIRE_rep1


title: C135_young_leaf_FAIRE_rep1

value: Xibaizhan


title: C139_young_leaf_FAIRE_rep1


title: C135_young_leaf_FAIRE_rep2


title: W105_young_leaf_FAIRE_rep2

value: HKG 98


title: W286_young_leaf_FAIRE_rep1

value: Garia


title: W286_young_leaf_FAIRE_rep2


title: W105_young_leaf_FAIRE_rep1


title: Nip_root_FAIRE_1

value: root

value: one-week old root after planting

value: Nipponare


title: Nip_mature_leaf_FAIRE_1


title: Nip_mature_leaf_FAIRE_2


title: C139_young_leaf_FAIRE_rep2

value: young leaf


title: ZS97_mature_leaf_FAIRE_rep1

value: mature leaves were flag leaf at floral induction phase


title: Nip_young_leaf_FAIRE_rep1


title: ZS97_mature_leaf_FAIRE_rep2


title: Nip_panicle_FAIRE_rep1

value: panicle

value: panicle (1.5-4.5 cm)


title: Nip_panicle_FAIRE_rep2


title: Nip_young_leaf_FAIRE_rep2


title: ZS97_root_FAIRE_rep2


title: ZS97_root_FAIRE_rep1


title: ZS97_young_leaf_FAIRE_rep2


title: MH63_mature_leaf_FAIRE_rep2

value: mature leaf

value: Minghui 63


title: ZS97_young_leaf_FAIRE_rep1

value: young leaves from two-week old seedlings


title: MH63_mature_leaf_FAIRE_rep1


title: MH63_root_FAIRE_rep1


title: MH63_panicle_FAIRE_rep2


title: MH63_root_FAIRE_rep2


title: W306_young_leaf_RNA_rep1

data_processing:
Trimmomatic fitered the raw reads
The cleaned reads were mapped to the MH63 or MSU7.0 reference genome using TopHat.
gene expression was quantified using Cufflinks v2.2.5
Genome_build: MH63,MSU7.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Total RNA was isolated from tissue using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. The RNA (2 mg) was used for library construction using an Illumina TruSeq RNA kit, according to the manufacturer’s recommendations.
The RNA was used for library construction using an Illumina TruSeq RNA kit, according to the manufacturer’s recommendations.

tag: genotype

value: BASMATI 385


title: W306_young_leaf_RNA_rep2


title: MH63_panicle_FAIRE_rep1


title: W081_young_leaf_RNA_rep1

value: Gasym Hany


title: Nip_root_FAIRE_2


title: MH63_young_leaf_FAIRE_rep1


title: MH63_young_leaf_FAIRE_rep2


title: W081_young_leaf_RNA_rep2


title: W257_young_leaf_RNA_rep2


title: ZS97_panicle_FAIRE_rep1


title: ZS97_panicle_FAIRE_rep2


title: W294_young_leaf_RNA_rep2

value: LABELLE


title: W257_young_leaf_RNA_rep1


title: W261_young_leaf_RNA_rep2

value: Ginga


title: W294_young_leaf_RNA_rep1


title: W128_young_leaf_RNA_rep2

value: TAINO 38


title: W125_young_leaf_RNA_rep2

value: Yong Chal Byo


title: W261_young_leaf_RNA_rep1


title: W125_young_leaf_RNA_rep1


title: W169_young_leaf_RNA_rep2


title: C051_young_leaf_RNA_rep2


title: C051_young_leaf_RNA_rep1


title: W169_young_leaf_RNA_rep1


title: W161_young_leaf_RNA_rep2


title: W128_young_leaf_RNA_rep1


title: C151_young_leaf_RNA_rep2


title: C151_young_leaf_RNA_rep1


title: C148_young_leaf_RNA_rep1


title: C148_young_leaf_RNA_rep2


title: C139_young_leaf_RNA_rep2


title: W286_young_leaf_RNA_rep2

value: Garia


title: C135_young_leaf_RNA_rep2

value: Xibaizhan


title: C019_young_leaf_RNA_rep2

value: Aijiaonante


title: C139_young_leaf_RNA_rep1


title: W286_young_leaf_RNA_rep1


title: C019_young_leaf_RNA_rep1


title: W105_young_leaf_RNA_rep2

value: HKG 98


title: W105_young_leaf_RNA_rep1

value: young leaf


title: Nip_mature_leaf_RNA_rep2

value: mature leaves were flag leaf at floral induction phase

value: Nipponare


title: Nip_root_RNA_rep2

value: root

value: one-week old root after planting


title: Nip_mature_leaf_RNA_rep1

value: mature leaf


title: W161_young_leaf_RNA_rep1

value: young leaves from two-week old seedlings


title: Nip_root_RNA_rep1


title: Nip_panicle_RNA_rep2

value: panicle

value: panicle (1.5–4.5 cm)


