title: Day5_CPC_Isl1_IP_ChIP_seq_rep1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

description:
Bigwig file from merge repetition 1 and 2
Day5_CPC_Isl1_IP_ChIP_seq_merge.bw
Day5_CPC_Isl1_peaks.txt

data_processing:
ChIP-Seq reads were mapped to the mouse reference genome mm9 (UCSC assembly) using the default settings of bowtie2. The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks were called with the use of MACS14 with the parameter (p1e8 --nomodel --shiftsize 80). Peaks overlapping blacklist defined by ENCODE were removed.
Bedtools v2.15 (intersect -wa) was used to find the common binding areas in experimental replicates.
ChIP-Seq peak annotation was performed using annotatePeaks.pl (default settings), which assigns each peak to the closest gene transcriptional start site (TSS).
For data visualization bam files were converted to BigWig files by the use of BamCoverage from deepTools2 (-b 20 -smooth 40 -e 150 --normalizeTo1x 2150570000).
Genome_build: mm9
Supplementary_files_format_and_content: bw, txt

source_name: Cardiac progenitors

growth_protocol: E14 Tg(Nkx2–5-EmGFP) ES cells were maintained on mitomycin treated MEF in Knockout DMEM medium containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, and 1,000 U/ml of leukemia inhibitory factor. For directed cardiomyocyte differentiation, ES cells were grown on gelatin in Neurobasal medium: DMEM/F12 (1:1) medium supplemented with 2,000 U/ml LIF and 10 ng/ml BMP4 for 2 days and differentiated by aggregation in low attachment bacterial dishes at a cell density of 75000 cells/ml in IMDM: F12 medium (3:1). After 48h aggregates were dissociated and re-aggregated in the presence of 5 ng/ml Activin A, 5ng/ml VEGF and 0.2ng/ml BMP4. 40h following the second aggregation, aggregates were dissociated and plated as a monolayer in Stempro-34 medium supplemented with Stempro34 nutrient supplement, L-Ascorbic Acid and 5ng/ml VEGF, 10ng/ml bFGF, and 25ng/ml FGF10 growth factors. ESC-derived cardiac progenitor cells were collected at day 5 for ChIP.

extract_protocol: mESC-derived CPCs were crosslinked with 1% formaldehyde at room temperature for 10 min. Crosslinking was terminated by adding 125 mM glycine followed by three washes with cold PBS. Nuclei were isolated by incubation in lysis buffer (50 mM Tris pH 8.0, 2 mM EDTA pH 8.0, 0.1% NP-40, 10% glycerol) along with protease and phosphatase inhibitors. Nuclei were frozen at −80 °C until further processing. Nuclei were lysed in nuclear lysis buffer supplemented with protease and phosphatase inhibitors (50 mM Tris pH 8.0, 1% SDS, 5 mM EDTA pH 8.0). Lysates were sonicated with Bioruptor (Diagenode) to achieve fragment sizes in the range of 200-500 bp. Lysates were diluted 1:10 in dilution buffer (50 mM Tris pH8.0, 200 mM NaCl, 5 mM EDTA pH8.0, 0.5% NP40) with protease and phosphatase inhibitors and precleared with Protein G Sepharose (GE Healthcare). Precleared lysates were incubated with 2-5 µg anti-Isl1 antibody (DSHB, clone 39.4D5) overnight at 4 °C followed by pulldown with BSA-presaturated protein G Sepharose beads. Immune complexes were washed with NaCl wash buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% NP-40), LiCl wash buffer (20 mM Tris pH 8.0, 500 mM LiCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% NP40) and TE wash buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0). Protein/DNA complexes were extracted in elution buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0 and 2% SDS) followed by reverse crosslinking at 65 °C overnight. DNA purification was performed using phenol-chloroform.

tag: cell line

value: E14 Tg(Nkx2-5-EmGFP) ES cells

value: Embryonic stem cells (ESC)

tag: sample description

value: ESC-derived cardiac progenitor cells

value: Isl1 (Developmental Studies Hybridoma Bank (DSHB) clone 39.4D5)


title: NMuMG RNA-seq vector replicate 1

status: Public on May 02 2019

type: SRA

city: Bethesda

first: Benjamin

last: Carter

state: MD

address: 10 Center Drive

department: NHLBI

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed using Trimmomatic and aligned to the appropriate reference genome using HISAT2 in paired-end mode. ATAC-seq reads were trimmed using Trimmomatic and mapped to the appropriate reference genome using Bowtie2 in very sensitive end-to-end mode.
For RNA-seq, gene expression levels were computed using htseq-count using default parameters. For ATAC-seq, BAM files were converted to BED files using BEDtools.
For RNA-seq, differential expression analysis was performed using edgeR with a FDR threshold of 0.05. For ATAC-seq, peaks of differential enrichment were identified using SICER-df with a false discovery rate threshold of 0.05. The annotatePeaks utility of HOMER was used to annotate statistically significant peaks.
Genome_build: hg19 for HK2. mm10 for NmuMG.
Supplementary_files_format_and_content: For RNA-seq, the raw counts matrix is provided as a tab-delimted text file. For ATAC-seq, files are tab-delimited text containing the annotated peaks obtained from HOMER.

molecule: total RNA

organism: Mus musculus

source_name: NMuMG cells

growth_protocol: HK-2 cells were cultured in RPMI supplemented with 10% FBS and 1% L -glutamine. NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10 µM/mL insulin, 1% L -glutamine, and 1% sodium pyruvate. All cell lines were grown at 37°C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA). Genomic DNA for ATAC-seq was obtained according to the ENCODE ATAC-seq pipeline.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stress treatments were performed immediately prior to RNA extraction. For peroxide stress, cells were treated with media containing 200 µM H2O2 for two hours. For low-glucose stress, cell media was replaced with glucose-free media for six hours.

tag: treatment

value: Lentiviral transfection of empty vector


title: Day5_CPC_Isl1_Input_ChIP_seq

library_source: genomic

data_processing:
ChIP-Seq reads were mapped to the mouse reference genome mm9 (UCSC assembly) using the default settings of bowtie2. The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks were called with the use of MACS14 with the parameter (p1e8 --nomodel --shiftsize 80). Peaks overlapping blacklist defined by ENCODE were removed.
Bedtools v2.15 (intersect -wa) was used to find the common binding areas in experimental replicates.
ChIP-Seq peak annotation was performed using annotatePeaks.pl (default settings), which assigns each peak to the closest gene transcriptional start site (TSS).
For data visualization bam files were converted to BigWig files by the use of BamCoverage from deepTools2 (-b 20 -smooth 40 -e 150 --normalizeTo1x 2150570000).
Genome_build: mm9
Supplementary_files_format_and_content: Bw

molecule: genomic DNA

extract_protocol: mESC-derived CPCs were crosslinked with 1% formaldehyde at room temperature for 10 min. Crosslinking was terminated by adding 125 mM glycine followed by three washes with cold PBS. Nuclei were isolated by incubation in lysis buffer (50 mM Tris pH 8.0, 2 mM EDTA pH 8.0, 0.1% NP-40, 10% glycerol) along with protease and phosphatase inhibitors. Nuclei were frozen at −80 °C until further processing. Nuclei were lysed in nuclear lysis buffer supplemented with protease and phosphatase inhibitors (50 mM Tris pH 8.0, 1% SDS, 5 mM EDTA pH 8.0). Lysates were sonicated with Bioruptor (Diagenode) to achieve fragment sizes in the range of 200-500 bp. Lysates were diluted 1:10 in dilution buffer (50 mM Tris pH8.0, 200 mM NaCl, 5 mM EDTA pH8.0, 0.5% NP40) with protease and phosphatase inhibitors and precleared with Protein G Sepharose (GE Healthcare). 10% of precleared lysates were taken as input. Protein/DNA complexes were extracted in elution buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0 and 2% SDS) followed by reverse crosslinking at 65 °C overnight. DNA purification was performed using phenol-chloroform.

tag: cell type

tag: chip antibody

value: none, input sample


title: Rhode Island Red-RIR_R32 [reanalyzed]

type: genomic

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

department: Animal Genetics and Breeding

country: China

institute: China Agricultural University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix Operating Software (AxAS version 4.0.1).
Genotype Call (SNP call): A/T/C/G

label: Biotin

organism: Gallus gallus

source_name: Rhode Island Red

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: chickens were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: tissue

value: Blood


title: cll_175_h3k27ac_bam

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave

department: HOPP

institute: MSKCC

data_processing:
ChIP-seq data were processed according to the ENCODE Histone ChIP-seq Data Standards and Processing Pipeline (https://www.encodeproject.org/chip-seq/histone/). Raw reads were mapped to the Human genome GRCh37 assembly using Burrows-Wheeler Aligner (BWA v0.7.17). Duplicate reads were removed using Picard (https://broadinstitute.github.io/picard/) and bigwig files were created for visualization. Peaks were identified with Macs2 (v2.0.10) with a q-value threshold of 0.01 and de novo motif enrichment analyses were performed using Homer against JASPAR CORE database. Peaks overlapping with Satellite repeat regions and Encode Blacklist were discarded. All ChIP-seq reads were normalized and displayed as read counts per million mapped reads.
Raw reads were mapped to the human genome GRCh37 using STAR (v2.5.2a) aligner49. We used several QC metrics for the RNA-seq library, including intron–exon ratio, intragenic reads fraction and GC bias. We quantified exon and gene expression using Salmon50 against the Homo sapiens transcriptome GRCh37.
Genome_build: GRCh37

organism: Homo sapiens

source_name: CLL

growth_protocol: Human subjects, sample collection and genotyping. The study was approved by the local ethics committee and by the Institutional Review Board (IRB) and conducted in accordance to the Declaration of Helsinki protocol. Blood samples were collected in EDTA blood collection tubes (BD Biosciences) from patient and healthy adult volunteers enrolled on clinical research protocols at the Dana-Faber/Harvard Cancer Center (DF/HCC), Memorial Sloan Kettering Cancer Center (MSKCC), and NewYork-Presbyterian/Weill Cornell Medical Center (NYP/WCMC). We note that the IRB does not permit collection of demographic information of healthy donors. The diagnosis of CLL according to World Health Organization (WHO) criteria was confirmed in all cases by flow cytometry, or by lymph node or bone marrow biopsy. Peripheral blood mononuclear cells (PBMCs) from normal donors and patients were isolated by Ficoll-Paque Plus (GE Healthcare) density gradient centrifugation. PBMCs were cryopreserved in 50%FBS/40%RPMI/10% DMSO and stored in vapor-phase liquid nitrogen until the time of analysis. Informed consent on DFCI and WCM IRB-approved protocols for genomic sequencing of patients’ samples was obtained prior to the initiation of sequencing studies. Immunoglobulin heavy-chain variable (IGHV) homology (unmutated was defined as greater than or equal to 98% homology to the closest germline match) were determined44. Cytogenetics were primarily evaluated by FISH analysis for the most common CLL abnormalities [del(13q), trisomy 12, del(11q), del(17p), del(6p)]

