title: 0F1: Foot regeneration ATAC-seq, 0 hours post amputation, replicate 1

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (0F1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0F_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Foot Regeneration

value: Untreated


title: 0F2: Foot regeneration ATAC-seq, 0 hours post amputation, replicate 2

status: Public on Jul 01 2020

type: SRA

city: Davis

first: Jack

last: Cazet

state: CA

address: 1 Shields Ave.

department: MCB

country: USA

institute: University of California, Davis

library_source: genomic

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (0F2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0F_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

molecule: genomic DNA

organism: Hydra vulgaris

source_name: Mid-Body Column Tissue

growth_protocol: Hydra vulgaris strain 105 polyps were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C and fed 1-2 times weekly with Artemia nauplii.

extract_protocol:
15 regenerating tips were homogenized using a dounce homogenizer and cells were lysed using a cocktail of mild detergents as described in the OMNI-ATAC-seq protocol (Corces et al., 2017). ~50000 nuclei were then spun down and used for tagmentation.
Libraries were prepared as described in the original ATAC-seq publication (Buenrostro et al., 2013)

treatment_protocol: For iCRT14 treatment, Hydra were pre-incubated in 5uM iCRT14 for two hours prior to amputation. Following amputation, iCRT14 treatment continued until tissue was collected for library preparation.

tag: strain

tag: tissue

value: Mid-Body Column

tag: timepoint

value: 0 hours post amputation

tag: regeneration type

tag: treatment


title: 0H2: Head regeneration ATAC-seq, 0 hours post amputation, replicate 2

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (0H2_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0H_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

value: Head Regeneration


title: WT2

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: rRNA depleted (sRNA-seq)

library_source: transcriptomic

data_processing:
Adapters and low quality bases were trimmed using Cutadapt
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2
Read counting was performed with HTSeq
Differential Gene expression analysis performed with DESeq2
Genome_build: Streptococcus pneumoniae D39 (RefSeq NC_008533) genome and D39 plasmid pDP1 sequence (RefSeq NC_005022)
Supplementary_files_format_and_content: WTvSPD1366DESeq2.xls: differential expression of sRNA genes (all sRNA genes)

molecule: total RNA

organism: Streptococcus pneumoniae D39

source_name: cells

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.15

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
Library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria.  rRNA depleted samples were then subjected to RNA fragmentation using the Ambion RNA fragmentation kit (AM8740). Fragmented RNA was subjected to RNA 5' polyphosphatase (Epicenter) treatment, which was performed to facilitate the 5' adapter ligation step. Small RNA libraries were generated by Macrogen using TruSeq® small RNA library kit (Illumina).

tag: genotype

value: Wildtype parent


title: NHP_41_Donor

city: Boston

first: James

middle: John

last: Kaminski

state: MA

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Boston Children's Hospital

data_processing:
Align with cellranger count (v3.1.0) to MMul10 with Ensembl98 annotations
Combine samples with cellranger aggregate, set “normalization=none”
Load matrix of UMI counts into Seurat v3.1
Retain cells with at least 800 genes detected and 1,500 transcripts detected.
Normalize data with SCTransform function in Seurat, using Lane as batch variable to correct for batch effects
Genome_build: mmul10
Supplementary_files_format_and_content: matrix.mtx.gz contains raw reads after aggregate command in cellranger. Normalized_Count_Matrix.mtx contains normalized counts after SCTransform
barcodes.tsv.gz: Barcodes file output by cellranger count
features.tsv.gz: Features file output by cellranger count
Supplementary_files_format_and_content: matrix.mtx.gz: Count matrix output by cellranger count
Normalized_Count_Matrix.mtx.gz: MatrixMarket formatted matrix of Normalized UMI counts for each gene in each cell, after QC and filtering
Normalized_Count_Matrix__ColumnNames.txt: Cell IDs for Normalized Count Matrix
Normalized_Count_Matrix__RowNames.txt: Genes for Normalized Count Matrix

organism: Macaca mulatta

extract_protocol:
Four colon samples from the allo-HCT cohort and four colon samples from the untransplanted healthy control cohort were aseptically thawed, labeled with the viability dye LIVE/DEAD Violet (Invitrogen), then stained with αCD45 antibodies, conjugated with PerCP-Cy5.5 (BD Biosciences), and PE-conjugated αMAMU-A001 antibodies (NHP Reagent Resource). Viable LIVE/DEAD Violet-negative CD45-positive cells were sorted from two out of four GVHD-derived samples into host and donor fractions, based on MAMU-A001 expression. Sorted samples were also CD45-AF488 (IVas)-negative. Donor- and host-derived cells were defined computationally from two additional GVHD samples (see the corresponding Methods section, below).
Single cell libraries from sorted samples were generated using a UMI-based droplet-partitioning platform with the Chromium single cell 3’ library and gel bead kit v2 and v3 (10X Genomics) and then sequenced using a NovaSeq S2 (Illumina).

tag: sample type

value: Donor sample

value: colon


title: 0H1: Head regeneration ATAC-seq, 0 hours post amputation, replicate 1

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (0H1_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0H_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: A16255_t1

type: RNA

city: Seattle

first: Matthew

middle: Price

last: Wood

state: WA

address: 307 Westlake Ave North

department: Global Infectious Diseases

institute: Seattle Children's Research Institute

hyb_protocol: 100 nanograms of RNA was directly hybridized for 18 hours using the Non-human Primate Immunology v2.0 chipset.

scan_protocol: Images were acquired from 280 fields for each sample

data_processing: Raw data were processed in nSolver 4.0 using Advanced Analysis with R version 3.3.2 by running Normalization with the default settings of a threshold count value of 20 and an observation frequency of 1 with automatic selection of optimal house keeping genes.

source_name: Draining Lymph node 2 weeks before vaccination

extract_protocol: Total RNA was extracted using the Macherey Nagel Nucleospin column purification system following the manufactureres instructions. Lymph node cells were lysed by resuspending the 3.0EE6-cell pellat in 300µL of buffer RA1 with 1% beta-mercaptoethanol and storing long term at -80˚C. Lysed cells were thawed and RNA was purified prior to nanostring analysis.

value: Submandibular Lymph Node


title: WT1

description: rRNA depleted (sRNA-seq)


title: NHP_40_Host

value: Host sample


title: NHP_43B_Host


title: NHP_45_Donor


title: 0H4: Head regeneration ATAC-seq, 0 hours post amputation, replicate 4

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (0H4_final_shift.bw) Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. (0H_MG_final_shift.bw) Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)


title: Z12209.W1

source_name: Buccal mucosa 1 week post IEP vaccination

extract_protocol: Total RNA was extracted using the Macherey Nagel Nucleospin column purification system following the manufactureres instructions. Buccal mucosal samples collected by oral cytobrush were stored in 2mL of buffer RA1 with 1% beta-mercaptoethanol and storing long term at -80˚C. Lysed cells were thawed and RNA was purified prior to nanostring analysis.

value: Buccal Mucosa


title: Z10036_t1


title: NHP_43_Host


title: NHP_42_HC

source_name: Healthy control_colon

value: Healthy control sample


title: Z12190.W1

source_name: Buccal mucosa 1 week post IM vaccination


title: Z12189.W1


title: CL Nitrogen control shoot, Rep 2

status: Public on Jun 30 2020

city: New Delhi

first: Pranab

middle: kumar

last: Mandal

state: Delhi

address: LBS building, Pusa Campus

department: National Research Centre on Plant Biotechnology

country: India

institute: Indian council of Agriculture Research

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) CL wheat variety, replicate 2

hyb_protocol: The biotinylated cDNAs were fragmented and hybridized to the Affymetrix GeneChip® Wheat Genome Array (Affymetrix, Inc., Carlsbad, CA) for 16 hours. The arrays were processed according to the manufacturer's specifications.