title: ZS97_mature_leaf_RNA_rep2


title: Nip_panicle_RNA_rep1


title: Nip_young_leaf_RNA_rep2


title: ZS97_mature_leaf_RNA_rep1


title: Nip_young_leaf_RNA_rep1


title: ZS_root_RNA_rep2


title: C135_young_leaf_RNA_rep1


title: MH63_mature_leaf_RNA_rep1

value: Minghui 63


title: ZS_panicle_RNA_rep1

source_name: ZS97 panicle leaf


title: ZS_root_RNA_rep1


title: ZS_young_leaf_RNA_rep1


title: ZS_young_leaf_RNA_rep2


title: MH63_root_RNA_rep2


title: MH63_mature_leaf_RNA_rep2


title: MH63_panicle_RNA_rep1


title: MH63_root_RNA_rep1


title: MH63_panicle_RNA_rep2


title: W306_young_leaf_RNAPII_rep2

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MSU.7.0/MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with narrow(H3K4me3,H3K27ac,PII)/broad(H3K27me3,H3K4me1,H3K9me2) parameters
Genome_build: MSU.7.0,MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

value: BASMATI 385

value: RNAPII


title: MH63_young_leaf_RNA_rep2


title: W306_young_leaf_H3K4me1_rep1


title: W306_young_leaf_RNAPII_rep1


title: W306_young_leaf_H3K9me2_rep1


title: W306_young_leaf_H3K4me1_rep2


title: ZS_panicle_RNA_rep2


title: W306_young_leaf_H3K9me2_rep2


title: W306_young_leaf_H3K27me3_rep2


title: W306_young_leaf_H3K4me3_rep2


title: W306_young_leaf_H3K27ac_rep2


title: W081_young_leaf_H3K9me2_rep1

value: Gasym Hany


title: W081_young_leaf_H3K9me2_rep2


title: W081_young_leaf_H3K27me3_rep2


title: W081_young_leaf_H3K4me1_rep1


title: W306_young_leaf_H3K27ac_rep1


title: W306_young_leaf_H3K4me3_rep1


title: W081_young_leaf_H3K27ac_rep2


title: W081_young_leaf_H3K4me1_rep2


title: MH63_young_leaf_RNA_rep1


title: W081_young_leaf_RNAPII_rep2


title: W257_young_leaf_RNAPII_rep1


title: W081_young_leaf_RNAPII_rep1


title: W257_young_leaf_H3K9me2_rep2


title: W257_young_leaf_H3K4me1_rep1


title: W257_young_leaf_H3K9me2_rep1


title: W257_young_leaf_H3K27me3_rep2


title: W081_young_leaf_H3K4me3_rep2


title: W257_young_leaf_RNAPII_rep2


title: W081_young_leaf_H3K4me3_rep1


title: W257_young_leaf_H3K4me1_rep2


title: W257_young_leaf_H3K27ac_rep2


title: W081_young_leaf_H3K27me3_rep1


title: W294_young_leaf_RNAPII_rep2

value: LABELLE


title: W294_young_leaf_H3K9me2_rep2


title: W081_young_leaf_H3K27ac_rep1


title: W257_young_leaf_H3K27ac_rep1


title: W257_young_leaf_H3K27me3_rep1


title: W294_young_leaf_RNAPII_rep1


title: W257_young_leaf_H3K4me3_rep1


title: W294_young_leaf_H3K9me2_rep1


title: W294_young_leaf_H3K4me1_rep1


title: W294_young_leaf_H3K4me1_rep2


title: W294_young_leaf_H3K27me3_rep1


title: W294_young_leaf_H3K27me3_rep2


title: W294_young_leaf_H3K27ac_rep2


title: W261_young_leaf_RNAPII_rep2

value: Ginga


title: W294_young_leaf_H3K4me3_rep2


title: W294_young_leaf_H3K27ac_rep1


title: W261_young_leaf_H3K4me1_rep2


title: W261_young_leaf_H3K27ac_rep1


title: W261_young_leaf_H3K4me3_rep2


title: W261_young_leaf_H3K9me2_rep1


title: W261_young_leaf_H3K4me1_rep1


title: W261_young_leaf_H3K27me3_rep2


title: W128_young_leaf_RNAPII_rep2

value: TAINO 38


title: W294_young_leaf_H3K4me3_rep1


title: W128_young_leaf_RNAPII_rep1


title: W128_young_leaf_H3K9me2_rep2


title: W128_young_leaf_H3K9me2_rep1