extract_protocol:
A minimum of 2 million purified human cells were used. Briefly, cells were fixed in a 1% methanol-free formaldehyde solution and then resuspended in sodium dodecyl sulfate (SDS) lysis buffer. Lysates were sonicated in an E220 focused-ultrasonicator (Covaris, Woburn, MA) to a desired fragment size distribution of 100–500 base pairs. Immunoprecipitation reactions were performed with the above-indicated antibodies, each on approximately 500,000 cells. ChIP assays were processed on an SX-8G IP-STAR Compact Automated System (Diagenode, Denville, NJ) using a direct ChIP protocol as previously described. Eluted chromatin fragments were then de-crosslinked and the DNA fragments purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Barcoded immunoprecipitated DNA and input DNA were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (#E6240, New England Biolabs, Ipswich, MA) and TruSeq Adaptors (Illumina) according to the manufacturer’s protocol on an SX-8G IP-STAR Compact Automated System (Diagenode). Phusion High-Fidelity DNA Polymerase (New England Biolabs) and TruSeq PCR Primers (Illumina, San Diego, CA) were used to amplify the libraries, which were then purified to remove adaptor dimers using AMPure XP beads and multiplexed on the HiSeq 2000 (Illumina, San Diego, CA).
dodecyl sulfate (SDS) lysis buffer. Lysates were sonicated in an E220 focused-ultrasonicator (Covaris, Woburn, MA) to a desired fragment size distribution of 100–500 base pairs. Immunoprecipitation reactions were performed with the above-indicated antibodies, each on approximately 500,000 cells. ChIP assays were processed on an SX-8G IP-STAR Compact Automated System (Diagenode, Denville, NJ) using a direct ChIP protocol as previously described45. Eluted chromatin fragments were then de-crosslinked and the DNA fragments purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Barcoded immunoprecipitated DNA and input DNA were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (#E6240, New England Biolabs, Ipswich, MA) and TruSeq Adaptors (Illumina) according to the manufacturer’s protocol on an SX-8G IP-STAR Compact Automated System (Diagenode). Phusion High-Fidelity DNA Polymerase (New England Biolabs) and TruSeq PCR Primers (Illumina, San Diego, CA) were used to amplify the libraries, which were then purified to remove adaptor dimers using AMPure XP beads and multiplexed on the HiSeq 2000 (Illumina, San Diego, CA). RNA was extracted using Qiagen (Hilden, Germany) RNeasy columns according to the manufacturer’s instructions. Subsequently, 500 ng of total RNA was used for polyA selection and TruSeq library preparation according to the instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 125 bp paired-end mode, using the TruSeq SBS Kit v.3 (Illumina, San Diego, CA). An average of 75 million paired reads was generated per sample.

treatment_protocol: Untreated

value: Peripheral Blood

value: CLL IGHV mutated

tag: antibody


title: Rhode Island Red-RIR_R31 [reanalyzed]


title: E8.25-E9_Isl1_Input

data_processing:
ChIP-Seq reads were mapped to the mouse reference genome mm9 (UCSC assembly) using the default settings of bowtie2. The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks were called with the use of MACS14 with the parameter (p1e8 --nomodel --shiftsize 80). Peaks overlapping blacklist defined by ENCODE were removed.
ChIP-Seq peak annotation was performed using annotatePeaks.pl (default settings), which assigns each peak to the closest gene transcriptional start site (TSS).
For data visualization bam files were converted to BigWig files by the use of BamCoverage from deepTools2 (-b 20 -smooth 40 -e 150 --normalizeTo1x 2150570000).
Genome_build: mm9
Supplementary_files_format_and_content: Bw

source_name: E 8.75 mouse embryos

extract_protocol: Cardiogenic mesoderm and heart region of E8.25-E9 mouse embryo was crosslinked with 1% formaldehyde at room temperature for 15 min. Crosslinking was terminated by adding 125 mM glycine followed by three washes with cold PBS. Single cells were obtained by disruption of the tissue using pestle and mortar and nuclei were isolated by incubation in lysis buffer (50 mM Tris pH 8.0, 2 mM EDTA pH 8.0, 0.1% NP-40, 10% glycerol) along with protease and phosphatase inhibitors. Nuclei were frozen at −80 °C until further processing. Around 60-80 E8.25 to E9.0 embryos were pooled and lysed in nuclear lysis buffer supplemented with protease and phosphatase inhibitors (50 mM Tris pH 8.0, 1% SDS, 5 mM EDTA pH 8.0). Lysates were sonicated with Bioruptor (Diagenode) to achieve fragment sizes in the range of 200-500 bp. Lysates were diluted 1:10 in dilution buffer (50 mM Tris pH8.0, 200 mM NaCl, 5 mM EDTA pH8.0, 0.5% NP40) with protease and phosphatase inhibitors and precleared with Protein G Sepharose (GE Healthcare). 10% of precleared lysates were taken as input. Protein/DNA complexes were extracted in elution buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0 and 2% SDS) followed by reverse crosslinking at 65 °C overnight. DNA purification was performed using phenol-chloroform.

tag: embryonic stage

tag: strain

value: none; Input sample


title: cd20_167_wce_bam

source_name: B cell CD20+

value: peripheral blood CD20+

value: wce


title: D35 IL-18Ra+_ILC1 Liver_ATAC_002

city: New Haven

first: Orrel

last: Weizman

state: CT

address: 333 Ceder Street

department: Immunology

institute: Yale

description: Table 2.csv

data_processing:
RNA sequencing reads were aligned using STAR (2.5.3a-foss-2016b) with  filters --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --  outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --  alignMatesGapMax 1000000 to allow for stringent alignment of unique reads to the  mouse (mm10) genome50.
Counts were made using BEDtools 2.27.1 coveragebed  function. Raw count files were processed using DESeq2, removing genes with less than  50 counts.
For ATAC sequencing peak-calling, read start sides aligned to the positive  strand and negative strands were offset by +4bp and -5bp, respectively, as described by51  Peak calling was performed on each time point (D0, D35 IL18+) individually by pooling  reads from biological replicates, and using MACS252, R137 with p-value threshold 0.2.  To exclude any peaks identified due to noise, we calculated an irreproducible discovery  rate (IDR)53. The IDR is an estimate of the threshold where two ranked lists of results, in  this case peak calls ranked by P value, no longer represent reproducible events. Using  this measure we excluded peaks that were not reproducible (IDR < 0.05) across replicates  for each time point. We created a single atlas of accessible sites across the two  timepoints by merging peaks from the IDR-reproducible peak list for each timepoint. In  this way, we created an atlas of 23016 reproducible peaks, and associated each peak to its  nearest gene in the mouse genome.
Differential expression and accessibility were  computed using DESeq2; genes were considered differentially expressed at FDR p = 0.05  and absolute value of log2FC < 1, and peaks were considered differentially accessible  between timepoints at FDR p = 0.2.
For heatmaps, the R package pheatmap and Broad  institute tool Morpheus was used to plot DESeq2 normalized counts. For visualization of  tracks with IGV (IGV 2.3.94), BAM files were indexed with SAMtools/1.5-foss-2016b  and then normalized and converted to a BigWig file using Python/2.7.13-foss-  2016b bamCoverage function.
Genome_build: mm10
Supplementary_files_format_and_content: .csv file with base mean, log2FC, Pval, Padju and normalized counts

source_name: Liver ILC1

extract_protocol:
To   isolate lymphocytes from liver, the tissues were physically dissociated using a glass  tissue homogenizer and purified using a discontinuous gradient of 40% over 60% Percoll. RBC were lysed using ACK lysis buffer
For ATAC sequencing, ATAC-seq libraries were prepared as previously described12 FACS-sorted cell populations (1x104 cells) were lysed and accessible chromatin was transposed using Nextera Tn5 transposase. Transposed DNA fragments were isolated using Qiagen MinElute kit and amplified 5-10 cycles using Nextera PCR primers. ATAC-seq libraries were submitted for paired-end sequencing on Illumina Hiseq.

value: liver

tag: age

value: 8 weeks

tag: days post infection

tag: Sex

value: female


title: Rhode Island Red-RIR_R34 [reanalyzed]


title: cd20_167_h3k4me1_bam


title: Rhode Island Red-RIR_R30 [reanalyzed]


title: D35 IL-18Ra+_ILC1 Liver_ATAC_001

description: Table 2.csv


title: Rhode Island Red-RIR_R29 [reanalyzed]


title: cd20_167_h3k36me3_bam


title: cd20_167_h3k27me3_bam


title: D0_ILC1 Liver_ATAC_002

description: Table 2.csv


title: Rhode Island Red-RIR_R27 [reanalyzed]


title: Day5_CPC_Isl1_IP_ChIP_seq_rep2


title: Rhode Island Red-RIR_R28 [reanalyzed]


title: cd20_167_h3k27ac_bam


title: Patient 37

type: RNA

city: Berlin

first: Ingeborg

last: Tinhofer

address: Chariteplatz 1

department: Dept of Radiooncology and Radiotherapy

institute: Charite University Hospital

hyb_protocol: Hybridization was carried out according to the standard Nanostring nCounter® XT Assay protocol.

scan_protocol: Data Collection was carried out in the nCounter® Digital Analyzer. Digital images were processed on the nCounter Digital Analyzer and the barcode counts were tabulated in a comma separated value (CSV) format.

data_processing: Raw expression data were normalized and analysed with the nSolver Analysis Software 4.0 using the PanCancer Immune Profiling Advanced Analysis Module (nanoString Technologies).

label: Nanostring

source_name: oropharynx

label_protocol: Biotinylated cRNA were prepared according to the standard Nanostring nCounter® XT Assay protocol from 100 ng total RNA.

extract_protocol: FFPE tissue blocks were cut in 5-µm thick slices. Haematoxylin and eosin (HE) staining was carried out for estimation of the tumor cell content on each slide by a pathologist. Tumor RNA was isolated using a fully automated Tissue Preparation System (TPS; Siemens Healthcare Diagnostics) according to manufacturer´s protocol.

value: oropharynx

tag: 3yr os status

value: alive

tag: hpv status

value: p16 and HPV DNA negative

tag: tumor mutational burden status

value: low

tag: disease state

value: advanced squamous cell carcinoma

tag: t stage

tag: n stage

tag: concurrent chemotherapy

value: cisplatin

tag: tumor mutational burden [n/megabase]

tag: gender

value: male

tag: never smoker

value: no

tag: never drinker

value: yes


title: D0_ILC1 Liver_ATAC_001

description: Table 2.csv

tag: tissue

tag: cell type


title: cd20_01835_wce_bam

value: Peripheral Blood

tag: antibody


title: Rhode Island Red-RIR_R26 [reanalyzed]

value: Blood


title: Rhode Island Red-RIR_R25 [reanalyzed]


title: cd20_01835_h3k9me3_bam


title: Rhode Island Red-RIR_R24 [reanalyzed]


title: D35 IL-18Ra+_ILC1 Liver_RNA_001

description: Table 1.csv

extract_protocol:
To   isolate lymphocytes from liver, the tissues were physically dissociated using a glass  tissue homogenizer and purified using a discontinuous gradient of 40% over 60% Percoll. RBC were lysed using ACK lysis buffer
For RNA sequencing, RNA was isolated from sorted cell populations from WT mice using TRIzol (Invitrogen) followed by SMARTer amplification and Illumina nextgeneration sequencing.