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using affymetrix GeneChip command console software (AGCC) and Robust MultiChip Average (RMA) used for normalization of data. Each array dataset was then imported into Agilent GeneSpring software 14.5 for analysis.

label: biotin

organism: Triticum aestivum

source_name: CL wheat genotype 15-d old shoot tissue N control

label_protocol: 250ng of total RNA were incubated with Oligo dT/T7 primers and reverse -transcribed into double stranded cDNA. The amplified RNA were purified and labeled by biotin with GeneChip® IVT labeling kit.

growth_protocol: Uniform size seeds of all four varieties were surface sterilized using 0.1% sodium hypochlorite for 5 min and then rinsed three times with sterile water. The sterilized seeds were germinated in water soaked filter paper placed in Petriplates at 25±1°C in the dark. When the primary roots were grown approximately 1cm in length, the germinating seeds were transferred in pots (5 seeds/pot) containing mixture of vermiculite and perlite in a ratio 2:1 and grown for 15 days in the culture room under a 16/8h light/ dark conditions.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen, Valencia, USA) and treated with DNaseI (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: All four genotypes were grown in two different conditions: MS modified (without N source) medium with standard nitrogen nutrition (control/+N) including 8mM Ca(NO3)2, and nitrogen starved condition (stressed/-N), with 0.08mM Ca(NO3)2 as source.

tag: genotype/variation

value: CL

tag: group

value: N control

value: 15 day old wheat shoot tissue


title: Z11114.W1


title: NHP_44_Host


title: CL Nitrogen control root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) CL wheat variety, replicate 2

source_name: CL wheat genotype 15-d old root tissue N control

value: 15 day old wheat root tissue


title: CL Nitrogen stressed shoot, Rep 2

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) CL wheat variety, replicate 2

source_name: CL wheat genotype 15-d old shoot tissue N stressed

value: N stressed


title: CL Nitrogen stressed shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) CL wheat variety, replicate 3


title: HD2967 Nitrogen control shoot, Rep 2

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) HD2967 wheat variety, replicate 2

source_name: HD2967 wheat genotype 15-d old shoot tissue N control


title: HD2967 Nitrogen control root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) HD2967 wheat variety, replicate 2

source_name: HD2967 wheat genotype 15-d old root tissue N control


title: spd_1366-1

description: rRNA depleted (sRNA-seq)

value: {delta}cvfD mutant


title: CL Nitrogen control root, Rep 3

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) CL wheat variety, replicate 3


title: HD2967 Nitrogen control shoot, Rep 1

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) HD2967 wheat variety, replicate 1


title: HD2967 Nitrogen control root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) HD2967 wheat variety, replicate 1


title: Z10070.W1


title: K307 Nitrogen control shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) K307 wheat variety, replicate 3

source_name: K307 wheat genotype 15-d old shoot tissue N control


title: CL Nitrogen stressed root, Rep 3

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) CL wheat variety, replicate 3

source_name: CL wheat genotype 15-d old root tissue N stressed


title: CL Nitrogen stressed root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) CL wheat variety, replicate 2


title: CL Nitrogen control root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) CL wheat variety, replicate 1


title: K307 Nitrogen control root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) K307 wheat variety, replicate 1

source_name: K307 wheat genotype 15-d old root tissue N control


title: CL Nitrogen stressed root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) CL wheat variety, replicate 1


title: K9107 Nitrogen stressed shoot, Rep 1

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) K9107 wheat variety, replicate 1

source_name: K9107 wheat genotype 15-d old shoot tissue N stressed


title: K9107 Nitrogen control shoot, Rep 1

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) K9107 wheat variety, replicate 1

source_name: K9107 wheat genotype 15-d old shoot tissue N control


title: K307 Nitrogen stressed shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) K307 wheat variety, replicate 3

source_name: K307 wheat genotype 15-d old shoot tissue N stressed


title: CL Nitrogen control shoot, Rep 1

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) CL wheat variety, replicate 1


title: CL Nitrogen control shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) CL wheat variety, replicate 3


title: K307 Nitrogen control root, Rep3

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) K307 wheat variety, replicate 3


title: HD2967 Nitrogen control shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) HD2967 wheat variety, replicate 3


title: HD2967 Nitrogen stressed root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) HD2967 wheat variety, replicate 2

source_name: HD2967 wheat genotype 15-d old root tissue N stressed


title: K307 Nitrogen stressed shoot, Rep 2

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) K307 wheat variety, replicate2


title: CL Nitrogen stressed shoot, Rep 1

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) CL wheat variety, replicate 1


title: K307 Nitrogen stressed root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) K307 wheat variety, replicate 1

source_name: K307 wheat genotype 15-d old root tissue N stressed


title: HD2967 Nitrogen stressed shoot, Rep 2

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) HD2967 wheat variety, replicate 2

source_name: HD2967 wheat genotype 15-d old shoot tissue N stressed


title: K307 Nitrogen stressed root, Rep 3

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) K307 wheat variety, replicate 3


title: 24wks_mfs_dta

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

description:
mixed sex (pooled samples)
24wk_MFS_D_S4_L007
24wk_MFS_D_S4_L008

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from HiSeq4000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) or human (GRCh38-3.0.0) transcriptome, cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline
The final output filtered expression matrices were imported into the Seurat package in R and built into Seurat objects using the CreateSeuratObject function.
Standard quality control measures were then taken to exclude outliers representing doublets/clumps and free RNA. Cells with greater than 7.5% mitochondrial gene content were excluded
Data normalization, scaling and regression by mitochondrial content were then performed using the SCTransform command in Seurat.
Genome_build: mm10-3.0.0, GRCh38-3.0.0
Supplementary_files_format_and_content: Processed data files(.csv format) are exported expression matrices from the SCT assay within the Seurat package in R. Columns represent individual cell barcodes, rows represent genex and numerical values represent the normalized expression data.

molecule: polyA RNA

organism: Mus musculus

source_name: Aortic tissue

extract_protocol:
For aortic root/ascending samples, the aortic root was dissected completely and divided below the aortic valve. The ascending aorta was divided midway between the aortic valve and the takeoff of the brachiocephalic artery (Figure 2A). For descending thoracic aorta, the vessel was transected proximally just beyond the ligamentum arteriosum and distally at the diaphragm. Aortas were transferred to a separate dish and rinsed in PBS. Specimens were combined into groups with age and genotype-matched animals as biologic replicates. The aortas were then digested in enzymatic solution containing 2U/mL Liberase TM (Roche #05401127001) and 2U/mL elastase (Worthington #LS002279) in Hanks buffered saline solution (HBSS) for one hour. The cell suspension was filtered through a 70uM strainer, centrifuged and resuspended in cold HBSS. Suspensions were processed with FACS to discriminate live/dead cells and clumps/debris. Samples were then diluted and proprocessed using a 10x Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions (GEMs) according to manufacturer protocols
Individual sample libraries were generate from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

value: Marfan (Fbn1 C1041G/+)

tag: age

value: 24 weeks

tag: Sex

value: pooled male and female

tag: anatomic segment

value: Descending thoracic aorta


title: K9107 Nitrogen control root, Rep 3

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) K9107 wheat variety, replicate 3

source_name: K9107 wheat genotype 15-d old root tissue N control


title: HD2967 Nitrogen stressed root, Rep 3

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) HD2967 wheat variety, replicate 3


title: K307 Nitrogen control shoot, Rep 2

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) K307 wheat variety, replicate 2


title: K9107 Nitrogen stressed root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) K9107 wheat variety, replicate1

source_name: K9107 wheat genotype 15-d old root tissue N stressed


title: K307 Nitrogen stressed root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) K307 wheat variety, replicate 2


title: K307 Nitrogen control shoot, Rep 1

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) K307 wheat variety, replicate 1


title: K9107 Nitrogen control root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) K9107 wheat variety, replicate1


title: HD2967 Nitrogen control root, Rep 3

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) HD2967 wheat variety, replicate 3


title: 4wks_mfs_root_asc

description:
mixed sex (pooled samples)
MFS_4wk_S1_L005

value: 4 weeks

value: Aortic root/ascending aorta


title: K9107 Nitrogen control shoot, Rep 2

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) K9107 wheat variety, replicate 2


title: 4wks_wt_root_asc

description:
mixed sex (pooled samples)
WT_4wk_S2_L005

value: Control (WT)


title: K9107 Nitrogen stressed root, Rep 3

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) K9107 wheat variety, replicate 3


title: 24wks_wt_dta

description:
mixed sex (pooled samples)
24wk_WT_D_S3_L007
24wk_WT_D_S3_L008


title: 24wks_mfs_female_root_asc

description:
female only (paired samples)
mfs_female_S1_L003

value: female


title: Experiment2

city: Dresden

first: Elisha

last: Krieg

state: Saxony

address: Hohe Str. 6

department: Institute of Biofunctional Polymer Materials

country: Germany

institute: The Leibniz Institute of Polymer Research Dresden (IPF)

data_processing:
bcl2fastq2 2.19.1
Kallisto (v. 0.43.1) was run on the sequencing data to generate TPM values. TThe tool needs to create an index for the TPM calculation. Here, the human transcriptome reference (v. 81)  from Ensembl was downloaded and used for the index creation. Afterwards files were read via a r script and summarised in a spreadsheet
Genome_build: hg38
Supplementary_files_format_and_content: Spreadsheet that shows Kallisto tpm values of the processed samples; each columns is a samples; the remaining columns are the annotation information of Ensembl81

organism: Homo sapiens

source_name: pancreatic islets

extract_protocol:
Extraction was not necessary because ready made libraries for Illumina sequencing were used
Complete cDNA was synthesized from 5 ng total RNA using the SmartScribe reverse transcriptase (Takara Bio) with a universally tailed poly-dT primer and a template switching oligo followed by amplification for 12 cycles with with the Advantage 2 DNA Polymerase (Takara Bio). After ultrasonic shearing (Covaris LE220), amplified cDNA samples were subjected to standard Illumina fragment library preparation using the NEBnext Ultra DNA library preparation chemistry (New England Biolabs). In brief, cDNA fragments were end-repaired, A-tailed and ligated to indexed Illumina Truseq adapters. Resulting libraries were PCR-amplified for 15 cycles using universal primers, purified using XP beads (Beckman Coulter) and then quantified with the Fragment Analyzer.