title: W261_young_leaf_H3K9me2_rep2


title: W261_young_leaf_H3K27ac_rep2


title: W128_young_leaf_H3K4me1_rep2


title: W128_young_leaf_H3K4me1_rep1


title: W128_young_leaf_H3K27me3_rep1


title: W128_young_leaf_H3K27ac_rep2


title: W125_young_leaf_RNAPII_rep1

value: Yong Chal Byo


title: W261_young_leaf_H3K27me3_rep1

value: young leaf


title: W125_young_leaf_H3K9me2_rep2


title: W128_young_leaf_H3K27ac_rep1


title: W125_young_leaf_RNAPII_rep2


title: W128_young_leaf_H3K4me3_rep2


title: W125_young_leaf_H3K4me1_rep2


title: W125_young_leaf_H3K4me3_rep1


title: W125_young_leaf_H3K4me1_rep1


title: W125_young_leaf_H3K9me2_rep1


title: C051_young_leaf_RNAPII_rep1


title: W125_young_leaf_H3K27me3_rep2


title: W125_young_leaf_H3K27ac_rep1


title: W125_young_leaf_H3K27me3_rep1


title: C051_young_leaf_H3K9me2_rep2


title: W125_young_leaf_H3K4me3_rep2


title: W128_young_leaf_H3K27me3_rep2


title: W128_young_leaf_H3K4me3_rep1


title: W125_young_leaf_H3K27ac_rep2


title: C051_young_leaf_RNAPII_rep2


title: C051_young_leaf_H3K4me1_rep2


title: C051_young_leaf_H3K27me3_rep2


title: C051_young_leaf_H3K9me2_rep1


title: C051_young_leaf_H3K27ac_rep1


title: C051_young_leaf_H3K4me3_rep2


title: C051_young_leaf_H3K27me3_rep1


title: C051_young_leaf_H3K27ac_rep2


title: W169_young_leaf_H3K9me2_rep2


title: W169_young_leaf_RNAPII_rep1


title: W169_young_leaf_RNAPII_rep2


title: C051_young_leaf_H3K4me3_rep1


title: W169_young_leaf_H3K4me1_rep1


title: W169_young_leaf_H3K4me1_rep2


title: W169_young_leaf_H3K27ac_rep2


title: W161_young_leaf_RNAPII_rep1


title: W169_young_leaf_H3K4me3_rep1


title: W161_young_leaf_RNAPII_rep2


title: W161_young_leaf_H3K9me2_rep2


title: W161_young_leaf_H3K9me2_rep1


title: W161_young_leaf_H3K4me1_rep1


title: W169_young_leaf_H3K27me3_rep2


title: W169_young_leaf_H3K27me3_rep1


title: W161_young_leaf_H3K27me3_rep2


title: W161_young_leaf_H3K4me1_rep2


title: W161_young_leaf_H3K27me3_rep1


title: W161_young_leaf_H3K27ac_rep2


title: W169_young_leaf_H3K9me2_rep1


title: W161_young_leaf_H3K27ac_rep1


title: W161_young_leaf_H3K4me3_rep2


title: C148_young_leaf_H3K4me1_rep2


title: C148_young_leaf_RNAPII_rep2


title: C148_young_leaf_H3K9me2_rep2


title: C148_young_leaf_RNAPII_rep1


title: W169_young_leaf_H3K27ac_rep1


title: W169_young_leaf_H3K4me3_rep2


title: C148_young_leaf_H3K27me3_rep2


title: C148_young_leaf_H3K27ac_rep2


title: C148_young_leaf_H3K27me3_rep1


title: C151_young_leaf_RNAPII_rep2


title: C148_young_leaf_H3K4me3_rep1


title: C148_young_leaf_H3K27ac_rep1


title: C148_young_leaf_H3K4me3_rep2


title: C151_young_leaf_RNAPII_rep1


title: C151_young_leaf_H3K4me1_rep1


title: C151_young_leaf_H3K9me2_rep1


title: C151_young_leaf_H3K27me3_rep1


title: C151_young_leaf_H3K27ac_rep2


title: C151_young_leaf_H3K27ac_rep1


title: C151_young_leaf_H3K27me3_rep2


title: C148_young_leaf_H3K4me1_rep1


title: W261_young_leaf_H3K4me3_rep1


title: W161_young_leaf_H3K4me3_rep1


title: C151_young_leaf_H3K4me3_rep2


title: C148_young_leaf_H3K9me2_rep1


title: C139_young_leaf_RNAPII_rep1


title: C139_young_leaf_H3K9me2_rep2


title: C139_young_leaf_H3K4me1_rep1


title: C139_young_leaf_RNAPII_rep2