tag: strain

tag: age


title: cd20_01835_h3k4me3_bam


title: D35 IL-18Ra+_ILC1 Liver_RNA_002

description: Table 1.csv

tag: days post infection

tag: Sex


title: E8.25-E9_Isl1_IP_ChIP_seq

data_processing:
ChIP-Seq reads were mapped to the mouse reference genome mm9 (UCSC assembly) using the default settings of bowtie2. The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks were called with the use of MACS14 with the parameter (p1e8 --nomodel --shiftsize 80). Peaks overlapping blacklist defined by ENCODE were removed.
ChIP-Seq peak annotation was performed using annotatePeaks.pl (default settings), which assigns each peak to the closest gene transcriptional start site (TSS).
For data visualization bam files were converted to BigWig files by the use of BamCoverage from deepTools2 (-b 20 -smooth 40 -e 150 --normalizeTo1x 2150570000).
Genome_build: mm9
Supplementary_files_format_and_content: bw, txt

source_name: Mouse Embryos

extract_protocol: Cardiogenic mesoderm and heart region of E8.25-E9 mouse embryo was crosslinked with 1% formaldehyde at room temperature for 15 min. Crosslinking was terminated by adding 125 mM glycine followed by three washes with cold PBS. Single cells were obtained by disruption of the tissue using pestle and mortar and nuclei were isolated by incubation in lysis buffer (50 mM Tris pH 8.0, 2 mM EDTA pH 8.0, 0.1% NP-40, 10% glycerol) along with protease and phosphatase inhibitors. Nuclei were frozen at −80 °C until further processing. Around 60-80 E8.25 to E9.0 embryos were pooled and lysed in nuclear lysis buffer supplemented with protease and phosphatase inhibitors (50 mM Tris pH 8.0, 1% SDS, 5 mM EDTA pH 8.0). Lysates were sonicated with Bioruptor (Diagenode) to achieve fragment sizes in the range of 200-500 bp. Lysates were diluted 1:10 in dilution buffer (50 mM Tris pH8.0, 200 mM NaCl, 5 mM EDTA pH8.0, 0.5% NP40) with protease and phosphatase inhibitors and precleared with Protein G Sepharose (GE Healthcare). Precleared lysates were incubated with 2-5 µg anti-Isl1 antibody (DSHB, clone 39.4D5) overnight at 4 °C followed by pulldown with BSA-presaturated protein G Sepharose beads. Immune complexes were washed with NaCl wash buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% NP-40), LiCl wash buffer (20 mM Tris pH 8.0, 500 mM LiCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% NP40) and TE wash buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0). Protein/DNA complexes were extracted in elution buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0 and 2% SDS) followed by reverse crosslinking at 65 °C overnight. DNA purification was performed using phenol-chloroform.

tag: embryonic stage

tag: chip antibody

value: Isl1 (Developmental Studies Hybridoma Bank (DSHB) clone 39.4D5)


title: Patient 34

source_name: hyopharynx

value: hyopharynx

tag: 3yr os status

value: deceased

tag: hpv status

tag: tumor mutational burden status

value: high

tag: disease state


title: D0_ILC1 Liver_RNA_002

description: Table 1.csv

value: liver

value: 8 weeks


title: D0_ILC1 Liver_RNA_001

description: Table 1.csv

value: female


title: Rhode Island Red-RIR_R23 [reanalyzed]


title: Patient 33

source_name: oral cavity

value: oral cavity

tag: t stage

tag: n stage

tag: concurrent chemotherapy

tag: tumor mutational burden [n/megabase]


title: Patient 35

tag: tissue

value: oropharynx

value: alive

value: p16 and HPV DNA negative

tag: gender

tag: never smoker

tag: never drinker


title: E8_75_Isl1_wt_RNA_seq_rep4

description:
E8_75_Isl1_wt_RNA_seq.bw
E8_75_Isl1_KO_quanty_transcripts_diff_expr.txt

data_processing:
RNA-Seq reads were mapped to the mm9 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000). Samples were quantified using analyzeRepeats.pl (mm9 –count exons –strand both –noadj). Differential expression (fold change >1.5; log2 fold change <−0.58, >0.58; p-value < 0.05) was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR. The KNIME 2.9.1 platform (Konstanz, Germany) was used to filter differentially regulated genes.
Genome_build: mm9
Supplementary_files_format_and_content: bw, differential expressed DESEq2 file

molecule: polyA RNA

extract_protocol: Pharyngeal mesoderm and hearts of E8.75 control and Isl1 KO embryos were dissected and stored at −80 °C in Qiazol. After genotyping, total RNA from single embryos was extracted using Rneasy Microarray Tissue Kit (Qiagen #73304). The integrity of RNA was assessed on Bioanalyzer 2100 (Agilent). For RNA-Seq of control and Isl1−/− tissue samples, 100 ng of total RNAs was used for library preparation and sequenced on NextSeq500 (Illumina).

value: E8.75 (6 somites)

value: pharyngeal mesoderm and hearts

tag: strain

tag: genotype

value: wild-type


title: Patient 32

value: low

value: advanced squamous cell carcinoma

value: cisplatin

value: male

value: no


title: Rhode Island Red-RIR_R22 [reanalyzed]

value: Blood


title: Patient 36

value: deceased

value: yes


title: Patient 31


title: Rhode Island Red-RIR_R21 [reanalyzed]


title: E8_75_Isl1_wt_RNA_seq_rep2


title: cd20_01835_h3k36me3_bam

value: Peripheral Blood

tag: cell type

value: peripheral blood CD20+

tag: antibody


title: E8_75_Isl1_wt_RNA_seq_rep3

tag: embryonic stage


title: nb_1_rnaseq

description:
nb_1
annotated_combined.counts.txt

source_name: Naïve B cell

value: peripheral blood NBCs [CD23+CD19+CD27-IgD+]


title: nb_2_rnaseq

description:
nb_2
annotated_combined.counts.txt


title: Rhode Island Red-RIR_R20 [reanalyzed]


title: Patient 29

value: oropharynx

tag: 3yr os status

value: female


title: Patient 30

tag: hpv status

value: p16 and HPV DNA negative


title: Rhode Island Red-RIR_R19 [reanalyzed]


title: cll_97_rnaseq

description:
cll_97
annotated_combined.counts.txt

value: CLL IGHV unmutated


title: cll_95_rnaseq

description:
cll_95
annotated_combined.counts.txt


title: Patient 27

value: alive

tag: tumor mutational burden status


title: cll_75_rnaseq

description:
cll_75
annotated_combined.counts.txt


title: Patient 28

value: high

tag: disease state


title: E8_75_Isl1_wt_RNA_seq_rep1

value: E8.75 (6 somites)

value: pharyngeal mesoderm and hearts

value: wild-type


title: E8_75_Isl1_KO_RNA_seq_rep3

description:
E8_75_Isl1_KO_RNA_seq.bw
E8_75_Isl1_KO_quanty_transcripts_diff_expr.txt


title: Rhode Island Red-RIR_R18 [reanalyzed]


title: cll_73_rnaseq

description:
cll_73
annotated_combined.counts.txt


title: E8_75_Isl1_KO_RNA_seq_rep2


title: Patient 25

value: low

value: advanced squamous cell carcinoma

tag: t stage

value: cisplatin


title: Rhode Island Red-RIR_R16 [reanalyzed]

value: Blood


title: cll_67_rnaseq

description:
cll_67
annotated_combined.counts.txt

value: CLL IGHV mutated


title: E8_75_Isl1_KO_RNA_seq_rep1


title: cll_5268_rnaseq

description:
cll_5268
annotated_combined.counts.txt

value: Peripheral Blood


title: Rhode Island Red-RIR_R15 [reanalyzed]


title: Day5_CPC_Isl1_KO_RNA_seq_rep2

description:
Day5_CPC_Isl1_KO_RNA_seq.bw
Day5_CPC_Isl1_quanty_transcripts_diff_expr.txt

data_processing:
RNA-Seq reads were mapped to the mm9 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000). Samples were quantified using analyzeRepeats.pl (mm9 –count exons –strand both –noadj). Differential expression (fold change >1.5; log2 fold change <−0.58, >0.58; p-value < 0.05) was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR. The KNIME 2.9.1 platform (Konstanz, Germany) was used to filter differentially regulated genes.
Genome_build: mm9
Supplementary_files_format_and_content: bw , differential expressed DESEq2 file

growth_protocol: Isl1-KO E14 Tg(Nkx2-5–EmGFP) ES cells were maintained on mitomycin treated MEF in Knockout DMEM medium containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, and 1,000 U/ml of leukemia inhibitory factor. ES cells were differentiated in cardiac progenitor cells and FACS sorted for GFP expression at day 5.

extract_protocol: Control and Isl1 KO Nkx2.5-GFP ES cell lines were differentiated into cardiac progenitors. Nkx2.5-GFP positive cells from two different control and Isl1−/− clones were sorted and RNA was isolated using RNeasy microarray kit (Qiagen #73304). The integrity of RNA was assessed on Bioanalyzer 2100 (Agilent). For RNA-Seq of control and Isl1−/−, 1 µg RNA was used as input for Truseq Stranded mRNA library preparation (Illumina). Sequencing was performed on NextSeq500 (Illumina) using V2 chemistry.

tag: cell line

value: Isl1-/- E14 Tg(Nkx2-5-EmGFP) ES cells

value: Embryonic stem cells (ESC)

tag: sample description

value: RNA-Seq of Isl1-/- ESC-derived cardiac progenitor cells


title: Rhode Island Red-RIR_R14 [reanalyzed]


title: E8_75_Isl1_KO_RNA_seq_rep4


title: cll_51_rnaseq

description:
cll_51
annotated_combined.counts.txt


title: Day5_CPC_Isl1_KO_RNA_seq_rep1


title: cll_4627_rnaseq

description:
cll_4627
annotated_combined.counts.txt


title: Rhode Island Red-RIR_R13 [reanalyzed]


title: Patient 24

value: hyopharynx

value: deceased

tag: n stage

tag: concurrent chemotherapy

tag: tumor mutational burden [n/megabase]

value: male

value: no

value: yes


title: Patient 23

tag: tissue

value: p16 and HPV DNA negative

tag: gender

tag: never smoker


title: Patient 26

value: oropharynx

value: alive

value: high

value: female

tag: never drinker


title: Rhode Island Red-RIR_R12 [reanalyzed]


title: cll_4605_rnaseq

description:
cll_4605
annotated_combined.counts.txt

tag: cell type


title: Day5_CPC_Isl1_control_RNA_seq_rep2

growth_protocol: Control E14 Tg(Nkx2-5–EmGFP) ES cells were maintained on mitomycin treated MEF in Knockout DMEM medium containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, and 1,000 U/ml of leukemia inhibitory factor. ES cells were differentiated in cardiac progenitor cells and FACS sorted for GFP expression at day 5.