tag: treated with merpy

tag: target-specific csl present

value: pancreatic islets


title: K9107 Nitrogen control root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) K9107 wheat variety, replicate 2


title: K9107 Nitrogen stressed shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) K9107 wheat variety, replicate 3


title: K307 Nitrogen control root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen control (8 mM) K307 wheat variety, replicate 2


title: Control3

data_processing:
bcl2fastq2 2.19.1
Kallisto (v. 0.43.1) was run on the sequencing data to generate TPM values. The tool needs to create an index for the TPM calculation. Here, the human transcriptome reference (v. 81)  from Ensembl was downloaded and used for the index creation. Afterwards files were read via a r script and summarised in a spreadsheet
Genome_build: hg38
Supplementary_files_format_and_content: Spreadsheet that shows Kallisto tpm values of the processed samples; each columns is a samples; the remaining columns are the annotation information of Ensembl81


title: K9107 Nitrogen control shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen control (8 mM) K9107 wheat variety, replicate 3


title: Control2


title: HD2967 Nitrogen stressed root, Rep 1

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) HD2967 wheat variety, replicate1


title: 24wks_wt_root_asc

description:
mixed sex (pooled samples)
24wk_WT_AS_S1_L007
24wk_WT_AS_S1_L008


title: HD2967 Nitrogen stressed shoot, Rep 1

description: Gene expression data from 15 day old roo tissue of nitrogen stressed (0.08 mM) HD2967 wheat variety, replicate1


title: K307 Nitrogen stressed shoot, Rep 1

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) K307 wheat variety, replicate 1


title: Experiment3


title: K9107 Nitrogen stressed shoot, Rep 2

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) K9107 wheat variety, replicate2


title: K9107 Nitrogen stressed root, Rep 2

description: Gene expression data from 15 day old root tissue of nitrogen stressed (0.08 mM) K9107 wheat variety, replicate2


title: HD2967 Nitrogen stressed shoot, Rep 3

description: Gene expression data from 15 day old shoot tissue of nitrogen stressed (0.08 mM) HD2967 wheat variety, replicate 3


title: Control1


title: Experiment1


title: Untreated2


title: Untreated1


title: Untreated3


title: 305589_S4_R1_001: K562 RNASE1-mutant RPMI RNA pretreatment with PNK only replicate 2

city: Woodbury

first: Thomas

middle: R

last: Gingeras

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description: small RNA from extracellular vesicle-depleted (non-EV) conditioned medium

data_processing:
Small RNAseq data were mapped with STAR with the following parameters: --clip3pAdapterSeq TGGAATTCTC --clip3pAfterAdapterNbases 4 --clip5pNbases 4 --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0.85 --outFilterMatchNmin 15 --outMultimapperOrder Random . Genome indices were generated with STAR v.2.6.1d using our custom transcript annotation file and with --sjdbOverhang 100 parameter. Custom transcript annotation file contains GENCODE comprehensive gene annotation for the primary assembly of the human genome GRCh38.p12 Release 28, complemented with the annotations of tRNA genes from GtRNAdb and with manually prepared annotations of the RNY5 gene and of its five pseudogenes (RNY5P1, RNY5P3, RNY5P4, RNY5P5, RNY5P8).
Primary read alignments for unique and multimapping reads were extracted with samtools v.0.1.19-44428cd. The resulting set of reads was used for all analyses of Y RNAs and tRNAs and of their fragments. Primary alignments were assigned to features in a strand-specific fashion with featureCounts v.1.6.1.
For analysis of Y RNAs, reads that were assigned to Y RNA genes and their corresponding annotated pseudogenes were counted. Primary alignments that were not assigned to any annotated features were further tested for overlap with Y RNA repeats by using bedtools v.2.17.0. Annotation of Y RNA repeats (annotated as HY1, HY3, HY4 and HY5) was obtained from RepeatMasker (last update date: 2018-08-10). RepeatMasker data were downloaded through the UCSC Table Browser. Reads that mapped to all pseudogenes of a particular Y RNA gene were grouped and counted together. Reads that mapped to all repeats that corresponded to a particular Y RNA gene were also grouped and counted together.
Reads for our analysis of tRNA fragments and of processing of tRNA CCA tails by RNase 1 were selected as outlined below. First, reads were filtered out if they had deletions, insertions or unannotated introns. Second, reads were excluded if they did not have 3’ adapter sequences. Remaining reads were trimmed of adapter sequences before further analysis. Mature human tRNAs are modified to contain a nontemplated CCA tail at their 3’ ends. In the next steps, potential presence of an intact CCA or a processed CC or C tail at the 3’ end was taken into account for the reads whose alignments reached the 3’ end of their corresponding tRNA gene annotations. We refer to those reads as “tailed” hereafter. Adapter-trimmed reads were included into the analysis, if their trimmed length was equal to the sum of alignment matches denoted in the CIGAR string. Tailed reads that contained exactly an intact CCA or a processed CC or C tail sequence at the 3’ end were allowed to be longer than the length of all alignment matches in the CIGAR string by the length of the tail sequence that did not map to the genome. Included reads were further required to not align to pre-tRNA sequences. A read was considered as aligning to pre-tRNA sequence, if its alignment overlapped by at least one nucleotide with either an intron of a tRNA gene or with a sequence outside the annotated mature tRNA. Of note, if a tailed tRNA read mapped to a gene that is followed in the genome by CCA, CC or C, the sequence of the intact CCA or a processed CC or C tail of this tailed read could completely or partially map outside of the corresponding tRNA gene annotation. Such reads were not considered as aligning to pre-tRNA and were included into our analysis.
Reads that qualified for analysis were used for quantification of 5’ and 3’ tRNA halves and for determination of CCA tail status. A read was classified as representing a 5’ tRNA half, if the alignment of such read started no farther than at the fifth nucleotide and ended within nucleotides 29 to 41 of the corresponding tRNA annotation. A read was considered as representing a 3’ tRNA half, if the alignment started within nucleotides 29 to 41 and ended within the last five nucleotides of the corresponding tRNA annotation.
For analyses of CCA tail status, we counted reads whose alignments reached the annotated end of a tRNA gene and did not have nontemplated nucleotides, or had only C, only CC or the intact CCA sequence following the annotated sequence.
Genome_build: GRCh38.p12 Release 28
Supplementary_files_format_and_content: Each raw data file is accompanied by two tab-delimited text files with processed data that were used for tRNA (file 1) and Y RNA (file 2) analyses. Processed data file 1 contains five fields: field #1 - with RNAseq read identifier, field #2 - with genomic feature as mapped by STAR and assigned by featureCounts, field #3 - with trimmed read length that was used for read length distribution plots, field #4 - with the sequence of nontemplated nucleotides if the read was eligible for tRNA 3' CCA analysis, field #5 - with classification of the read as tRNA half, if applicable. Note that tRNA genes, whose annotation is followed by C, CC or CCA in the genome often got precedence in assignment of tRNA reads that cover processed or intact CCA tails. Processed data file 2 contains two fields: field #1 - with a feature name, field #2 - with read counts that correspond to the feature in field #1.

source_name: K562 RNASE1-mutant

growth_protocol: Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific), penicillin (100 units/ml), streptomycin (100 µg/ml) and glutamine (4 mM) (Thermo Fisher Scientific), or in QBSF-55 serum-free medium (Quality Biological).