title: C151_young_leaf_H3K4me3_rep1


title: C139_young_leaf_H3K9me2_rep1


title: C139_young_leaf_H3K4me1_rep2


title: C139_young_leaf_H3K27me3_rep2


title: C151_young_leaf_H3K9me2_rep2


title: C151_young_leaf_H3K4me1_rep2


title: C139_young_leaf_H3K27me3_rep1


title: C139_young_leaf_H3K4me3_rep2


title: W261_young_leaf_RNAPII_rep1


title: C139_young_leaf_H3K4me3_rep1


title: W306_young_leaf_H3K27me3_rep1


title: C135_young_leaf_RNAPII_rep1

value: Xibaizhan


title: C135_young_leaf_H3K4me1_rep2


title: C135_young_leaf_H3K4me1_rep1


title: C135_young_leaf_H3K27me3_rep2


title: C135_young_leaf_H3K9me2_rep2


title: C135_young_leaf_H3K27ac_rep2


title: C135_young_leaf_H3K27me3_rep1


title: C135_young_leaf_H3K27ac_rep1


title: C019_young_leaf_RNAPII_rep2

value: Aijiaonante


title: C135_young_leaf_H3K4me3_rep1


title: C019_young_leaf_RNAPII_rep1


title: C019_young_leaf_H3K9me2_rep1


title: C019_young_leaf_H3K4me1_rep2


title: C019_young_leaf_H3K27me3_rep1


title: C139_young_leaf_H3K27ac_rep2


title: C019_young_leaf_H3K9me2_rep2


title: C019_young_leaf_H3K27me3_rep2


title: C135_young_leaf_RNAPII_rep2


title: C139_young_leaf_H3K27ac_rep1


title: C135_young_leaf_H3K9me2_rep1


title: C019_young_leaf_H3K27ac_rep1


title: C019_young_leaf_H3K4me3_rep1


title: W286_young_leaf_RNAPII_rep2

value: Garia


title: C019_young_leaf_H3K27ac_rep2


title: W286_young_leaf_RNAPII_rep1


title: W286_young_leaf_H3K9me2_rep2


title: C019_young_leaf_H3K4me3_rep2


title: C019_young_leaf_H3K4me1_rep1


title: W286_young_leaf_H3K9me2_rep1


title: W286_young_leaf_H3K27ac_rep1


title: W286_young_leaf_H3K4me1_rep2


title: W286_young_leaf_H3K27me3_rep1


title: W286_young_leaf_H3K27ac_rep2


title: W286_young_leaf_H3K4me3_rep2


title: W286_young_leaf_H3K4me3_rep1


title: W286_young_leaf_H3K27me3_rep2


title: W105_young_leaf_RNAPII_rep2

value: HKG 98


title: C135_young_leaf_H3K4me3_rep2


title: W105_young_leaf_H3K9me2_rep1


title: W105_young_leaf_RNAPII_rep1


title: W105_young_leaf_H3K9me2_rep2


title: W105_young_leaf_H3K4me1_rep1


title: W105_young_leaf_H3K4me1_rep2


title: W105_young_leaf_H3K27me3_rep2


title: W105_young_leaf_H3K27ac_rep2


title: W105_young_leaf_H3K27ac_rep1


title: W105_young_leaf_H3K4me3_rep2


title: NIP_INPUT

value: Nipponare


title: W105_young_leaf_H3K4me3_rep1

value: young leaves from two-week old seedlings


title: ZS_Input


title: MH_Input


title: ZS97_H3K4me3_0.05g_2


title: ZS97_H3K4me3_0.01g_2


title: W286_young_leaf_H3K4me1_rep1


title: ZS97_H3K4me3_0.01g_1


title: ZS97_H3K4me3_5g_standard


title: MH63_H3K9me2_0.2g_2


title: MH63_H3K9me2_0.05g_2


title: MH63_H3K9me2_0.01g_2


title: Nip_mature_leaf_RNAPII_rep1

value: mature leaf

value: mature leaves were flag leaf at floral induction phase


title: Nip_mature_leaf_H3K27me3_rep1


title: Nip_mature_leaf_H3K4me1_rep2


title: W105_young_leaf_H3K27me3_rep1


title: Nip_mature_leaf_H3K4me1_rep1


title: Nip_mature_leaf_RNAPII_rep2


title: Nip_mature_leaf_H3K27me3_rep2


title: MH63_H3K9me2_5g_standard

value: Minghui 63


title: Nip_mature_leaf_H3K27ac_rep2


title: Nip_mature_leaf_H3K27ac_rep1


title: ZS97_H3K4me3_0.2g_2


title: TPR1-HA_aGFP_r3 (ChIP-Seq)