value: Control E14 Tg(Nkx2-5-EmGFP) ES cells

value: RNA-Seq of Control ESC-derived cardiac progenitor cells


title: Day5_CPC_Isl1_control_RNA_seq_rep1


title: cll_32545_rnaseq

description:
cll_32545
annotated_combined.counts.txt

value: CLL IGHV mutated


title: Patient 21

value: low

value: advanced squamous cell carcinoma

value: cisplatin


title: Patient 22


title: Rhode Island Red-RIR_R11 [reanalyzed]

value: Blood


title: Patient 20


title: Rhode Island Red-RIR_R10 [reanalyzed]


title: cll_253_rnaseq

description:
cll_253
annotated_combined.counts.txt

value: Peripheral Blood

value: CLL IGHV unmutated


title: Rhode Island Red-RIR_R17 [reanalyzed]


title: cll_22526t_h3k27ac_bam

tag: antibody


title: cll_248_rnaseq

description:
cll_248
annotated_combined.counts.txt


title: Rhode Island Red-RIR_R8 [reanalyzed]


title: Rhode Island Red-RIR_R6 [reanalyzed]


title: E8_75_control_ATAC-seq_Rep2

description:
E8_75_control_ATAC-seq.bw
E8_75_control_ATAC-seq_peaks_annot.txt

data_processing:
ATAC-Seq reads were mapped with bowtie2 to mm9 mouse genome. Samtools view (-F 1804 -f2) was used to remove unmapped, mate unmapped, not primary aligned reads.
The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks calling was performed with MACS14 (p1e5 –nomodel and –shiftsize 100), and peaks overlapping blacklist defined by ENCODE with the help of Bedtools v2.15 (intersect -wa).
Bedtools v2.15 (intersect -wa) was used to obtain open chromatin regions overlapping by at least 1 bp in the replicates.
 BamCoverage function of deepTools2 (-b 20 -smooth 40 -e 150) was used to create normalized bigwig files (reads per genome coverage, RPGC). Further, bigWigAverageOverBed (https://github.com/ENCODE-DCC/kentUtils) was used to quantify mapped reads on peaks areas.
Heatmap and densitity plots were created using computeMatrix followed by plotHeatmap or plotProfile from deepTools2. To permit a comparative display of data within a deeptools profile heatmap, size factors produced by edgeR based on unified peak counts were used to scale samples to account for differences in sequencing depth, library composition, and ATAC-Seq efficiency.
Genome_build: mm9
Supplementary_files_format_and_content: Bw

extract_protocol: Pharyngeal mesoderm and hearts were dissected from E8.75 embryos (6 somites stage). Tissues were resuspended in 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) and used for ATAC Library preparation using Tn5 Transposase from Nextera DNA Library Prep Kit (Illumina #15028211). After centrifugation (10 min, 500 g at 4 °C), cell pellet was resuspended in transposition reaction mix (25 µl TD-Buffer, 2.5 µl Tn5, 22.5 µl water) and incubated for 30 min at 37 °C with gentle mixing. Immediately following the transposition reaction, purification was carried out using MinElute PCR Purification Kit (Qiagen #28004).

tag: genotype

value: wt


title: E8_75_Isl1_KO_ATAC-seq_Rep1


title: cll_21626_rnaseq

description:
cll_21626
annotated_combined.counts.txt


title: cll_242_rnaseq

description:
cll_242
annotated_combined.counts.txt


title: Rhode Island Red-RIR_R7 [reanalyzed]


title: Rhode Island Red-RIR_R4 [reanalyzed]


title: cll_20792_rnaseq

description:
cll_20792
annotated_combined.counts.txt


title: Rhode Island Red-RIR_R9 [reanalyzed]


title: Patient 17

value: hyopharynx

tag: 3yr os status

value: deceased

value: mitomycin C

value: male

value: no


title: E8_75_Isl1_KO_ATAC-seq_Rep3

data_processing:
ATAC-Seq reads were mapped with bowtie2 to mm9 mouse genome. Samtools view (-F 1804 -f2) was used to remove unmapped, mate unmapped, not primary aligned reads.
The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks calling was performed with MACS14 (p1e5 –nomodel and –shiftsize 100), and peaks overlapping blacklist defined by ENCODE with the help of Bedtools v2.15 (intersect -wa).
Bedtools v2.15 (intersect -wa) was used to obtain open chromatin regions overlapping by at least 1 bp in the replicates.
BamCoverage function of deepTools2 (-b 20 -smooth 40 -e 150) was used to create normalized bigwig files (reads per genome coverage, RPGC). Further, bigWigAverageOverBed (https://github.com/ENCODE-DCC/kentUtils) was used to quantify mapped reads on peaks areas.
Heatmap and densitity plots were created using computeMatrix followed by plotHeatmap or plotProfile from deepTools2. To permit a comparative display of data within a deeptools profile heatmap, size factors produced by edgeR based on unified peak counts were used to scale samples to account for differences in sequencing depth, library composition, and ATAC-Seq efficiency.
Genome_build: mm9
Supplementary_files_format_and_content: Bw


title: cll_20788_rnaseq

description:
cll_20788
annotated_combined.counts.txt


title: E8_75_control_ATAC-seq_Rep3


title: Patient 19

value: oropharynx

tag: hpv status

value: p16 and HPV DNA negative

value: yes


title: Patient 18

value: alive

tag: tumor mutational burden status


title: Rhode Island Red-RIR_R5 [reanalyzed]


title: E8_75_Brg1_KO_ATAC-seq_Rep3

value: Isl1Cre+/-/ Brg1fl/fl


title: Patient 15

value: low

tag: disease state


title: E8_75_Isl1_KO_ATAC-seq_Rep2


title: Patient 16

value: high

value: advanced squamous cell carcinoma

tag: t stage


title: Patient 12

value: cisplatin


title: E8_75_Brg1_KO_ATAC-seq_Rep2


title: Patient 13

value: oral cavity


title: NMuMG RNA-seq PBKD H2O2 replicate 3

tag: treatment

value: Lentiviral transfection of shPBRM1 with H2O2 stress


title: cll_20796_rnaseq

description:
cll_20796
annotated_combined.counts.txt

value: Peripheral Blood

value: CLL IGHV unmutated


title: E8_75_control_ATAC-seq_Rep1

value: wt


title: cll_189_rnaseq

description:
cll_189
annotated_combined.counts.txt

value: CLL IGHV mutated


title: cll_20506_rnaseq

description:
cll_20506
annotated_combined.counts.txt


title: Rhode Island Red-RIR_R2 [reanalyzed]

value: Blood


title: E8_75_Brg1_KO_ATAC-seq_Rep1


title: Rhode Island Red-RIR_R3 [reanalyzed]


title: Patient 11

value: male

value: no


title: Dwarf chicken-80

source_name: Dwarf chicken


title: Rhode Island Red-RIR_R1 [reanalyzed]


title: Patient 10

value: oropharynx

value: p16 and HPV DNA negative

value: female


title: cll_151_rnaseq

description:
cll_151
annotated_combined.counts.txt


title: Dwarf chicken-79


title: BUS2_c

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

description:
Ramie
circRNA
processed data file: circRNA_expression.txt

data_processing:
The raw reads for each sample were filtered, generating clean reads used in next analysis.
The clean reads for transcriptome sequencing were aligned into ramie genome (accession ID: PHNS00000000), using the software HISAT. The StringTie program (Pertea et al. 2015) was used for the assembly of transcripts, with the default parameters. To identify new transcripts, the genomic positions of all transcripts were compared with those of known genes annotated from genome, using the cuffcompare program of cufflinks.
The clean reads from circRNA sequencing were aligned into ramie genome (accession ID: PHNS00000000). Then, two softwares, CIRI and find_circ (Memczak et al. 2013), were used to predicted the circRNAs, with the default parameters.
The clean reads from small RNA sequencing were aligned into miRBase and Rfam databases, using AASRA and cmsearch software, respectively. The reads unaligned into these two databases were used to predict the novel miRNA by RIPmiR program, with the default parameters.
Genome_build: PHNS00000000.1
Supplementary_files_format_and_content: *.txt: Tab-delimited text files contain the gene name, sample name, read count, and FPKM value.

organism: Boehmeria nivea

source_name: stem bark

extract_protocol:
The TPS and MPS barks were separately collected from five individuals of Zhongzhu 1, immediately frozen in liquid nitrogen. Three replicates were sampled for TPS and MPS barks, respectively. Total RNA of this sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the manufacturer’s protocol.
Total RNAs from six samples were used separately to construct the small RNAs, circRNAs and cDNA libraries, respectively.

tag: cultivar

value: Zhongzhu No. 1

value: Barks from the top part of stem where the secondary cellular walls of fiber cell have not initiated growth

tag: age

value: 40 days


title: BUS3_c


title: BUS1_c


title: Patient 09

value: hyopharynx

value: alive

value: high

value: advanced squamous cell carcinoma

tag: n stage

tag: concurrent chemotherapy

value: yes


title: Dwarf chicken-78

tag: tissue


title: cb_2_rnaseq

description:
cb_2
annotated_combined.counts.txt

source_name: Germinal center B cell

value: Peripheral Blood

value: peripheral blood memory B cells [GCBs; CD23+CD19+CD27+IgD-]


title: BLS2_c

value: Barks from the middle part of stem where the secondary cellular walls of fiber cell are thickening


title: Dwarf chicken-77

value: Blood


title: cb_1_rnaseq

description:
cb_1
annotated_combined.counts.txt


title: Patient 08

value: low

value: cisplatin

tag: tumor mutational burden [n/megabase]

tag: gender

value: male


title: BLS1_c


title: Patient 14

value: not available

value: p16 and HPV DNA negative

value: mitomycin C

tag: never smoker

value: no

tag: never drinker


title: Dwarf chicken-76


title: cll_175_rnaseq

description:
cll_175
annotated_combined.counts.txt

tag: cell type

value: CLL IGHV mutated


title: Dwarf chicken-75


title: WTC11 WT replicate 8

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S21_r3_R1

data_processing:
RNA-Seq data was aligned to the human hg19 reference genome and transcriptome (Ensembl 72) using the software STAR. To accurately detect diverse alternative splicing events in iPSC-CM RNA-Seq, we adapted a recently developed Percent Spliced In (PSI) splicing method called MultiPath-PSI. MultiPath-PSI is available through AltAnalyze version 2.1.1, requiring aligned BAM files as input and was extensively benchmarked against other local splicing variation approaches (http://altanalyze.readthedocs.io/en/latest/Algorithms/#multipath-psi-splicing-algorithm).
For gene expression Quantification Kallisto (https://pachterlab.github.io/kallisto/) was used.
Genome_build: hg19
Supplementary_files_format_and_content: Kallisto-gene expression Quantification data

source_name: iPS cell-derived cardiomyocytes

growth_protocol: The iPS cell lines were differentiated into iPS-CMs using the method that controls WNT signaling by small molecules 16. Briefly, iPS cells were seeded at 1.25–2.5x104 cells/cm2 onto 12-well plates coated with 80 μg/μl growth factor-reduced Matrigel (BD Biosciences) in mTeSR1 supplemented with 10 μM Y-27632 (Selleckchem) for 24 h (day –3). mTeSR1 medium was changed daily for the next 2 days. On day 0, iPS cells were treated with 12 μM CHIR99021 (CHIR) (Tocris) in RPMI supplemented with B-27 (RPMI/B27) without insulin (Life Technologies) for exactly 24 h. On day 1, the culture medium was replaced with fresh RPMI/B27 without insulin and maintained for 48 h. On day 3, cells were treated with 5 μM IWP2 (Tocris) in RPMI/B27 without insulin and maintained for 48 h. On day 5, fresh RPMI/B27 without insulin was added to the cells, and on day 7, the medium was switched to RPMI/B27 with insulin. Afterward, fresh RPMI/B27 with insulin was added to the cells every 3 days. We used a metabolic selection protocol with glucose-free DMEM containing lactate to purify iPS-CMs. Cells were replated on day 15–18 of differentiation, and then on day 20–22 media were replaced with DMEM (without glucose, with sodium pyruvate, Thermo Fisher Scientific) supplemented with Glutamax, non-essential amino acids, and buffered lactate (4 mM). Stock-buffered lactate solution was prepared by dissolving sodium L-lactate powder (Sigma-Aldrich) at 1 M concentration in 1 M HEPES solution. Lactate media were exchanged 2–3 times, with a total exposure of 48 hours for each treatment. After the final lactate treatment (day 24–28), media were changed to RPMI/B27. The purified iPS-CMs at day 30 were harvested for RNA-Seq or cryopreserved for further analyses.