extract_protocol:
Before RNA isolation, vesicle-depleted (non-EV) conditioned medium was concentrated at 4 °C from 15 ml to 1 ml on 3 kDa cutoff Amicon filters (Millipore-Sigma), as per manufacturer’s instructions. RNA was isolated with a mirVana miRNA isolation kit (Thermo Fisher Scientific). The manufacturer’s protocol for total RNA isolation was used, with the following exceptions. RNA isolation was started by addition of two volumes of mirVana Lysis Buffer, and volumes in subsequent steps were scaled up accordingly; organic extraction was spun at 9,400 g instead of 10,000 g. RNA intended for sequencing was treated with DNase using a TURBO DNA-free kit (Thermo Fisher Scientific). Up to 10 µg of RNA were incubated with 2 units of TURBO DNase in 1× DNase buffer (kit-supplied) for 25 min at 37 °C. Reactions were inactivated by using the kit-supplied inactivation reagent. RNA was ethanol-precipitated, resuspended in diethyl pyrocarbonate (DEPC)-treated water (Thermo Fisher Scientific). All RNA samples for sequencing were decapped with Cap-Clip acid pyrophosphatase (Cellscript). RNA (up to 1 µg in 21 µl DEPC-treated water) was incubated 2 min at 85 °C and transferred to ice for 1 min. 2.5 µl of manufacturer supplied Cap-Clip buffer, 20 units of RNase inhibitor (ANTI-RNase; Ambion) and 2.5 units of Cap-Clip enzyme were added and the reaction (final volume- 25 µl) was incubated for 1 h at 37 °C. Following incubation, RNA was phenol-chloroform extracted and ethanol-precipitated. Unless otherwise noted, RNA samples were also treated with polynucleotide kinase (PNK; New England BioLabs). RNA (up to 1 µg in 37.5 µl DEPC-treated water) was combined with 5 µl manufacturer supplied PNK buffer and 2.5 µl (25 units) PNK. The reaction was incubated 10 min 37 °C, then 5 µl 10 mM ATP were added, followed by 30 min incubation at 37 °C. RNA was phenol-chloroform extracted and ethanol-precipitated. Where applicable, the aforementioned PNK treatment was replaced by treatment with the rtStar tRF&tiRNA Pretreatment Kit (Arraystar) as per the manufacturer’s protocol. The kit workflow includes 3’ deacylation, followed by end-healing with PNK and demethylation by AlkB.
Starting material for all sequencing reactions was 100 ng (before pretreatments as described above). Libraries were prepared using the Bioo NEXTFLEX Small RNA-Seq Kit v3 (Bioo Scientific) following the manufacturer’s protocol. Reverse transcription reaction bead cleanup was performed in accordance with the manufacturer’s alternative protocol without size selection. Libraries were amplified using 16 PCR cycles. Products were size selected on 2% agarose gels to include products larger than the adapter dimer and up to 350 bp (corresponding to RNA inserts up to ~225 nt). The resulting libraries were sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: Stable Cas9 overexpression was established in the K562 chronic myelogenous leukemia cell line (ATCC CCL-243) by lentiviral transduction of the pLentiV-Cas9-puro transfer vector. Upon 48 hours post-infection (high multiplicity of infection), cells were subjected to puromycin selection to obtain an antibiotic-resistant bulk population. sgRNAs were cloned into the lentiviral sgRNA expression vector, LRG2.1 (gift from the Chris Vakoc Lab; available from Addgene). This vector expresses the GFP reporter from the EFS promoter. The sgRNA construct was infected at single copy (MOI < 0.2) into K562-Cas9 cells and GFP-positive populations were derived by fluorescence-activated cell sorting. Clonal lines were generated by sorting for single GFP-positive cells. The RNASE1 null clone that was chosen for use in the present work carries a homozygous 19 bp deletion in the coding sequence of RNASE1. This deletion creates a nonsense mutation that is expected to truncate the 128 amino acid wild type mature protein into an N-terminal 45 amino acid polypeptide. The resulting polypeptide would lack two of the three catalytic residues conserved in all catalytically active family members. Cells carrying wild type RNASE1 that were used in this work represent a bulk population of GFP-positive K562-Cas9 cells infected with sgRNA that targets the Rosa26 locus in mice, which is absent from human cells.

tag: cell line

value: K562 RNASE1-mutant

tag: growth medium of cells

value: RPMI 1640

tag: differential rna pretreatment before sequencing

value: pretreatment with PNK, no deacylation, no demethylation

tag: insert size

value: up to 225 nt


title: 305591_S6_R1_001: K562 RNASE1-mutant RPMI RNA pretreatment with PNK only replicate 4


title: 305590_S5_R1_001: K562 RNASE1-mutant RPMI RNA pretreatment with PNK only replicate 3


title: 302190_S4_R1_001: K562 RNASE1-mutant RPMI RNA pretreatment with PNK only replicate 1


title: 302195_S8_R1_001: K562 RNASE1-mutant QBSF RNA pretreatment with PNK only replicate 1


title: MCF7_RBneg-PF-3

city: Buffalo

first: Ram

middle: Mohan

last: Nambiar

address: 665 Elm Street

institute: Roswell Park

data_processing:
The adaptors of the sample files were removed using Trimmomatic in Single End (SE) mode and. Trimmomatic also removes leading and trailing low quality bases (below quality 3),reads whose average quality score per base falls below 15 for 4 base wide sliding window and those reads whose length is below 20.
After the Fastq files are preprocessed, they were aligned to the Human genome(hg38) using tophat2 with default parametrs(i.e read-mismatch=2,read-gap-length=2) for each samples to create a bam file
Finally, the corresponding bam files are collected and sorted using samtools sort and the number of reads for each genes in each samples are computed using HTSeq.
Genome_build: hg38

source_name: mammary gland, breast

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using the RNeasy kit from Quiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO(0.1%) and PF006873600(200nM+0.1% DMSO) upto 48 hrs

tag: tissue

value: mammary gland, breast

tag: disease state

value: breast cancer

value: RB Knockout

tag: agent


title: 305595_S10_R1_001: K562 RNASE1-WT RPMI RNA pretreatment with PNK + deacylation and demethylation replicate 2

source_name: K562 RNASE1-WT

value: K562 RNASE1-WT

value: pretreatment with PNK plus deacylation and demethylation


title: 305594_S9_R1_001: K562 RNASE1-WT RPMI RNA pretreatment with PNK + deacylation and demethylation replicate 1


title: 305585_S3_R1_001: K562 RNASE1-WT RPMI RNA pretreatment with PNK only replicate 4


title: MCF7_RBneg-PF-2


title: 302193_S6_R1_001: K562 RNASE1-WT QBSF RNA pretreatment with PNK only replicate 1


title: 305583_S1_R1_001: K562 RNASE1-WT RPMI RNA pretreatment with PNK only replicate 2


title: 302187_S1_R1_001: K562 RNASE1-WT RPMI no RNA pretreatment replicate 1

value: no PNK, no deacylation, no demethylation


title: 305592_S7_R1_001: K562 RNASE1-WT RPMI no RNA pretreatment replicate 2


title: 305584_S2_R1_001: K562 RNASE1-WT RPMI RNA pretreatment with PNK only replicate 3


title: MCF7_RBneg-PF-1


title: 302188_S2_R1_001: K562 RNASE1-WT RPMI RNA pretreatment with PNK only replicate 1


title: MCF7_RBpos-PF-3

value: wild type


title: MCF7_RBpos-PF-2


title: 226-PF-3

source_name: Pancreas

value: Pancreas

value: PDAC


title: MCF7_RBpos-PF-1


title: 226-PF-1


title: 226-PF-2


title: 519-PF-1


title: 519-PF-3


title: 519-PF-2


title: 24wks_mfs_male_root_asc

description:
male only (paired samples)
mfs_male_S2_L003

value: Marfan (Fbn1 C1041G/+)

value: 24 weeks

value: male

value: Aortic root/ascending aorta


title: ChIP-seq of H3K27me3 in LNCaP/MYC KD 627 Rep 1

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

data_processing:
Libraries were sequenced 76 cycles single-end.
FASTQ files were adaptor trimmed using TrimGalore, aligned with BWA to b37, and sorted using PICARD.
Read pileups were summarized into bigwig files using DeepTools
Genome_build: b37
Supplementary_files_format_and_content: bigwig format of sequence read pileups

source_name: prostate cancer

extract_protocol:
Crosslinked chromatin was extracted from cells using the Active Motif ChIP-it kit
Cells were crosslinked and lysed, and chromatin was sheared to 200-1000bp. 30 micrograms of chromatin were incubated with H3K27me3 antibody overnight, immunoprecipiated, and DNA was purified using the Active Motif ChIP-IT High Sensitivity Kit. DNA was constructed into libraries using the Illumina TruSeq ChIP Library Preparation Kit.