city: Cologne

first: Thomas

last: Griebel

address: Carl-von-Linne-Weg 10

department: Department of Plant Microbe Interactions

institute: Max-Planck Institute for Plant Breeding Research

description: negative control for peak calling

data_processing:
Before mapping, remaining LinDA adapters and low quality sequences were removed from the sequencing data using a two-step procedure. Here, first Bpm and t7-Bpm sites were trimmed from the 5′ end using cutadapt (version 1.2.1) with options–e 0.2, -n 2 and–m 36 (otherwise default settings were used), and subsequently poly-A and poly-T tails and low quality ends were trimmed and reads with overall low quality or with less than 36 bases remaining after trimming were removed using PRINSEQ lite (version 0.20.2) (Schmieder and Edwards, 2011) with options–trim_qual_right/left 20, trim_tail_right/left 3 –min_len 36, -min_qual_mean 25. After the preprocessing steps, remaining high quality reads were mapped to the A. thaliana reference genome TAIR10 (http://www.arabidopsis.org) using Bowtie (version 2.0.5; default settings) (Langmead and Salzberg, 2012). For subsequent removal of non-uniquely mapping reads, the alignment output was filtered for mapping quality using samtools (version 0.1.18) (Li et al., 2009) view with option -q 10.
To identify genomic DNA regions (‘peak regions’) enriched in sequencing reads in the ChIP sample compared to the input control and TPR1-HA negative control, the peak calling algorithm of the QuEST program (version 2.4) (Valouev et al., 2008) was applied using the TF mode (option ‘2’), with permissive parameter settings for peak calling (option ‘3’). Each of three biological replicates was first analyzed separately. To obtain more exact peak locations for consistent peaks, mapped reads of the three replicates were additionally pooled and peaks called for the pooled samples. Further analyses were performed on peak regions identified from the pooled samples . To annotate peak locations with respect to annotated gene features in TAIR10 the annotatePeaks.pl function from the Homer suite (Heinz et al., 2010) was used with default settings.
Bed files for gene regions were prepared based on TAIR10 annotation (TAIR10_GFF3_genes_transposons, 11-07-2019). Raw sequence reads were trimmed with cutadapt (version 1.9.1, -e 0.2 -n 2 -m 30) to remove overrepresented sequences detected with fastqc (version 0.11.9) (Andrews et al., 2010) and then mapped to TAIR10 using bowtie2 (version 2.2.8). The resulting BAM files from individual biological replicates were deduplicated, filtered for low-quality mapping (-q 10 in view function in samtools version 1.9) and finally merged with samtools v1.9 (Li et al., 2009; Li, 2011). BAM/BAI files of the pooled samples are provided here.
The bigwig file provided for visualization in IGV (Thorvaldsdóttir et al., 2013) was prepared with bamCompare (--operation subtract --binSize 1) using merged BAM files for input and TPR1-GFP samples.
Genome_build: A. thaliana reference genome TAIR10
Supplementary_files_format_and_content: The bigwig file provided for visualization in IGV (Thorvaldsdóttir et al., 2013) was prepared with bamCompare (--operation subtract --binSize 1) using merged BAM files for input and TPR1-GFP samples.

organism: Arabidopsis thaliana

source_name: 6-week old leaves

growth_protocol: Plants were grown on soil with a daily 10 h light period (150-200 μE/m2s) at 22 °C and 60 % relative humidity. Plant leaf material was harvested after 6 weeks of growth.

extract_protocol:
ChIP was performed on 2 g leaf tissues of 6-week-old plants according to Gendrel et al. (2005) with modifications (Birkenbihl et al., 2012). Leaf samples were cross-linked twice by infiltration with 1% formaldehyde under a vacuum for 2x 7.5 minutes. Nuclei were disrupted by sonication 10 times for 30 s each and 30 s of cooling in a Bioruptor (Diagenode). IPs were performed using α-GFP (Ab6556, Abcam) antibodies and Protein A agarose beads (Sigma). After elution of immune complexes, cross-linking was reversed with an overnight incubation at 65°C in 200 mM NaCl followed by proteinase K digestion. DNA was extracted with phenol-chloroform and precipitated with ethanol in the presence of 0.3 M sodium acetate (pH=5.2) and 10 μg/mL glycogen (overnight at -20°C). After centrifugation, DNA pellets were washed with 70% ethanol, air-dried and resuspended in water before PCR.
MiniElute PCR Purification Kit (Qiagen, Germany) was used for cleaning ChIP DNA and two rounds of in vitro transcription by T7 RNA polymerase followed according to a linear DNA amplification (LinDA) protocol (Shankaranarayanan et al., 2011). Sequencing libraries were barcoded and generated using Ovation® Ultralow DR Multiplex system (NuGEN Technologies Inc.) including a 16-cycles PCR amplification. Libraries were size-selected (200-350 bp) with an agarose gel extraction using the MinElute Gel Extraction Kit (Qiagen, Germany).