extract_protocol: Total RNA was purified from iPS-CMs by using TRIzol and PureLink RNA Mini Kit (Thermo Fisher Scientific) according manufactures’ instructions. The RNAseq libraries were prepared from the purified RNA by using TruSeq RNA Library Prep Kit v2 (Illumina). Paired-end 100 bp RNAseq was performed with HiSeq (Illumina). An average of ~90 million reads were obtained from this iPS-cell RNA-Seq data (45-182 million PE reads).

tag: cell line

tag: disease

value: healthy

tag: Sex

tag: differentiation

value: WNT modulation method day 26

tag: purification

value: Lactate method (PMID:23168164)

tag: genotype/variation

value: WT


title: BUS3_t

description:
Ramie
cDNA

value: Zhongzhu No. 1

value: Barks from the top part of stem where the secondary cellular walls of fiber cell have not initiated growth

value: 40 days


title: Patient 07

value: hyopharynx

tag: 3yr os status

value: alive

tag: hpv status

tag: tumor mutational burden status

tag: disease state

value: advanced squamous cell carcinoma

tag: t stage

value: yes


title: WTC11 WT replicate 7

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S18_r3_R1

value: male


title: Dwarf chicken-74

tag: tissue

value: Blood


title: BLS3_c

tag: cultivar

value: Barks from the middle part of stem where the secondary cellular walls of fiber cell are thickening

tag: age


title: BUS2_t

description:
Ramie
cDNA


title: Patient 06

value: p16 and HPV DNA negative

value: high

tag: n stage

tag: concurrent chemotherapy

value: cisplatin

tag: tumor mutational burden [n/megabase]

tag: gender

value: female

tag: never smoker


title: Patient 05

value: oropharynx

value: no

tag: never drinker


title: Dwarf chicken-73


title: Patient 03

value: oral cavity


title: Patient 04

value: low


title: BUS1_t

description:
Ramie
cDNA

value: Zhongzhu No. 1

value: Barks from the top part of stem where the secondary cellular walls of fiber cell have not initiated growth


title: Dwarf chicken-72


title: WTC11 WT replicate 6

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S15_r4_R1

tag: cell line

tag: disease

value: healthy

tag: Sex

tag: differentiation

value: WNT modulation method day 26

value: Lactate method (PMID:23168164)

value: WT


title: WTC11 WT replicate 5

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S15_r3_R1

value: male

tag: purification

tag: genotype/variation


title: WTC11 WT replicate 4

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S14_r4_R1


title: Patient 02

tag: 3yr os status

value: deceased

tag: hpv status

tag: tumor mutational burden status

tag: disease state

value: advanced squamous cell carcinoma


title: Dwarf chicken-71

tag: tissue

value: Blood


title: BLS2_t

description:
Ramie
cDNA

tag: cultivar

value: Barks from the middle part of stem where the secondary cellular walls of fiber cell are thickening

tag: age

value: 40 days


title: WTC11 WT replicate 3

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S3_r2_R1


title: Patient 01

value: hyopharynx

value: p16 and HPV DNA negative

tag: t stage

tag: n stage

tag: concurrent chemotherapy

value: cisplatin

tag: tumor mutational burden [n/megabase]

value: yes


title: validation cohort 2 patient 36

hyb_protocol: Hybridization was carried out according to the standard NanoString nCounter® XT Assay protocol.

data_processing:
Raw expression data were analyzed with the nSolver Analysis Software version 4.0 using the Advanced Analysis Module (NanoString Technologies).
For background correction, the geometric mean of negative controls was subtracted from the counts of each gene. The geometric mean of the housekeeping genes was used to calculate a normalization factor for each sample.

label: biotin

source_name: primary oropharyngeal carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard NanoString nCounter® XT Assay protocol from 100 ng total RNA.

extract_protocol: FFPE tissue slides (5-µm) were stained with hematoxylin and eosin (HE) and reviewed by a pathologist to delineate tumor areas. RNA was isolated from macrodissected tumor areas using the High Pure FFPE RNA Micro Kit (Roche) according to the manufacturer’s protocol.

tag: cohort

value: validation 2

tag: disease status

value: oropharyngeal squamous cell carcinoma (OPSCC)

value: primary oropharyngeal carcinoma

tag: 3-year os status

value: alive


title: cll_10126_rnaseq

description:
cll_10126
annotated_combined.counts.txt

value: Peripheral Blood

tag: cell type

value: CLL IGHV mutated


title: BLS1_t

description:
Ramie
cDNA

value: Zhongzhu No. 1


title: validation cohort 2 patient 35


title: Dwarf chicken-69


title: BLS3_t

description:
Ramie
cDNA


title: WTC11 WT replicate 2

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S2_r2_R1

tag: cell line

tag: disease

value: healthy

tag: Sex

value: male

tag: differentiation

value: WNT modulation method day 26

tag: purification

value: Lactate method (PMID:23168164)

value: WT


title: WTC11 WT replicate 1

description:
GCaMP6 is expressed from AAVS1
WTC_WT-S1_r2_R1

tag: genotype/variation


title: Dwarf chicken-68

tag: tissue

value: Blood


title: WTC11 RBM20 R636S Homo replicate 3

description:
GCaMP6 is expressed from AAVS1
WTC_Homo_R636-S23_r3_R1

value: RBM20 R636S Homo


title: Dwarf chicken-66


title: validation cohort 2 patient 34

tag: hpv status


title: WTC11 RBM20 R636S Homo replicate 2

description:
GCaMP6 is expressed from AAVS1
WTC_Homo_R636-S20_r3_R1


title: WTC11 RBM20 R636S Homo replicate 1

description:
GCaMP6 is expressed from AAVS1
WTC_Homo_R636-S17_r3_R1


title: Dwarf chicken-65


title: validation cohort 2 patient 32


title: Dwarf chicken-64


title: Dwarf chicken-63


title: WTC11 RBM20 R636S Het replicate 6

description:
GCaMP6 is expressed from AAVS1
WTC_Het_R636-S22_r3_R1

value: RBM20 R636S Het


title: WTC11 RBM20 R636S Het replicate 5

description:
GCaMP6 is expressed from AAVS1
WTC_Het_R636-S19_r3_R1


title: WTC11 RBM20 R636S Het replicate 4

description:
GCaMP6 is expressed from AAVS1
WTC_Het_R636-S16_r3_R1


title: validation cohort 2 patient 31

value: deceased


title: validation cohort 2 patient 30


title: validation cohort 2 patient 29


title: Dwarf chicken-67


title: WTC11 RBM20 R636S Het replicate 3

description:
GCaMP6 is expressed from AAVS1
WTC_Het_R636-S3_r2_R1


title: Dwarf chicken-62


title: validation cohort 2 patient 33


title: validation cohort 2 patient 28


title: WTC11 RBM20 R636S Het replicate 2

description:
GCaMP6 is expressed from AAVS1
WTC_Het_R636-S2_r2_R1


title: validation cohort 2 patient 27


title: validation cohort 2 patient 26


title: Dwarf chicken-60


title: WTC11 RBM20 R636S Het replicate 1

description:
GCaMP6 is expressed from AAVS1
WTC_Het_R636-S1_r2_R1


title: Dwarf chicken-59


title: Dwarf chicken-58


title: WTC11 RBM20 8-bp deletion Homo replicate 3

description:
GCaMP6 is expressed from AAVS1
WTC_638_Del_8_3-S8_r4_R1

value: RBM20 8-bp deletion


title: WTC11 RBM20 8-bp deletion Homo replicate 4

description:
GCaMP6 is expressed from AAVS1
WTC_638_Del_8_4_S9_r4_R1


title: validation cohort 2 patient 25

value: validation 2


title: validation cohort 2 patient 24

value: oropharyngeal squamous cell carcinoma (OPSCC)


title: Dwarf chicken-61


title: Dwarf chicken-57


title: WTC11 RBM20 8-bp deletion Homo replicate 2

description:
GCaMP6 is expressed from AAVS1
WTC_638_Del_8_2-S7_r4_R1


title: WTC11 RBM20 8-bp deletion Homo replicate 1

description:
GCaMP6 is expressed from AAVS1
WTC_638_Del_8_1-S6_r4_R1


title: Dwarf chicken-70


title: validation cohort 2 patient 22

value: primary oropharyngeal carcinoma


title: validation cohort 2 patient 21


title: Dwarf chicken-55


title: UbxDegrad_Pho-ChIP_experiment_input_R3

city: Heidelberg

first: Katrin

last: Domsch

address: INF 230

department: COS - Developmental Biology

institute: Heidelberg University

description: mef2-Nslmb_Pho-ChIP_input_R3_Ibberson_lane6KD90

data_processing:
reads were first analysed with FastQC and aligned with bowtie
peaks were called by using MACS2
Genome_build: dm6
Supplementary_files_format_and_content: bed

organism: Drosophila melanogaster

source_name: mesoderm stage 14-17

extract_protocol:
tissue specific nuclei were extracted vis the INTACT method (Steiner et al., 2012)
Samples were amplified using the ThruPLEX DNA-Seq Kit (Rubicon). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: twi-INTACT, Mef2>Nslmb,GFP-Ubx

tag: developmental stage

value: mesoderm stage 14-17

value: mesoderm

tag: chip antibody


title: UbxDegrad_Pho-ChIP_experiment_Pho_R3

description: mef2-Nslmb_Pho-ChIP_Pho_R3_Ibberson_lane6KD91

value: Rb-Pho 2-382 (gift from Jürg Müller)


title: validation cohort 2 patient 19

value: alive


title: validation cohort 2 patient 23


title: validation cohort 2 patient 20


title: Dwarf chicken-54


title: validation cohort 2 patient 18


title: UbxDegrad_Pho-ChIP_experiment_Pho_R2

description: mef2-Nslmb_Pho-ChIP_Pho_R2_Ibberson_lane6KD87


title: validation cohort 2 patient 17


title: Dwarf chicken-52


title: 2811_sarcoidosis

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: Following fragmentaion, single-stranded cDNA were hybridized for 20 hours at 48 ℃ with HuGene2.1ST Array Strip (Affymetrix) and GeneChip Expression 3'-Amplification Reagents Hybridization Control kit (Affymetrix).

scan_protocol: The array was scanned using Imaging Station (Affymetrix) according to the manufacture's instructions.

data_processing: R 3.4.1, rma function from oligo package, version 1.40.2, default options, target=probeset

source_name: BALf

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Amplification Kit Module 1(Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: The total RNA was isolated using Nucleo Spin RNA II Columns Kit (Machery & Nagel; Düren, Germany).