value: LNCaP

tag: condition

value: MYC Knockdown Construct 627

tag: chip antibody

value: H3K27me3 (39155, Active Motif)

tag: replicate


title: ChIP-seq of H3K27me3 in LNCaP/MYC KD 512 Rep 1

value: MYC Knockdown Construct 512


title: ChIP-seq of H3K27me3 in LNCaP/WT Rep 1

value: Wild-type


title: ChIP-seq of H3K27me3 in LNCaP/Control Rep 1

value: Control


title: ChIP-seq of RNAP2 in LNCaP/MYC KD 637 Rep 2

extract_protocol:
Crosslinked chromatin was extracted from cells using the Active Motif ChIP-it kit
Cells were crosslinked and lysed, and chromatin was sheared to 200-1000bp. 30 micrograms of chromatin were incubated with RNAP2 antibody overnight, immunoprecipiated, and DNA was purified using the Active Motif ChIP-IT High Sensitivity Kit. DNA was constructed into libraries using the Illumina TruSeq ChIP Library Preparation Kit.

value: MYC Knockdown Construct 637

value: RNAP2 (39097, Active Motif)


title: ChIP-seq of RNAP2 in LNCaP/WT Rep 2


title: ChIP-seq of H3K27ac in LNCaP/MYC KD 637 Rep 2

extract_protocol:
Crosslinked chromatin was extracted from cells using the Active Motif ChIP-it kit
Cells were crosslinked and lysed, and chromatin was sheared to 200-1000bp. 30 micrograms of chromatin were incubated with H3K27ac antibody overnight, immunoprecipiated, and DNA was purified using the Active Motif ChIP-IT High Sensitivity Kit. DNA was constructed into libraries using the Illumina TruSeq ChIP Library Preparation Kit.

value: H3K27ac (39133, Active Motif)


title: ChIP-seq of RNAP2 in LNCaP/Control Rep 2


title: ChIP-seq of H3K27ac in LNCaP/MYC KD 512 Rep 2


title: ChIP-seq of H3K27ac in LNCaP/MYC KD 627 Rep 2


title: ChIP-seq of H3K27ac in LNCaP/Control Rep 2


title: ChIP-seq of H3K27ac in LNCaP/WT Rep 2


title: ChIP-seq of MYC in LNCaP/Control Rep 2

extract_protocol:
Crosslinked chromatin was extracted from cells using the Active Motif ChIP-it kit
Cells were crosslinked and lysed, and chromatin was sheared to 200-1000bp. 30 micrograms of chromatin were incubated with MYC antibody overnight, immunoprecipiated, and DNA was purified using the Active Motif ChIP-IT High Sensitivity Kit. DNA was constructed into libraries using the Illumina TruSeq ChIP Library Preparation Kit.

value: MYC (ab56, Abcam)


title: ChIP-seq of MYC in LNCaP/MYC KD 627 Rep 2


title: ChIP-seq of H3K27ac in LNCaP/MYC KD 627 Rep 1


title: ChIP-seq of MYC in LNCaP/WT Rep 2


title: ChIP-seq of MYC in LNCaP/MYC KD 637 Rep 2


title: ChIP-seq of H3K27me3 in LNCaP/MYC KD 637 Rep 1


title: ChIP-seq of H3K27ac in LNCaP/MYC KD 512 Rep 1


title: ChIP-seq of H3K27ac in LNCaP/MYC KD 637 Rep 1


title: ChIP-seq of H3K27ac in LNCaP/Control Rep 1


title: ChIP-seq of RNAP2 in LNCaP/MYC KD 637 Rep 1


title: ChIP-seq of H3K27ac in LNCaP/WT Rep 1


title: ChIP-seq of RNAP2 in LNCaP/MYC KD 512 Rep 1


title: ChIP-seq of RNAP2 in LNCaP/Control Rep 1


title: ChIP-seq of RNAP2 in LNCaP/MYC KD 512 Rep 2


title: ChIP-seq of RNAP2 in LNCaP/MYC KD 627 Rep 2


title: ChIP-seq of RNAP2 in LNCaP/MYC KD 627 Rep 1


title: ChIP-seq of MYC in LNCaP/MYC KD 512 Rep 2


title: ChIP-seq of MYC in LNCaP/MYC KD 637 Rep 1

data_processing:
Libraries were sequenced 76 cycles single-end.
FASTQ files were adaptor trimmed using TrimGalore, aligned with BWA to b37, and sorted using PICARD.
Read pileups were summarized into bigwig files using DeepTools
Peaks were scaled using the trimmed mean of M-values.
Peaks were scaled to Drosophila Dm6 spike-in controls.
Genome_build: b37
Supplementary_files_format_and_content: bigwig format of sequence read pileups

value: MYC (ab32072, Abcam)


title: ChIP-seq of MYC in LNCaP/MYC KD 627 Rep 1


title: ChIP-seq of MYC in LNCaP/MYC KD 512 Rep 1


title: ChIP-seq of MYC in LNCaP/WT Rep 1


title: ChIP-seq of MYC in LNCaP/Control Rep 1


title: IMR90 cells, IR TSA Rep1

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were demultiplexed using the bcl2fastq tool, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

source_name: IMR90 cells

growth_protocol: Human primary IMR90 fibroblasts were grown in DMEM +20% FBS, 100 u/mL penicillin, 100 ug/ml streptomycin and 2mM glutamine, at 37 degrees celcius in a humidified atmosphere with 5% CO2.

extract_protocol:
Poly-A mRNA was extracted using a Qiagen RNeasy Mini kit with on-column Dnase1 digestion, according to the manufacturer’s protocol.
mRNA libraries were prepared using an Illumina TruSeq Stranded LT kit according to the manufacturer’s protocol.

treatment_protocol: Cells were treated with control or 100 nM Trichostatin A (TSA) for 10 days, and the medium was refreshed daily. To induce senescence, cells were irradiated 8 hrs after commencement of treatment, where indicated.

tag: cell state

value: Senescent

tag: drug treatment

value: TSA


title: IMR90 cells, IR No TSA Rep3


title: ChIP-seq of RNAP2 in LNCaP/WT Rep 1


title: IMR90 cells, IR No TSA Rep2


title: IMR90 cells, Prolif No TSA Rep2

value: Proliferating


title: IMR90 cells, Prolif TSA Rep3


title: IMR90 cells, Prolif TSA Rep2


title: IMR90 cells, IR No TSA Rep1


title: IMR90 cells, Prolif TSA Rep1


title: IMR90 cells, Prolif No TSA Rep3


title: IMR90 cells, Prolif Parkin Rep3

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were demultiplexed using the bcl2fastq tool, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

treatment_protocol:
[infection protocol]  Retroviral vectors LZRS or LZRS-YFP_Parkin were used to transfect Phoenix packaging cells, and virus was harvested after 24 hrs. Filtered viral supernatent was then mixed 1:1 with culture medium, supplemented with 8 ug/ml polybrene, and cultured with IMR90 cells for 20 hrs. Infected cells were selected with 250 uM zeocin.
Infected cells were treated for 48 hrs with 12.5uM CCCP where appropriate.

tag: gene transduction

value: Parkin

value: DMSO

value: proliferating


title: IMR90 cells, Prolif Parkin Rep2


title: IMR90 cells, Prolif EV Rep3

value: Empty vector control


title: IMR90 cells, Prolif EV Rep1


title: IMR90 cells, Prolif Parkin Rep1


title: IMR90 cells, IR Parkin Rep3

value: senescent


title: IMR90 cells, IR Parkin Rep2


title: IMR90 cells, IR TSA Rep3


title: IMR90 cells, IR Parkin CCCP Rep3

value: CCCP


title: IMR90 cells, IR Parkin CCCP Rep1


title: IMR90 cells, IR CCCP Rep3


title: IMR90 cells, IR Parkin Rep1


title: IMR90 cells, IR TSA Rep2


title: IMR90 cells, IR CCCP Rep1


title: IMR90 cells, IR EV Rep2


title: IMR90 cells, IR EV Rep3


title: IMR90 cells, Prolif No TSA Rep1


title: IMR90 cells, Prolif EV Rep2


title: Ctsd-KO-1%FCS-LT rep3

city: Freiburg

first: Maria

middle: Elena

last: Hess

address: Breisacherstr. 153

department: Institute for Medical Bioinformatics and Systemsmedicine

institute: Universitaetsklinikum Freiburg

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR with parameters--readFilesCommand zcat --twopassMode Basic --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10--alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 12 --limitBAMsortRAM 31532137230 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample.