treatment_protocol: untreated

tag: chip/antibody

value: anti-GFP


title: Nip_root_H3K4me1_rep1

value: root

value: one-week old root after planting


title: Nip_mature_leaf_H3K9me2_rep1


title: ZS97_H3K4me3_0.05g_1


title: Nip_mature_leaf_H3K4me3_rep2


title: Nip_mature_leaf_H3K4me3_rep1


title: Nip_root_H3K9me2_rep2


title: Nip_root_H3K4me1_rep2


title: TPR1-HA_aGFP_r2 (ChIP-Seq)

description: negative control for peak calling


title: TPR1-GFP_Input_r3 (ChIP-Seq)

description: negative control for peak calling

value: Input


title: Nip_mature_leaf_H3K9me2_rep2


title: Nip_root_H3K9me2_rep1


title: Nip_root_H3K27ac_rep2


title: Nip_root_H3K27ac_rep1


title: TPR1-GFP_Input_r2 (ChIP-Seq)

description: negative control for peak calling


title: Nip_root_H3K27me3_rep1


title: Nip_root_H3K4me3_rep2


title: TPR1-GFP_aGFP_r2 (ChIP-Seq)

description: TPR1-GFP ChIP


title: Nip_root_H3K4me3_rep1


title: TPR1-HA_aGFP_r1 (ChIP-Seq)

description: negative control for peak calling


title: TPR1-GFP_aGFP_r1 (ChIP-Seq)

description: TPR1-GFP ChIP


title: Nip_root_H3K27me3_rep2


title: Nip_panicle_RNAPII_2

value: panicle

value: panicle (1.5-4.5 cm)

value: RNAPII


title: TPR1-GFP_Input_r1 (ChIP-Seq)

description: negative control for peak calling


title: Nip_panicle_RNAPII_1


title: TPR1-GFP_aGFP_r3 (ChIP-Seq)

description: TPR1-GFP ChIP


title: Nip_panicle_H3K9me2_2


title: Nip_panicle_H3K9me2_1


title: MCF-10A Onco M + LPS+ LIGHT (RNA seq)

city: Boston

first: Rabih

last: Darwiche

state: MA

address: 240 longwwod ave

department: BCMP

institute: Harvard Medical School

description: Squencing used barcode

data_processing:
This program takes raw paired end Illumina fastq data from 3'READS RNA-seq and prepares both matched R1 and R2 fastq files for mapping. Strips off the 4 random nucleotides from each 5' end.  Counts and removes intial Ts. Checks for far read seqs and truncates before going beyond them into the far primer.  Appends the initial T count from the R1 read to the read ids of both the R1 and R2 reads. n.b. does NOT chop off the first non-random nt of R2, as we have done for other applications
bowtie -p24 -n0 -l27 -x700 -m1
Genome_build: Hg19

source_name: MCF-10A Breast cells

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) according to the manufacturer’s instructions. RNA obtained was further purified using QIAGEN RNeasy columns with DNase I treatment according to the manufacturer’s instructions. Libraries construction and amplified libraries were purified with SizeSelector-I beads (Aline Biosciences) as were prepared as described (Jin et al., 2015). Purified barcoded libraries were then examined and quantified via Bioanalyzer (Agilent). RNA-seq libraries were sequenced by Harvard Bauer Core Facility using Hiseq 2000. Sequence analysis was performed as described (Yi J, et al. 2015).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transcriptome level mRNA profiling was performed by 3’READS as described previously (Jin, Y. et al. Mapping 3' mRNA isoforms on a genomic scale. Curr. Protoc. Mol. Biol. 110, 4.23.21-24.23.17 (2015))

value: mammary gland; breast

tag: cell line

tag: passages

value: 3 to 5


title: MCF-10A Onco M + LPS (RNA seq)

description: Squencing used barcode


title: Nip_panicle_H3K4me1_2


title: Nip_panicle_H3K4me1_1


title: Nip_panicle_H3K27me3_2


title: MCF-10A LIGHT (RNA seq)

description: Squencing used barcode


title: MCF-10A Onco M + LIGHT (RNA seq)

description: Squencing used barcode


title: Nip_panicle_H3K27me3_1


title: Nip_panicle_H3K27ac_2


title: MCF-10A Onco M + TGF-a + HGF + IFN-Y (RNA seq)

description: Squencing used barcode


title: MCF-10A LPS (RNA seq)

description: Squencing used barcode


title: Nip_panicle_H3K27ac_1


title: Nip_panicle_H3K4me3_2


title: MCF-10A Onco M + TGF-a + HGF (RNA seq)

description: Squencing used barcode


title: MCF-10A Onco M+ TGF-a + IFN-Y (RNA seq)

description: Squencing used barcode


title: MCF-10A Onco M + HGF + IFN-Y (RNA seq)

description: Squencing used barcode


title: Nip_panicle_H3K4me3_1


title: Nip_young_leaf_RNAPII_2

value: young leaf


title: MCF-10A Onco M + TGF-a (RNA seq)

description: Squencing used barcode


title: MCF-10A Onco M + IFN-Y (RNA seq)

description: Squencing used barcode


title: CTL_0030: Control subjects 30

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

institute: Kyoto University Graduate School of Medicine

description: Control sample

hyb_protocol: Sandard Illumina protocol using bisulfite converted genomic DNA

scan_protocol: Standard protocol using the Illumina iScan system

data_processing: ChAMP analysis pipeline [ Y.Tian et al.,  Bioinformatics (2017)]