value: bronchoalveolar lavage fluid (BALf)

tag: diagnosis

value: sarcoidosis


title: validation cohort 2 patient 16


title: Dwarf chicken-51


title: 2803_sarcoidosis


title: 2802_sarcoidosis


title: 2875_sarcoidosis


title: 2791_sarcoidosis


title: 2799_sarcoidosis


title: 2724_sarcoidosis


title: 2663_sarcoidosis


title: 2889_IPF

value: IPF


title: 2765_sarcoidosis


title: 2753_sarcoidosis


title: 2878_IPF


title: 2794_sarcoidosis


title: 2836_IPF


title: 2823_sarcoidosis


title: UbxDegrad_Pho-ChIP_experiment_input_R2

description: mef2-Nslmb_Pho-ChIP_input_R2_Ibberson_lane6KD86


title: UbxDegrad_Pho-ChIP_experiment_input_R1

description: mef2-Nslmb_Pho-ChIP_input_R1_Ibberson_lane5KD82


title: UbxDegrad_Pho-ChIP_control_Pho_R3

description: UAS-Nslmb_Pho-ChIP_Pho_R3_Ibberson_lane6KD89

value: twi-INTACT; UAS-Nslmb,GFP-Ubx


title: 2879_IPF


title: 2882_IPF


title: Dwarf chicken-48

value: Blood


title: UbxDegrad_Pho-ChIP_control_input_R3

description: UAS-Nslmb_Pho-ChIP_input_R3_Ibberson_lane6KD88


title: Dwarf chicken-53


title: Dwarf chicken-50


title: GM12878-qc-5000beads

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to hg19 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
NA
Genome_build: hg19
Supplementary_files_format_and_content: Decomposed counts matrix. CountsData is indexed by peak (row), cell (column), and count where the Bed file and CellData provide annotations for rows and columns. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data.

organism:
Homo sapiens
Mus musculus

source_name: Cell line mixutre

growth_protocol: GM12878 cells were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) (ATCC) supplemented with 10% FBS and 1% Pen/Strep. NIH/3T3 (ATCC) mouse embryonic fibroblast cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) (ATCC) supplemented with 10% Calf Bovine Serum and 1% Pen/Strep. All cell lines were maintained at 37°C and 5% CO2 at recommended density and were harvested at mid-log phase for all experiments. All suspension cells were harvested using standard cell culture procedure, and adherent cells were detached using TrypLE Express Enzyme (Gibco). After harvesting, cells were washed twice with ice cold 1x PBS (Gibco) supplemented with 0.1% BSA (MilliporeSigma). Cells were then filtered with a 35 μm cell strainer (Corning) and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter (Bio-Rad). Cell viability was greater than 90% for all samples.

extract_protocol:
A protocol based on Omni-ATAC was followed. Briefly, washed and pelleted cells were lysed with the Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 10 mM NaCl, 3 mM MgCl2, and 10 mM Tris-HCl pH7.4 for 3 min on ice. The lysis buffer was diluted with ATAC-Tween buffer that only contains 0.1% Tween-20 as a detergent. Cells were collected and resuspended in Omni Tagmentation Mix containing ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme that are parts of the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad). The Omni Tagmentation Mix was buffered with 1X PBS supplemented with 0.1% BSA. Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).
SureCell scATAC-seq

tag: celltype

value: GM12878 and 3T3 cell line mixture

tag: bead concentration

value: 5000 beads/uL


title: UbxDegrad_Pho-ChIP_control_Pho_R2

description: UAS-Nslmb_Pho-ChIP_Pho_R2_Ibberson_lane5KD85


title: UbxDegrad_Pho-ChIP_experiment_Pho_R1

description: mef2-Nslmb_Pho-ChIP_Pho_R1_Ibberson_lane5KD83


title: validation cohort 2 patient 14

tag: cohort


title: Dwarf chicken-46


title: Mix-ht-sciATAC-seq-160k-input-48Tn5-rep2

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to hg19 or mm10 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
NA
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Per-sample quality-control statistics used for species-mixing inference. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data.

source_name: Cell line mixture

growth_protocol: K562 (ATCC) human chronic myelogenous leukemia cells were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) (ATCC) supplemented with 10% FBS and 1% Pen/Strep. NIH/3T3 (ATCC) mouse embryonic fibroblast cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) (ATCC) supplemented with 10% Calf Bovine Serum and 1% Pen/Strep. All cell lines were maintained at 37°C and 5% CO2 at recommended density and were harvested at mid-log phase for all experiments. All suspension cells were harvested using standard cell culture procedure, and adherent cells were detached using TrypLE Express Enzyme (Gibco). After harvesting, cells were washed twice with ice cold 1x PBS (Gibco) supplemented with 0.1% BSA (MilliporeSigma). Cells were then filtered with a 35 μm cell strainer (Corning) and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter (Bio-Rad). Cell viability was greater than 90% for all samples.

extract_protocol:
A protocol based on Omni-ATAC was followed. Briefly, washed and pelleted cells were lysed with the Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 10 mM NaCl, 3 mM MgCl2, and 10 mM Tris-HCl pH7.4 for 3 min on ice. The lysis buffer was diluted with ATAC-Tween buffer that only contains 0.1% Tween-20 as a detergent. Cells were collected and resuspended in Omni Tagmentation Mix containing ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme that are parts of the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad). The Omni Tagmentation Mix was buffered with 1X PBS supplemented with 0.1% BSA. Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).
dsciATAC-seq (Barcoded-transposition SureCell scATAC-seq)

value: K562 and 3T3 cell line mixture

tag: cell input


title: UbxDegrad_Pho-ChIP_control_input_R2

description: UAS-Nslmb_Pho-ChIP_input_R2_Ibberson_lane5HD84


title: validation cohort 2 patient 15

tag: disease status

tag: 3-year os status


title: 2845_IPF


title: validation cohort 2 patient 13


title: Dwarf chicken-56

data_processing:
The array image was acquired using Affymetrix Operating Software (AxAS version 4.0.1).
Genotype Call (SNP call): A/T/C/G

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.


title: Dwarf chicken-49


title: Dwarf chicken-45


title: Mix-ht-sciATAC-seq-160k-input-48Tn5


title: UbxDegrad_Pho-ChIP_control_Pho_R1

description: UAS-Nslmb_Pho-ChIP_Pho_R1_Ibberson_lane5KD81

tag: cell type


title: Dwarf chicken-47


title: UbxDegrad_Pho-ChIP_control_input_R1

description: UAS-Nslmb_Pho-ChIP_input_R1_Ibberson_lane5KD80


title: validation cohort 2 patient 10

value: deceased


title: Dwarf chicken-43


title: Mix-ht-sciATAC-seq-80k-input-48Tn5


title: Mix-ht-sciATAC-seq-40k-input-48Tn5


title: validation cohort 2 patient 09

value: validation 2


title: 2841_IPF


title: validation cohort 2 patient 11

value: oropharyngeal squamous cell carcinoma (OPSCC)


title: validation cohort 2 patient 12

value: primary oropharyngeal carcinoma


title: Dwarf chicken-44


title: validation cohort 2 patient 07


title: validation cohort 2 patient 08


title: Dwarf chicken-42


title: Mix-ht-sciATAC-seq-16k-input-48Tn5


title: meUbx_R

source_name: mesoderm stage 10-13

value: twi-INTACT

value: mesoderm stage 10-13

value: gp-Ubx (home-made)


title: Dwarf chicken-40


title: 2827_IPF


title: Dwarf chicken-41

description:
W82_3116061041.CEL
no processed data; was filtered after QC (DQC > 0.82 and call rate > 97 %) in genotyping software (AxiomAnalysisSuite_4.0.3).


title: meUbx_input_R

value: mesoderm


title: Mix-ht-sciATAC-seq-8k-input-48Tn5


title: UbxDegrad_experiment_H3K27me3_R3

tag: chip-antibody

value: H3K27me3 (ab6002, Abcam)

tag: genotype

value: twi-INTACT, Mef2>Nslmb,GFP-Ubx


title: validation cohort 2 patient 06

value: not available


title: validation cohort 2 patient 05

value: alive


title: UbxDegrad_experiment_input_R3


title: UbxDegrad_experiment_H3K27me3_R2


title: UbxDegrad_experiment_H3K27ac_R3

value: H3K27ac (ab4729, Abcam)


title: 2800_IPF

value: bronchoalveolar lavage fluid (BALf)

value: IPF


title: Mix-ht-sciATAC-seq-160k-input

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to hg19 or mm10 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Per-sample quality-control statistics used for species-mixing inference. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data.

extract_protocol:
A protocol based on Omni-ATAC was followed. Briefly, washed and pelleted cells were lysed with the Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 10 mM NaCl, 3 mM MgCl2, and 10 mM Tris-HCl pH7.4 for 3 min on ice. The lysis buffer was diluted with ATAC-Tween buffer that only contains 0.1% Tween-20 as a detergent. Cells were collected and resuspended in Omni Tagmentation Mix containing ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme that are parts of the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad). The Omni Tagmentation Mix was buffered with 1X PBS supplemented with 0.1% BSA. Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

value: mixture of K562 / 3T3


title: UbxDegrad_experiment_H3K27ac_R2


title: Mix-ht-sciATAC-seq-40k-input


title: Mix-ht-sciATAC-seq-80k-input


title: Dwarf chicken-39

value: Blood


title: Dwarf chicken-37


title: Mix-ht-sciATAC-seq-16k-input


title: validation cohort 2 patient 04


title: validation cohort 2 patient 02


title: GM12878-qc-800beads

value: GM12878 and 3T3 cell line mixture

value: 800 beads/uL


title: Dwarf chicken-36


title: Mix-ht-sciATAC-seq-8k-input


title: UbxDegrad_experiment_input_R2


title: validation cohort 2 patient 01

value: validation 2

value: oropharyngeal squamous cell carcinoma (OPSCC)

value: deceased


title: GM12878-3T3-qc-5000beads

source_name: Cell line

value: 5000 beads/uL


title: validation cohort 1 patient 31

value: validation 1

value: primary oropharyngeal carcinoma


title: Dwarf chicken-35


title: UbxDegrad_experiment_H3K27me3_R1

value: mesoderm

value: H3K27me3 (ab6002, Abcam)


title: GM12878-3T3-qc-800beads


title: Dwarf chicken-34


title: Dwarf chicken-38


title: UbxDegrad_experiment_H3K27ac_R1

value: twi-INTACT, Mef2>Nslmb,GFP-Ubx


title: validation cohort 2 patient 03

value: alive


title: CFTRneg_Treated_6

city: Cleveland

first: Aura

last: Perez

address: 10900 Euclid Avenue

department: Pediatrics

institute: CWRU

description: Generated using CRISPR/Cas9-mediated mutagenesis of CFTR

data_processing:
Trimming and filtering of the reads to remove adaptor sequences and low-quality nucleotides were performed using Trimmomatic (v 0.36). 100bp samples were trimmed to 75bp before continuing with the rest of the analysis.
The filtered reads were aligned to the UCSC human genome hg19 as a reference using Bowtie2 (v 2.3.4.3) and Tophat (v 2.1.1). Assembly of transcriptomes and quantification of their expression was performed using Cufflinks (v 2.2.1).  Expression levels were expressed as fragments per kilobase of exon per million fragments mapped (FPKM).
Statistical significance in differential gene expression between groups was determined with Cuffdiff (v 2.2.1).  Both p and q values were determined and defined as uncorrected p-value of the test statistic and FDR-adjusted p-value of test-statistic, respectively.
Data were further analyzed and visualized using CummeRbund run under the R package (v 3.4.4)
Hierarchical clustering (heat map) of genes with differential expression was generated using Complete Linkage as the clustering method, Euclidian distance as the similarity measure, and Z-Score as normalization with TIBCO Spotfire Software (Palo Alto, CA). Pathway analysis was done using Gene Set Enrichment Analysis (GSEA) (Broad Institute, software.broadinstitute.org/gsea), a computational method that determines statistical significance of a priori defined set of genes between two groups. The Hallmark gene set from the Molecular Signature Database (MSigDB) collection was used to explore overrepresented pathways. It comprises of 50 hallmarks condensed from over 4,000 overlapping gene sets from v4.0 MSigDB collections C1 through C6.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file for each sample including FPKM values and locus

source_name: Caco2 cells

growth_protocol: Caco-2 cells obtained from the American Type Culture Collection (ATCC) were maintained in Eagle’s minimum essential medium with 10% FBS, 1% glutamine, and 1% penicillin-streptomycin. Cells were cultured at 37°C in an atmosphere of 95% O2 - 5% CO2

extract_protocol:
Total RNA was harvested using RNAeasy kit per manufacturer instructions, Qiagen Inc, Valencia, CA)
RNA-Seq libraries were generated using TruSeq stranded Total RNA Ribo-Zero human gold kit (Illumina, San Diego, CA) and the quality of resulting libraries was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). Sequencing was carried out using either an Illumina HiSeq 2500 Rapid Run flowcell – 2x100bp run or an Illumina NextSeq 550 HO - 2x75bp run, as indicated below.