growth_protocol: Mice were maintained under specific-pathogen-free (SPF) conditions. Cells were cultured for 10 days (1% FCS) or 12 weeks (1% FCS LT) in a mild starvation medium (DMEM/F12 medium supplemented with 1% FCS, 2 mM L-glutamine, and 1% Penicillin-Streptomycin) at 37 °C in humidified air containing 5% CO2.

extract_protocol:
Total RNA was extracted using the Universal RNA purification kit (Roboklon) following the manufacturer’s recommendations. RNA integrity (RIN) was verified using a Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: origin

value: spontaneously immortalized primary breast tumor cells

tag: genotype/background

value: Ctsd-/-

tag: medium

value: 1% FCS

tag: cultivation time

value: 12 weeks


title: Ctsd-KO-1%FCS-LT rep2


title: IMR90 cells, IR CCCP Rep2

tag: cell line


title: IMR90 cells, IR EV Rep1


title: WT-1%FCS-LT rep1

value: wild type


title: Ctsd-KO-1%FCS rep1

value: 10 days


title: WT-1%FCS rep2


title: WT-1%FCS rep3


title: WT-1%FCS rep1


title: Ctsd-KO-1%FCS-LT rep1


title: Ctsd-KO-1%FCS rep2


title: Ctsd-KO-1%FCS rep3


title: human_mfs_root

description:
Male (single patient)
g131_mfs_root_S1_L007

tag: genotype

value: Marfan

tag: Sex

value: male

tag: anatomic segment

value: Aortic root


title: RNA-seq of LNCaP/MYC KD 637 Rep 5

data_processing:
Libraries were sequenced with 150 cycles paired-end. FASTQ files were aligned with STAR to grch37-ercc.
FASTQ files were trimmed using TrimGalore and aligned with STAR to grch37-ercc.
Gene level counts were determined using FeatureCounts.
Genome_build: grch37 and ERCC
Supplementary_files_format_and_content: semicolon separated values for gene level counts

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Mini Plus kit
1 microgram of RNA was extracted from cells, combined with ERCC spike-in control, and assembled into PolyA selected libraries using the Illumina TruSeq Stranded Total RNA Kit. Libraries were sequenced with 150 cycles paired-end. FASTQ files were aligned with STAR to grch37-ercc.

value: LNCaP

value: MYC Knockdown Construct 637


title: RNA-seq of LNCaP/MYC KD 627 Rep 5

value: MYC Knockdown Construct 627


title: RNA-seq of LNCaP/MYC KD 512 Rep 3

value: MYC Knockdown Construct 512


title: WT_346

first: Alexander

last: Herrmann

address: Fetscherstraße 74

department: Clinic of Internal Medicine I

institute: Technical University Dresden, University Hospital Carl Gustav Carus

data_processing:
Illumina Casava 2.17 software used for basecalling.
Reads were trimmed with flexbar v3.5.0 for adapter contamination.
The reads were then aligned to the mouse genome reference GRCm38 with the STAR v2.6.1d and the per-sample 2-pass mapping strategy processing all reads in both passes as described in the documentation.
Read counts were summarized to Gencode gene models vM21 with featureCounts v1.6.1 counting primary alignments only.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts per gene for each sample

source_name: Whole Liver

extract_protocol:
After the treatment period, the livers were perfused with PBS and extracted from the mice were, and kept on RNA later for 24 hours at 4 C. The total RNA was extracted using RNAeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-8 week old mice were fed with HFCDD for 6 weeks. Or 10wk old mice fed CHOW diet.

tag: tissue

value: Whole Liver

value: Mboat7 wildtype

tag: diet treatment

value: CHOW diet

tag: treatment duration

value: 10Wk old


title: WT_327


title: WT_335


title: OCI-C5x nanostring

first: Reid

last: Shaw

address: 401 Terry Ave

institute: Cure First

hyb_protocol: NanoString  standard protocol

scan_protocol: NanoString  standard protocol

data_processing: Raw expression data was normalized using R package 'NanoStringNorm' v. 1.2.1

label: nCounter

source_name: ovarian carcinoma

label_protocol: NanoString  standard protocol

growth_protocol: Cells were grown in previously defined media and culture conditions (Ince et al. 2015)

extract_protocol: RNA was extracted from the cells using Qiagen RNeasy kit per manufacturer's protocol.

treatment_protocol: Cells were untreated.

tag: cell type

value: ovarian carcinoma patient-derived cells

tag: histology

value: Clear cell


title: OCI-P5x nanostring

value: Papillary serous


title: WT_319


title: RNA-seq of LNCaP/Control Rep 5

tag: condition

value: Control

tag: replicate


title: WT_107

value: High fat methionine low choline deficient diet


title: WT_317


title: IMR90 cells, IR Parkin CCCP Rep2

value: Parkin

tag: drug treatment

value: CCCP

tag: cell state

value: senescent


title: RNA-seq of LNCaP/MYC KD 637 Rep 4


title: WT-1%FCS-LT rep2

tag: origin

value: spontaneously immortalized primary breast tumor cells

value: wild type

value: 1% FCS

value: 12 weeks


title: WT_102


title: RNA-seq of LNCaP/Control Rep 4

value: LNCaP


title: WT_103

value: Whole Liver


title: WT_333

value: Mboat7 wildtype


title: WT_106


title: KO_337

value: Mboat7 deleted in hepatocytes

value: CHOW diet


title: RNA-seq of LNCaP/MYC KD 637 Rep 3

value: MYC Knockdown Construct 637


title: KO_326

value: 10Wk old


title: KO_328


title: KO_321


title: Ctsd-KO rep4

source_name: Ctsd-KO

value: breast tumor tissue

tag: age

value: 18 weeks

tag: genotype/background

value: Ctsd-/-


title: WT-1%FCS-LT rep3

tag: medium

tag: cultivation time


title: KO_334

tag: genotype


title: RNA-seq of LNCaP/MYC KD 512 Rep 1

tag: cell line

value: MYC Knockdown Construct 512


title: RNA-seq of LNCaP/Control Rep 3

data_processing:
Libraries were sequenced with 150 cycles paired-end.
FASTQ files were trimmed using TrimGalore and aligned with STAR to grch37-ercc.
Gene level counts were determined using FeatureCounts.
Genome_build: grch37 and ERCC
Supplementary_files_format_and_content: semicolon separated values for gene level counts

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Mini Plus kit
1 microgram of RNA was extracted from cells, combined with ERCC spike-in control, and assembled into PolyA selected libraries using the Illumina TruSeq Stranded Total RNA Kit.

value: Control


title: Ctsd-KO rep3


title: RNA-seq of LNCaP/MYC KD 512 Rep 2


title: WT rep4

source_name: WT


title: WT rep3


title: Ctsd-KO rep2


title: Ctsd-KO rep1


title: KO_110

value: High fat methionine low choline deficient diet


title: WT rep2


title: RNA-seq of LNCaP/MYC KD 627 Rep 3

value: MYC Knockdown Construct 627


title: KO_108


title: KO_320


title: KO_105


title: WT rep1

value: wild type


title: riboH27nsun3

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
Library strategy: Ribo-Seq
Pipeline 1 - Raw reads were assessed for quality using FastQC (Andrews, 2010) and Trimmed for low quality bases and adapter sequences using Trimmomatic (version 0.39, parameters - ILLUMINACLIP:2:30:10 SLIDINGWINDOW:4:20 MINLEN:20) (Bolger et al., 2014). SortMERNA (Kopylova et al., 2012) was used to remove any rRNA sequences. Remaining reads were uniquely aligned to the C. elegans (WBCel235) reference genome using HISAT2 (Kim et al., 2015) (version 2.1.0). The longest transcript was chosen for each gene from the WBCel235 reference genome and the CDS for these transcripts was extracted. Reads were length stratified and checked for periodicity, only read lengths showing periodicity over the 3 frames were retained for further analysis (26 bp -30 bp). Reads aligned to the genome were shifted 12 bp from the 5′-end towards the 3′-end (Ingolia et al., 2009). Any reads aligned to the first 10 codons of each gene were then removed and the remaining reads with a 5′ end aligning to a CDS were kept for further analysis (Lecanda et al., 2016). Ribosome occupancy for gene in a sample was calculated as the number of shifted in frame RPFs aligned to the CDS of the gene (not including the first 10 codons). These values were inputted into DESeq2 (Love et al., 2014).
Pipeline 2 - Raw reads were assessed for quality using FastQC (Andrews, 2010) and Trimmed for low quality bases and adapter sequences using Trimmomatic (version 0.39, parameters - ILLUMINACLIP:2:30:10 SLIDINGWINDOW:4:20 MINLEN:25) (Bolger et al., 2014). SortMERNA (Kopylova et al., 2012) was used to remove any reads matching rRNA sequences. Remaining reads were aligned to the C. elegans reference genome (WBCel235) using HISAT2 (Kim et al., 2015) (version 2.1.0, default parameters). Read alignments were then counted using HTSeq-count (Anders et al., 2015) and gene counts inputted into DESeq2 (Love et al., 2014).
Genome_build: WBCel235
Supplementary_files_format_and_content: rawCounts.txt