label: Cy3 and Cy5

source_name: Peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from peripheral blood samples using the QIAamp DNA blood midi kit

tag: diagnosis

value: Control

tag: gender

value: Female

value: whole blood


title: MCF-10A TGF-a + HGF + IFN-Y (RNA seq)

description: Squencing used barcode


title: CTL_0032: Control subjects 32

description: Control sample


title: Nip_young_leaf_RNAPII_1

value: young leaves from two-week old seedlings

value: Nipponare


title: CTL_0034: Control subjects 34

description: Control sample

value: Male


title: CTL_0020: Control subjects 20

description: Control sample


title: CTL_0023: Control subjects 23

description: Control sample


title: CTL_0029: Control subjects 29

description: Control sample


title: CTL_0027: Control subjects 27

description: Control sample


title: CTL_0033: Control subjects 33

description: Control sample


title: MCF-10A TGF-a + IFN-Y (RNA seq)

description: Squencing used barcode


title: CTL_0019: Control subjects 19

description: Control sample


title: CTL_0024: Control subjects 24

description: Control sample


title: Nip_young_leaf_H3K9me2_1


title: CTL_0031: Control subjects 31

description: Control sample


title: MCF-10A TGF-a + HGF (RNA seq)

description: Squencing used barcode


title: CTL_0026: Control subjects 26

description: Control sample


title: CTL_0025: Control subjects 25

description: Control sample


title: CTL_0017: Control subjects 17

description: Control sample


title: CTL_0021: Control subjects 21

description: Control sample


title: CTL_0018: Control subjects 18

description: Control sample


title: MCF-10A HGF + IFN-Y (RNA seq)

description: Squencing used barcode


title: CTL_0007: Control subjects 7

description: Control sample


title: CTL_0028: Control subjects 28

description: Control sample


title: Nip_young_leaf_H3K4me1_2


title: CTL_0016: Control subjects 16

description: Control sample


title: Nip_young_leaf_H3K4me1_1


title: CTL_0022: Control subjects 22

description: Control sample


title: MCF-10A IFN-Y (RNA seq)

description: Squencing used barcode


title: CTL_0012: Control subjects 12

description: Control sample


title: Nip_young_leaf_H3K27me3_2


title: MCF-10A Onco M (RNA seq)

description: Squencing used barcode


title: CTL_0013: Control subjects 13

description: Control sample


title: CTL_0014: Control subjects 14

description: Control sample


title: Nip_young_leaf_H3K27me3_1


title: CTL_0010: Control subjects 10

description: Control sample


title: CTL_0015: Control subjects 15

description: Control sample


title: CTL_0011: Control subjects 11

description: Control sample


title: Nip_young_leaf_H3K9me2_2


title: MCF-10A w/o Cytokines (RNA seq)

description: Squencing used barcode


title: CTL_0009: Control subjects 9

description: Control sample


title: Nip_young_leaf_H3K27ac_2


title: preTHigh_3

city: Philadelphia

first: Eduardo

middle: A

last: Torre

state: PA

department: Bioengineering

institute: University of Pennsylvania

data_processing:
We aligned reads to hg19 and quantified reads per gene using STAR and HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: .tsv files conain reads per gene (unnormalized)

source_name: melanoma cells

growth_protocol: We grew these cells at 37°C in Tu2% media (78% MCDB, 20% Leibovitz’s L-15 media, 2% FBS, and 1.68mM CaCl2)

extract_protocol:
For each sample, we isolated mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module
We built the RNA sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina
We sequenced the libraries via paired-end sequencing on a NextSeq 500

treatment_protocol: We either treated cells with 4uM EPZ5676 or with DMSO for seven days

tag: cell type

value: melanoma

tag: treatment

value: Pre-treated with EPZ5676 for one week

tag: cell population

value: Only cells with high levels of NGFR and EGFR expression


title: preTBulk_3

value: Bulk population


title: preTLow_2

value: Only cells with low levels of NGFR and EGFR expression


title: Nip_young_leaf_H3K4me3_1

tag: tissue


title: ZS97_mature_leaf_RNAPII_rep2

value: mature leaf

value: mature leaves were flag leaf at floral induction phase


title: CTL_0005: Control subjects 5

description: Control sample


title: CTL_0003: Control subjects 3

description: Control sample


title: CTL_0006: Control subjects 6

description: Control sample


title: preTLow_3


title: Nip_young_leaf_H3K27ac_1

source_name: NIPyoung leaf


title: CTL_0008: Control subjects 8

description: Control sample


title: Nip_young_leaf_H3K4me3_2


title: preTHigh_2


title: WS_0034: WS patients 34

description: WS sample

value: Williams syndrome (WS)