treatment_protocol: Cells were exposed to 100ng/ml TNFa for 2 hours prior to harvesting RNA for RT PCR and RNAseq

value: Colonic adenocarcinoma-derived cell line

value: CFTR null

tag: clone

tag: treatment

value: 100ng/ml TNFa for 2 hours


title: Dwarf chicken-32


title: validation cohort 1 patient 30

value: not available


title: Dwarf chicken-31

value: Blood


title: UbxDegrad_control_H3K27me3_R3

value: twi-INTACT; UAS-Nslmb,GFP-Ubx


title: CFTRneg_Treated_5


title: UbxDegrad_control_H3K27ac_R3

value: H3K27ac (ab4729, Abcam)


title: UbxDegrad_experiment_input_R1


title: CFTRneg_Treated_4


title: Dwarf chicken-30


title: validation cohort 1 patient 28


title: validation cohort 1 patient 27


title: validation cohort 1 patient 26


title: UbxDegrad_control_input_R3


title: UbxDegrad_control_H3K27me3_R2


title: Dwarf chicken-28


title: CFTRneg_Nontreated_4


title: UbxDegrad_control_H3K27ac_R2


title: Dwarf chicken-27


title: CFTRpos_Treated_6

value: NonCF


title: validation cohort 1 patient 29

value: oropharyngeal squamous cell carcinoma (OPSCC)


title: validation cohort 1 patient 25

value: deceased


title: UbxDegrad_control_input_R2


title: validation cohort 1 patient 24


title: Dwarf chicken-33


title: Dwarf chicken-25


title: CFTRneg_Nontreated_6


title: CFTRpos_Treated_5


title: validation cohort 1 patient 22


title: UbxDegrad_control_H3K27ac_R1


title: Dwarf chicken-24


title: UbxDegrad_control_H3K27me3_R1


title: CFTRpos_Treated_4


title: validation cohort 1 patient 21


title: Dwarf chicken-29


title: CFTRneg_Nontreated_5


title: UbxDegrad_control_input_R1


title: CFTRpos_Nontreated_6


title: Dwarf chicken-23


title: mlH3K27me3_R3

value: twi-INTACT


title: validation cohort 1 patient 19

value: validation 1


title: validation cohort 1 patient 20

value: primary oropharyngeal carcinoma


title: Dwarf chicken-22


title: CFTRpos_Nontreated_4


title: mlH3K27ac_R3

value: mesoderm


title: Dwarf chicken-21


title: Dwarf chicken-20


title: validation cohort 1 patient 18


title: mlH3K27me3_R2

value: H3K27me3 (ab6002, Abcam)


title: validation cohort 1 patient 17


title: validation cohort 1 patient 23


title: Dwarf chicken-18


title: mlH3K27ac_R2


title: ml_input_R2


title: meH3K27me3_R2


title: Dwarf chicken-17


title: ml_input_R3


title: CFTRpos_Nontreated_5


title: Dwarf chicken-19


title: meH3K27ac_R2


title: validation cohort 1 patient 14


title: Dwarf chicken-15


title: Dwarf chicken-14


title: validation cohort 1 patient 15


title: validation cohort 1 patient 12


title: Dwarf chicken-16


title: me_input_R2


title: validation cohort 1 patient 13


title: validation cohort 1 patient 11


title: Dwarf chicken-13


title: meH3K27me3_R1


title: validation cohort 1 patient 10


title: validation cohort 1 patient 16


title: validation cohort 1 patient 09


title: meH3K27ac_R1


title: Dwarf chicken-12


title: me_input_R1


title: Dwarf chicken-11


title: Dwarf chicken-26


title: nlUbx_S

source_name: neuronal stage 14-17

value: neuronal

value: gp-Ubx (home made)

value: elav>INTACT


title: Dwarf chicken-10


title: nlUbx_input_S


title: Dwarf chicken-9


title: nlUbx_R


title: validation cohort 1 patient 08

value: alive


title: validation cohort 1 patient 07


title: validation cohort 1 patient 06


title: nlUbx_input_R


title: Dwarf chicken-7


title: validation cohort 1 patient 04


title: Dwarf chicken-8


title: validation cohort 1 patient 05


title: Dwarf chicken-6


title: neUbx_R

source_name: neuronal stage 10-13


title: neUbx_S


title: neUbx_input_S


title: validation cohort 1 patient 03


title: NK-Human-Channel3

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode module.
Paired-end reads were aligned to hg19 using bwa.
Duplicate reads and all downstream processing was performed using the bead-based scATAC-seq processing (bap) tool.
Samples of common biological origin were pooled into single ranged summarized experiment obejcts using bap and shown below.
Genome_build: hg19
Supplementary_files_format_and_content: Decomposed counts matrix. CountsData is indexed by peak (row), cell (column), and count where the Bed file and CellData provide annotations for rows and columns. Barcode translate file maps raw sequence barcode (many) to cell barcode (one) from the bap output. The BarcodeLogic Excel file contains the information needed to parse the cell barcode from the sequencing data.

source_name: NK Cells

growth_protocol: Cryopreserved human isolated bone marrow CD34+ stem/progenitor cells, and isolated peripheral blood CD4+ T cells, CD8+ T cells, CD14+ (Monocytes), CD19+ (B cells) and CD56+ (NK) cells were purchased from Allcells. Cells were quickly thawed in a 37°C water bath, rinsed with culture medium (IMDM medium supplemented with 10% FBS and 1% Pen/Strep) and then treated with 0.2 U/μL DNase I (Thermo Fisher Scientific) in 10 mL of culture medium at 37°C for 30 min. After DNase I treatment, cells were washed with medium once and then twice with ice cold 1x PBS + 0.1% BSA. Cells were then filtered with a 35 μm cell strainer (Corning) and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter (Bio-Rad). Cell viability was greater than 80% for all samples.

extract_protocol:
Lysis was performed simultaneously with tagmentation. Washed and pelleted cells were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1X PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (parts of the SureCell ATAC-Seq Library Prep Kit - 17004620, Bio-Rad). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

value: NK Cells


title: Dwarf chicken-3


title: validation cohort 1 patient 02


title: Dwarf chicken-4


title: mlUbx_S


title: training cohort patient 32

value: training


title: neUbx_input_R


title: Dwarf chicken-5

value: Blood


title: NK-Human-Channel2


title: Dwarf chicken-2


title: training cohort patient 33


title: mlUbx_input_S


title: training cohort patient 31


title: Dwarf chicken-1


title: training cohort patient 30


title: mlUbx_R


title: NK-Human-Channel1


title: Bcell-Human-Channel4

source_name: B Cells

value: B Cells


title: Bcell-Human-Channel3


title: validation cohort 1 patient 01


title: BUS3_s

description:
Ramie
Small RNA

tag: cultivar

value: Zhongzhu No. 1

value: Barks from the top part of stem where the secondary cellular walls of fiber cell have not initiated growth

tag: age

value: 40 days


title: mlUbx_input_R


title: NK-Human-Channel4


title: Bcell-Human-Channel2


title: meUbx_S


title: Bcell-Human-Channel1


title: training cohort patient 28

value: oropharyngeal squamous cell carcinoma (OPSCC)

tag: tissue

value: deceased

tag: hpv status


title: meUbx_input_S

value: twi-INTACT


title: training cohort patient 29

value: primary oropharyngeal carcinoma


title: BUS1_s

description:
Ramie
Small RNA


title: BUS2_s

description:
Ramie
Small RNA


title: training cohort patient 27


title: Mono-Human-Channel4

source_name: Monocytes

value: Monocytes


title: BLS3_s

description:
Ramie
Small RNA

value: Barks from the middle part of stem where the secondary cellular walls of fiber cell are thickening


title: Mono-Human-Channel3


title: meUbx_input_R2

value: mesoderm


title: BLS2_s

description:
Ramie
Small RNA


title: BLS1_s

description:
Ramie
Small RNA


title: training cohort patient 26


title: training cohort patient 25


title: Treated replicate 3

city: Coventry

first: Alexia

last: Hapeshi

address: Gibbet Hill

country: United Kingdom

institute: University of Warwick

description: rRNA depleted RNA

data_processing:
Basecalling and adapter trimming was done on the MiSEQ instrument
Fastq reads were checked for quality using fastqc and aligned to the reference using Bowtie2 v2.1.0 in --very-sensitive-local mode.
SAMtools was used to create bam files from the mapped reads.
BEDtools coveragebed was used to obtain read counts for each feature in the reference.
The coverageBed output was filtered to create text files consisting of two columns whereby on column contains gene names and the other one read depth.
The filtered text files were used as input for DESeq2
Genome_build: GCF_000008865.1; NC_002695 (chromosome), NC_002128 pOSAK1), NC_002127 (pO157). For alignment the fasta files of the chromosome and two plasmids were concatenated.
Supplementary_files_format_and_content: _filt.txt files contain read depth counts for each gene as calculated using coverageBed; norm_counts_paired.csv file contains the normalised counts as calculated using DESeq2

organism: Escherichia coli O157:H7 str. Sakai

source_name: Bacterial culture

growth_protocol: The bacteria were grown in cation-adjusted Mueller-Hinton broth at 37 ˚C, shaking

extract_protocol:
Enzymatic lysis was performed using TE buffer with proteinase K and 1 mg/ml lysozyme. RNA was then purified using the miRNeasy kit (Qiagen) with the inclusion of a double on-column DNA digestion. Ribosomal RNA was depleted using the Ribo-Zero bacterial rRNA removal kit (Illumina).
Illumina TruSeqTM stranded mRNA kit (5 µl of rRNA-depleted sample were directly mixed with 13 µl of TruSeqTM ‘Fragment, Prime, Finish mix’. Then, the kit guidelines were followed).

treatment_protocol: At an OD600 of 0.5 cultures were split in two and one sample treated with  methanol while the other was treated with 0.5 µg/ml of Λ-5b (dissolved in methanol). The cultures were incubated for a further 40 min and then 1 ml of each sample was harvested in RNAprotect reagent (Qiagen).