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: wild type and noNSUN animals were cultured at 15°C and 25°C for three generations

extract_protocol: Libraries were prepared using a NEB NEXT Small RNA Library Prep Set for Illumina (Multiplex compatible) E7330 Kit, following the manufacturer’s instructions. cDNA libraries were purified according to the manual, followed by a QIAQuick PCR Purification Kit and a 6% polyacrylamide gel, where a band of 150 bp (120 bp adapter + 28-32 footprint fragments) was excised.

treatment_protocol: Empty vector, nsun-1 (W07E6.1), nsun-2 (Y48G8AL.5), nsun-4 (Y39G10AR.21), and nsun-5 (Y53F4B.4) bacterial feeding clones were kindly provided by Prof. Julie Ahringer’s lab (82). Single colonies were inoculated in LB-Ampicillin 100 μg/ml and cultured for 8 h at 37°C. Bacterial cultures were seeded onto 50 mm NGM agar plates containing 1 mM IPTG and 25 μg/ml Carbenicillin at a volume of 200 μl of bacterial culture per plate, and left to dry for 48 hours. 50 synchronized L1 larvae were placed onto RNAi plates and left to grow until adult stage.

tag: datapipeline

tag: temperature

value: noNSUN


title: riboH27nsun2


title: riboH27WT3

value: WT


title: riboH27nsun1


title: riboL20nsun3


title: riboL20nsun1


title: riboH27WT2


title: riboL20WT3


title: KO_318

tag: tissue

tag: diet treatment


title: KO_104

tag: treatment duration


title: riboL20WT1


title: rnaH27nsun3

data_processing:
Pipeline 1 - Raw reads were assessed for quality using FastQC (Andrews, 2010) and Trimmed for low quality bases and adapter sequences using Trimmomatic (version 0.39, parameters - ILLUMINACLIP:2:30:10 SLIDINGWINDOW:4:20 MINLEN:20) (Bolger et al., 2014). SortMERNA (Kopylova et al., 2012) was used to remove any rRNA sequences. Remaining reads were uniquely aligned to the C. elegans (WBCel235) reference genome using HISAT2 (Kim et al., 2015) (version 2.1.0). The longest transcript was chosen for each gene from the WBCel235 reference genome and the CDS for these transcripts was extracted. Reads were length stratified and checked for periodicity, only read lengths showing periodicity over the 3 frames were retained for further analysis (26 bp -30 bp). Reads aligned to the genome were shifted 12 bp from the 5′-end towards the 3′-end (Ingolia et al., 2009). Any reads aligned to the first 10 codons of each gene were then removed and the remaining reads with a 5′ end aligning to a CDS were kept for further analysis (Lecanda et al., 2016). Ribosome occupancy for gene in a sample was calculated as the number of shifted in frame RPFs aligned to the CDS of the gene (not including the first 10 codons). These values were inputted into DESeq2 (Love et al., 2014).
Pipeline 2 - Raw reads were assessed for quality using FastQC (Andrews, 2010) and Trimmed for low quality bases and adapter sequences using Trimmomatic (version 0.39, parameters - ILLUMINACLIP:2:30:10 SLIDINGWINDOW:4:20 MINLEN:25) (Bolger et al., 2014). SortMERNA (Kopylova et al., 2012) was used to remove any reads matching rRNA sequences. Remaining reads were aligned to the C. elegans reference genome (WBCel235) using HISAT2 (Kim et al., 2015) (version 2.1.0, default parameters). Read alignments were then counted using HTSeq-count (Anders et al., 2015) and gene counts inputted into DESeq2 (Love et al., 2014).
Genome_build: WBCel235
Supplementary_files_format_and_content: rawCounts.txt

extract_protocol: Input RNA was extracted from the supernatant of the same samples used for polysome profiling and ribosome footprinting. RNA was depleted of DNA with a TURBO DNA-free kit (Invitrogen), according to the manufacturer’s instructions. Libraries were prepared with 750 ng of starting material using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following rRNA depletion using a NEBNext rRNA Depletion Kit (Human/Mouse/Rat)


title: rnaH27nsun2


title: shTET1-2 5hmC-seq

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description:
shTET1-2
hMe-Seal

data_processing:
Library strategy: 5hmC-seq
Sequence reads were aligned to the human genome (hg19) by using bowtie2 v2.2.9.
Aligned reads were quality filtered with samtools view with following parameters -bh -f 2 - F 1548, sorted (samtools sort) and duplicated reads were removed with samtools rmdup. Bed files were generated with samtools view awk 'OFS="\t" {print $3, $4-1, $4+sqrt($9*$9)-1, $1, ".","+"}.
Peaks were called with MACS v1.4.2 20120305 with pvalue cutoff = 1.00e-05.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: *.bw: bedWig files were generated with following code: scale=$(bc -l <<< '10000000/'$reads) bedtools genomecov -i "$line".bed -g hg19.genome -bg -scale $scale > "$line".bedGraph sort -k1,1 -k2,2n "$line".bedGraph >"$line".sorted.bedGraph bedGraphToBigWig "$line".sorted.bedGraph hg19.chrom.sizes "$line".bw
Supplementary_files_format_and_content: *_peaks.xls: Excel files

extract_protocol:
Genomic DNA was extracted using DNeasy blood and tissue kit (Qiagen).
Library was prepared by KAPA Hyper Prep kit (KK8504). Briefly, genomic DNA was fragmented with dsDNA Fragmentase (NEB, M0348S) and then end-repaired and adaptor-ligated with KAPA Hyper Prep kit. Adaptor-ligated DNA was processed with hMe-Seal method to labelled 5hmC and labelled fragments were pull-downed on Dynabeads™ M-270 Streptavidin (Invitrogen, 65306). Final libraries were amplified with KAPA HiFi HotStart ReadyMix (2X).

tag: tumor

value: acute monocytic leukemia

tag: shRNA


title: rnaL20WT3


title: rnaH27WT1


title: rnaL20WT1


title: rnaL20nsun1


title: rnaL20nsun2


title: rnaL20WT2


title: riboH27WT1


title: rnaH27WT3


title: rnaL20nsun3


title: shNS 5hmC-seq

description:
shNS
hMe-Seal

value: shNS (non-specific control)


title: riboL20nsun2


title: Myc RNAi rep3

city: Canberra

first: Olga

last: Zaytseva

state: ACT

address: 131 Garran Road

country: Australia

institute: John Curtin School of Medical Research

description: Myc RNAi

data_processing:
Sequence quality was verified using FastQC v0.11.6
Alignment was performed using Tophat2 2.1.1
Gene counts were performed using HTSeq 0.6.1
Significant differential expression was analysed using DESeq2 1.12.0
Significant differential splicing was analysed using rMATS 4.0.2
Genome_build: dmel-r6.10 (Flybase)
Supplementary_files_format_and_content: Plain text (.txt) file containing raw gene-level counts for each sample
Supplementary_files_format_and_content: Comma separated values (.csv) files containing output of DESeq2 (differential gene expression). Each column contains: FlybaseID, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, geneSymbol, EntrezID, normalised counts for each sample
Supplementary_files_format_and_content: Microsoft Excel workbook (.xls) file containing combined output of rMATS (differential splicing), arranged into tabs according to splice events: alternative 3’splice site (A3SS.MATS.JCEC), alternative 5’ splice site (A5SS.MATS.JCEC), mutually exclusive exons (MXE.MATS.JCEC),  retained intron (RI.MATS.JCEC), skipped exon (SE.MATS.JCEC),

organism: Drosophila melanogaster

source_name: imaginal wing disc

growth_protocol: Drosophila melanogaster wandering third instar larvae were grown at 18 degrees C for 4 days following 25 degrees C for 3 days

extract_protocol:
RNA was extracted using the Promega ReliaPrep RNA Cell miniprep system (Z6012) following the manufacturer’s protocol and eluted in 50 μL nuclease-free water. RNA purity and integrity were assessed using an automated electrophoresis system (2200 TapeStation, Agilent Technologies)
RNA was prepared using the standard TruSeq Illumina protocol preserving strandedness information, with Oligo-dT beads used to enrich for mRNA

treatment_protocol: RNAi using tubulin-GAL4 driver in the background of temperature-sensitive GAL80

value: tsGAL80;tubG4/Myc RNAi

tag: stock number

tag: developmental stage

value: mid-third instar larvae

value: wing imaginal disc


title: Myc RNAi rep1

description: Myc RNAi


title: riboL20WT2


title: Psi RNAi rep2

description: Psi RNAi

value: tsGAL80;tubG4/Psi RNAi


title: Psi RNAi rep1

description: Psi RNAi


title: Psi RNAi rep3

description: Psi RNAi


title: rnaH27nsun1


title: rnaH27WT2


title: shTET1-1 5hmC-seq

description:
shTET1-1
hMe-Seal


title: Control juvenile (Cy5) vs trf mutant (Cy3) 2

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

country: Japan

institute: Okayama University

description: Dye swap of M5Cj3-2. Biological replicate 2 of 2.