title: ZS97_mature_leaf_RNAPII_rep1

source_name: ZS97 mature leaf

value: RNAPII


title: WS_0030: WS patients 30

description: WS sample


title: WS_0033: WS patients 33

description: WS sample


title: CTL_0001: Control subjects 1

description: Control sample


title: preTBulk_2


title: ZS97_mature_leaf_H3K9me2_rep2


title: preTLow_1


title: ZS97_mature_leaf_H3K9me2_rep1


title: WS_0029: WS patients 29

description: WS sample


title: preTHigh_1


title: preTBulk_1


title: CTL_0002: Control subjects 2

description: Control sample


title: ZS97_mature_leaf_H3K4me1_rep1


title: WS_0032: WS patients 32

description: WS sample


title: dmsoLow_3

value: Pre-treated with DMSO for 1 week


title: WS_0027: WS patients 27

description: WS sample


title: ZS97_mature_leaf_H3K27me3_rep2


title: WS_0026: WS patients 26

description: WS sample


title: ZS97_mature_leaf_H3K4me1_rep2


title: dmsoHigh_3


title: WS_0024: WS patients 24

description: WS sample


title: ZS97_mature_leaf_H3K27me3_rep1


title: dmsoBulk_3


title: WS_0025: WS patients 25

description: WS sample


title: WS_0020: WS patients 20

description: WS sample


title: WS_0022: WS patients 22

description: WS sample


title: WS_0019: WS patients 19

description: WS sample


title: WS_0028: WS patients 28

description: WS sample


title: CTL_0004: Control subjects 4

description: Control sample


title: dmsoLow_2


title: ZS97_mature_leaf_H3K4me3_rep2


title: ZS97_mature_leaf_H3K27ac_rep1


title: RVC_95901

city: Tucson

first: Eugene

middle: H

last: Chang

state: AZ

address: 1501 N. Campbell Avenue

department: Department of Otolaryngology

institute: The University of Arizona

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15
We processed the discovery and validation data sets separately through making use of NOISeq library in order to filter out the genes with low count, specifically cpm <30 with method one. This procedure resulted in 7,474 and 7,905 unique genes, respectively, for discovery and validation cohorts.
We then utilized the function “ARSyNseq” (Nueda et al. 2012) implemented in R package NOISeq together with TMM normalization in order to remove the known batch effects in addition to other hidden and noisy systematic variation from each cohort separately.
Through the use of function “voomWithQualityWeights” (Ritchie et al. 2006, Law et al. 2014, Liu et al. 2015) from LIMMA package we further made the processed RNA count values ready for downstream statistical analysis with linear model implemented in LIMMA R library.
genome build: hg38
Supplementary_files_format_and_content:tab-delimited text file include rsem inferred count values for each Sample

growth_protocol: We developed well-differentiated ciliated air-liquid interface (ALI) cultures from nasal tissues biopsied from thirty adults with physician-diagnosed asthma.

extract_protocol:
RNA was extracted from whole-cell lysates, mapped to the UCSC transcript set using Bowtie2 (v2.1.0) and the gene expression level was estimated using standard techniques.
Libraries for RNA-Seq were prepared with Kapa Stranded mRNA. The workflow consisted of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: We infected ALI cultures with common RV strains RV-A16 (1x105 RNA copies/well), RV-C15 (1x105 RNA copies/well, courtesy of Dr. James Gern), or DMEM/F12 media (control) for 4 hrs at 34°C, 5% CO2.

value: RVC

tag: clinical _w

value: No

tag: Sex

value: H

tag: race

value: W

tag: cohort

value: validataion


title: RVA_95901

value: RVA

value: Female


title: dmsoHigh_2

value: melanoma


title: Control_95901

value: Control


title: ZS97_mature_leaf_H3K4me3_rep1

tag: development stage

tag: cultivar

tag: chip antibody


title: dmsoBulk_2


title: WS_0014: WS patients 14

description: WS sample

value: Male

value: whole blood


title: WS_0012: WS patients 12

description: WS sample


title: WS_0011: WS patients 11

description: WS sample


title: WS_0015: WS patients 15

description: WS sample


title: dmsoLow_1

value: Only cells with low levels of NGFR and EGFR expression


title: ZS97_root_H3K9me2_rep2

value: root

value: one-week old root after planting


title: RVC_49101

value: NH

tag: age


title: WS_0010: WS patients 10

description: WS sample

value: Williams syndrome (WS)


title: dmsoHigh_1

value: Pre-treated with DMSO for 1 week

value: Only cells with high levels of NGFR and EGFR expression


title: WS_0031: WS patients 31

description: WS sample


title: WS_0016: WS patients 16

description: WS sample


title: WS_0017: WS patients 17

description: WS sample


title: RVA_49101

value: No


title: Control_49101


title: ZS97_root_H3K9me2_rep1


title: WS_0006: WS patients 6

description: WS sample


title: RVC_20501

value: RVC

value: Yes


title: RVA_20501

value: W

value: validataion


title: WS_0003: WS patients 3

description: WS sample

value: Female


title: Control_20501