value: 0.5 ug/ml of lambda-5b

tag: streain

value: E. coli Sakai O157:H7 stx-


title: Mono-Human-Channel2


title: CD8-Human-Channel3

source_name: CD8+ T Cells

value: CD8+ T Cells


title: CD8-Human-Channel4


title: Treated replicate 2

description: rRNA depleted RNA


title: Mono-Human-Channel1


title: Treated replicate 1

description: rRNA depleted RNA


title: T2+7_MCP_rep3

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

description: Processed data file: Matrix_FPKM.txt

data_processing:
RNA-Seq data were aligned to the Malus x domestica genome assembly v1.0 using TopHat2 software (Kim et al. 2013) and processed with Cufflinks (Trapnell et al. 2012) to assemble transcript isoforms. Malus x domestica whole genome annotation 1.0 was used to guide RABT assembly using default parameters. Gene expression was quantified as fragments per kilobase of exon model per million mapped reads (FPKM). Differential expression analysis was performed using Cuffdiff program from Cufflinks suite with FDR threshold of 0.05 and a Log2 FC ≥ 1.
Genome_build: MalDomGD1.0 (GCF_000148765.1)
Supplementary_files_format_and_content: Matrix_FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Malus domestica

source_name: apple skin, 1-MCP, cold storage + shelf life

extract_protocol:
RNA extraction was performed, for each of the three biological replicates with the Spectrum Plant total RNA kit (Sigma-Aldrich Co., St. Luis, MO, USA). RNA was quantified using a NanoDrop ND-8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), while its purity and integrity were assessed with a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
For each replicate/sample, 3 mg of RNA was used for the construction of a non-directional Illumina RNA-seq library, using TruSeq RNA sample preparation kits, v2 (Illumina, San Diego, CA, USA). Libraries were quantified using quantitative PCR and quality control was performed with the DNA 1000 series II chip bioanalyzer (Agilent, Santa Clara, CA, USA). Sequencing of libraries was performed with an Illumina HiSeq 1000 Sequencer using TruSeq SBS v3-HS kit (100 cycles) and TruSeq SR Cluster v3-cBot-HS kits (Illumina, San Diego, CA, USA) generating 100-bp reads.

treatment_protocol: The 1-MCP treatment was performed with 0.14% of active ingredient, reaching a final concentration of 0.7 μl/L, according to the instruction provided by AgroFresh.

value: apple skin

tag: Stage

value: 7 days of shelf-life after 2 month of cold storage

tag: storage

value: Yes


title: training cohort patient 23

value: training


title: T2+7_MCP_rep2

description: Processed data file: Matrix_FPKM.txt


title: training cohort patient 22


title: T2_MCP_rep3

description: Processed data file: Matrix_FPKM.txt

source_name: apple skin, 1-MCP, cold storage

value: 2 months of cold storage


title: CD8-Human-Channel2

tag: bead concentration


title: CD8-Human-Channel1


title: Control replicate 2

description: rRNA depleted RNA

value: methanol


title: meUbx_R2

value: gp-Ubx (home made)


title: training cohort patient 20

source_name: primary oropharyngeal carcinoma

tag: cohort

value: oropharyngeal squamous cell carcinoma (OPSCC)


title: training cohort patient 21

value: deceased


title: T2_MCP_rep2

description: Processed data file: Matrix_FPKM.txt


title: training cohort patient 19

value: alive


title: T2_MCP_rep1

description: Processed data file: Matrix_FPKM.txt


title: Control replicate 1

description: rRNA depleted RNA


title: CD4-Human-Channel3

source_name: CD4+ T Cells

value: CD4+ T Cells


title: CD4-Human-Channel4


title: training cohort patient 24

value: primary oropharyngeal carcinoma


title: training cohort patient 18


title: training cohort patient 17


title: CD4-Human-Channel2


title: T2+7_MCP_rep1

description: Processed data file: Matrix_FPKM.txt


title: Control replicate 3

description: rRNA depleted RNA


title: T2+7_CTRL_rep2

description: Processed data file: Matrix_FPKM.txt

source_name: apple skin, control, cold storage + shelf-life

value: Control


title: training cohort patient 16


title: T2+7_CTRL_rep1

description: Processed data file: Matrix_FPKM.txt


title: CD34-Human-Channel8

source_name: CD34+ stem/progenitor cells

value: CD34+ stem/progenitor cells


title: CD4-Human-Channel1


title: training cohort patient 13


title: T2_CTRL_rep3

description: Processed data file: Matrix_FPKM.txt

source_name: apple skin, control, cold storage


title: training cohort patient 14


title: dme-2_nDMECTD-1_BS-seq_endo

city: kannapolis

first: Tzung-Fu

last: Hsieh

state: NORTH CAROLINA

address: 600 Laureate way

department: Plant and Microbial Biology

institute: North Carolina State University

data_processing:
We used Perl scripts to convert all the Cs in the ‘forward’ reads to Ts, and all the Gs in the ‘reverse’ reads to As. The converted reads were then aligned to the equivalently converted TAIR10 reference genome, allowing up to two mismatches per read.
Single_C: We use Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR10
Supplementary_files_format_and_content: All processed files are in GFF format. Files contain fractional methylation data for individual cytosines (single-c) or in 50 bp windows.

organism: Arabidopsis thaliana

source_name: dme nDMECTD endosperm

growth_protocol: Long day condition (16 hours light, 8 hours dark) at 23 °C

extract_protocol:
Genomic DNA were isolated from hand dissected, 5-6 DAP (torpedo to early-bend stage seed stage) dme-2 endosperm that has been complemented by nDMECTD (dme-2/dme-2; nDMECTD/nDMECTD).
Approximately 20-50 ng of purified genomic DNA was sheared to about 300bp using Covaris M220 (Covaris Inc., Woburn, Massachusetts). The sheared DNA was cleaned up and recovered by 1.2x AMPure XP beads then followed by end repaired and A-tailing (NEBNext Ultra II DNA Library Prep Kit for Illumina, NEB) before ligated to the NEBNext methylated multiplex adaptors (NEBNext Multiplex Oligos for Illumina, NEB) according to the manufacturer’s instructions. Adaptor-ligated DNA was cleaned up with 1x AMPure XP beads. The purified adaptor-ligated DNA was subjected to one round of sodium bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research Corporation, Irvine, CA) as outlined in the manufacturer’s instruction with 80 min of conversion time. Half of the bisulfite-converted DNA molecules was PCR amplified with the following condition: 2.5 U of ExTaq DNA polymerase (Takara), 5 ul of 10 x Extaq reaction buffer, 25 µM dNTPs, 1 ul of universal and index primers (10 uM) in 50 uL reaction. The thermocyling condition was as follows: 95 °C for 2 min and then 10 cycles each of 95 °C for 30 s, 65 °C for 30 s, and 72 °C for 60 s. The enriched libraries were purified twice with 0.8x (v/v) AMPure XP beads to remove adaptor dimers. High throughput sequencing was performed by Novogene Corporation (USA).

value: endosperm

tag: ecotype

value: Col-gl

value: dme-2/dme-2; nDMECTD/nDMECTD


title: T2_CTRL_rep2

description: Processed data file: Matrix_FPKM.txt

value: apple skin


title: dme-2_nDMECTD-3_BS-seq_endo


title: CD34-Human-Channel7


title: T2+7_CTRL_rep3

description: Processed data file: Matrix_FPKM.txt

value: 7 days of shelf-life after 2 month of cold storage


title: T0_rep3

description: Processed data file: Matrix_FPKM.txt

source_name: apple skin, control

value: harvest

value: No


title: CD34-Human-Channel5


title: T2_CTRL_rep1

description: Processed data file: Matrix_FPKM.txt

value: 2 months of cold storage

value: Yes


title: dme-2_nDMECTD-2_BS-seq_endo


title: training cohort patient 12

value: training

tag: disease status


title: training cohort patient 11

value: oropharyngeal squamous cell carcinoma (OPSCC)

tag: 3-year os status


title: CD34-Human-Channel4

tag: cell type


title: training cohort patient 10

value: deceased

value: not available


title: T0_rep2

description: Processed data file: Matrix_FPKM.txt


title: T0_rep1

description: Processed data file: Matrix_FPKM.txt


title: training cohort patient 15


title: training cohort patient 09


title: CD34-Human-Channel3


title: CD34-Human-Channel6


title: training cohort patient 08


title: CD34-Human-Channel2


title: CD34-Human-Channel1


title: E10_5_Isl1_hypo_OFT_RV_RNA_seq_rep3

description:
E10_5_Isl1_hypo_OFT_RV_RNA_seq.bw
E10_5_Isl1_hypo_OFT_RV_quanty_transcripts_diff_expr.txt

data_processing:
RNA-Seq reads were mapped to the mm9 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000). Samples were quantified using analyzeRepeats.pl (mm9 –count exons –strand both –noadj). Differential expression (fold change >1.5; log2 fold change <−0.58, >0.58; p-value < 0.05) was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR. The KNIME 2.9.1 platform (Konstanz, Germany) was used to filter differentially regulated genes.
Genome_build: mm9
Supplementary_files_format_and_content: bw, differential expressed DESEq2 file

extract_protocol: Outflow tract and right ventricle of E10.5 control and Isl1 hypomorphic embryos were dissected and stored at −80 °C in Qiazol. After genotyping, total RNA from single embryos was extracted using Rneasy Microarray Tissue Kit (Qiagen #73304). The integrity of RNA was assessed on Bioanalyzer 2100 (Agilent). For RNA-Seq of control and Isl1 hypomorphic tissue samples, 100 ng of total RNAs was used for library preparation and sequenced on BGISEQ-500.

tag: embryonic stage

value: dissected outflow tract and right ventricle

tag: strain

value: Isl1 hypomorph


title: E10_5_Isl1_hypo_OFT_RV_RNA_seq_rep4

tag: genotype


title: E10_5_Isl1_hypo_OFT_RV_RNA_seq_rep2


title: VDHG_Man2

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description:
RNA sample 2 of V. sp. dhg which was grown in mannitol medium
Total RNA without ribosomal RNA

data_processing:
The quality of the sequence reads obtained from RNA-seq was checked by FastQC.
The sequence reads were aligned to the reference genome using bowtie2.
The Cufflink package (http://cufflinks.cbcb.umd.edu/) was run to obtain transcriptomic data.
Genome_build: The genome sequence of V. sp. dhg has been uploaded to Genbank (accession number: CP028943, CP028944, and CP028945).
Supplementary_files_format_and_content: gtf, FPKM values for each gene
*_1_transcripts.gtf corresponds to CP028943
*_2_transcripts.gtf corresponds to CP028944
*_3_transcripts.gtf corresponds to CP028945

organism: Vibrio sp. dhg

source_name: KCTC 13229BP

growth_protocol: For expression profiling, V. sp. dhg was cultured in buffered minimal medium supplemented with alginate, mannitol, or glucose as a sole carbon source, and harvested at early exponential phase (OD600=0.6).

extract_protocol:
Total RNA including small RNAs was extracted by using an RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Then, the ribosomal RNAs were removed from the total RNA using the Ribo-Zero rRNA Removal Kit for Gram-negative bacteria (Illumina, San Diego, USA).
The strand-specific RNA-seq library was constructed using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina platforms according to the manufacturer’s instructions.

treatment_protocol: The cells were treated with RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany).

value: sp. dhg

value: wildtype

tag: carbon source

value: mannitol


title: VDHG_Man1

description:
RNA sample 1 of V. sp. dhg which was grown in mannitol medium
Total RNA without ribosomal RNA


title: E10_5_Isl1_hypo_OFT_RV_RNA_seq_rep1


title: training cohort patient 07

value: primary oropharyngeal carcinoma

value: alive


title: training cohort patient 06