hyb_protocol: A set of fluorescently labeled cRNA targets (750ng for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.

scan_protocol: Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.

data_processing: The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.5 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default condition of the software. Some probes which were judged beyond analysis by Feature Extraction 10.5 software were eliminated from the following analysis.

organism: Ciona intestinalis

source_name: Control juvenile

label_protocol: Cyanine-5 (Cy5) or cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng of total RNA using the Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: trf is a mutant line of Ciona intestinalis isolated from a wild population. trf heterozygous mutants were kept under constant light to induce oocyte maturation.

extract_protocol: Total RNA was extracted from each sample by the acid guanidium thiocyanate-phenol-chloroform method.

treatment_protocol: To obtain a progeny group including homozygous trf mutant larvae, trf heterozygous mutant at the reproductive stage was subjected to self-fertilization. At 42 hours post fertilization, approximately 50 swimming larvae which showed trf/trf phenotype were collected. As controls with normal phenotype, swimming larvae which have not started metamorphosis yet and juvenile which have completed tail regression were obtained from the same batch of trf mutant.

tag: phenotype

value: Normal

tag: morphology

value: juvenile

source_name: trf/trf mutant larva

value: trf/trf mutant

value: swimming larva initiating body axis rotation without tail regression


title: trf mutant (Cy5) and control juvenile (Cy3) 2

description: Dye swap of Cj5M3-2. Biological replicate 2 of 2.

source_name: trf mutant larvae


title: control rep2

description: control


title: control rep1

description: control


title: Myc RNAi rep2

description: Myc RNAi


title: trf mutant (Cy5) and control swimming larva (Cy3) 2

description: Dye swap of Cl5M3-2. Biological replicate 2 of 2.

source_name: Control swimming larva

value: swimming larva


title: LCP_sorted_D10_rep2

last: Edge

state: Massachusetts

address: 243 Charles St

institute: Harvard Medical School

data_processing:
Alignment to mm10 with STAR.
Reads and alignments were assessed for quality using a combination of FastQC, Qualimap and custom scripts
Transcript level per-transcript quantification was performed with Salmon.
Transcript counts were collapsed to gene level counts using Tximport
Differential expression was evaluated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: *tpm.tsv: Tab delimited file containing the transcripts per million for each gene in the sample. The first column is the ensembl id and the second one, the tpm value.

source_name: Primary cochlear organoids

growth_protocol: Mice were maintained at MEEI ACF accodring to IACUC regulations

extract_protocol:
Cochlear sensory epithelia were dissected out and incubated with Cell Recovery Solution (Corning) to separate hair cells and supporting cells from mesenchyme and neurons. RNA was extracted using RNeasy Micro Kit (Qiagen) from hair cells and supporting cells alone. Every sample is from 2 ears of 1 pup.
cDNA was synthesized from 2.5 ng of RNA using SMARTer V4 Kit (Clontech). Fragmentation was done using M220 Focused-Ultrasonicator (Covaris) and 2 ng of sheared cDNA were taken for library preparation using ThruPLEX DNA-seq kit (Rubicon Genomics)
NextSeq500 Single-End 75bp (SE75) Sequencing (Illumina)

treatment_protocol: For Cre activation in neonatal mice, mothers were given 100 μl tamoxifen (50 μg/μl, Sigma-Aldrich) via intraperitoneal injection 1 or 4 days after delivery. Sox2-CreER; β-cateninflox(Exon3)/+ pups and β-cateninflox(Exon3)/+ littermate controls were exposed to tamoxifen at P1 or P4 through the mother’s milk and sacrificed 72 hours later at P4 or P7, respectively.

value: Primary cochlear organoids

tag: sequencing date

tag: sorted

value: Y


title: LCP_D4_rep2

value: N


title: trf mutant (Cy5) and control swimming larva (Cy3) 1

description: Dye swap of Cl5M3-1. Biological replicate 1 of 2.


title: Control swimming larva (Cy5) vs trf mutant (Cy3) 2

description: Dye swap of M5Cl3-2. Biological replicate 2 of 2.

source_name: Control swimming larvae


title: LCP_sorted_D0_RNA_rep2


title: LCP_D2_rep2


title: Lgr5_P2_rep2

source_name: Cochlear sensory epithelium

value: Cochlear sensory epithelium


title: rad3_K48R_UV_0hr

city: Albuquerque

first: Peng

last: Mao

state: NM

address: 915 Camino de Salud. NE

institute: The University of New Mexico Comprehensive Cancer Center

data_processing:
Library strategy: CPD-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes. The barcode sequences and the last nucleotide of  the read were trimmed, using a custom Python script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS bamtoBed
Damage coordinates and dinucleotide sequences were obtained using the flank and getfasta functions of BEDTOOLS. The reverse complementary sequence of the dinucleotide on the opposite strand was obtained using a custum Python script
Only reads mapping to dipyrimidines such as TT, TC, CT, and CC, corresponding to CPD lesions were retained in BED file using a custom python script
BED files were split to plus and minus strands, sorted, and converted to 1-based WIG files using COUNT function of IGVTools
Genome_build: SacCer3
Supplementary_files_format_and_content: WIG files containing counts of CPD damage reads filtered for dipyrimidine mapping sequences. Note, rep1 and rep2 represent two biological repeats.

organism: Saccharomyces cerevisiae

source_name: rad3_K48R_UV_0hr_yeast cells

growth_protocol: Yeast strains were grown in YPD (yeast extract, peptone, dextrose) to OD600=0.8 in a yeast shaker at 30 0C.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 12 μg of DNA was used for each sequencing library preparation.
CPD-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, genomic DNA was sonicated to ~400 bp. Sonicated DNA fragments were purified, end-repaired, dA-tailed and ligated to a double-stranded adaptor DNA trP1. Free 3'-OHs were blocked by terminal transferase and dideoxy-ATP. CPD lesions were cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor A. Five different barcoded A adaptors (A1: AAGAGGAT, A2: TTCGTGAT, A3: CCTGAGAT, A4: ATCGCGAT, and A5: TACTGGAT) were used to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for 5-6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing using an Ion Torrent sequencer.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. After UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at different repair time points as indicated. Cells were spun down and kept at -80˚C until genomic DNA isolation.

tag: strain background

tag: genotype/variation

value: TFIIH (Rad3) helicase-dead mutant

tag: treatment

value: UV irradiated 100 J/m2

tag: repair time


title: Sox2_P2_rep2


title: LCP_D10_rep2


title: LCP_D10_rep1


title: Control swimming larva (Cy5) vs trf mutant (Cy3) 1

description: Dye swap of M5Cl3-1. Biological replicate 1 of 2.


title: Atoh1_P2_rep2


title: rad3_K48R_UV_2hr

source_name: rad3_K48R_UV_2hr_yeast cells


title: LCP_sorted_D10_rep1


title: rad26rad16_UV_2hr

source_name: rad26rad16_UV_2hr_yeast cells

value: RAD26 RAD16 double deletion

value: UV irradiated 125 J/m2


title: rad26rad16_UV_0hr

source_name: rad26rad16_UV_0hr_yeast cells


title: LCP_D2_rep1


title: Control juvenile (Cy5) vs trf mutant (Cy3) 1

description: Dye swap of M5Cj3-1. Biological replicate 1 of 2.


title: trf mutant (Cy5) and control juvenile (Cy3) 1

description: Dye swap of Cj5M3-1. Biological replicate 1 of 2.


title: LCP_D0_rep1


title: LCP_sorted_D0_RNA_rep1


title: rad26spt4_UV_0hr_repeat

source_name: rad26spt4_UV_0hr_yeast cells

value: RAD26 SPT4 double deletion


title: Sox2_P2_rep1


title: rad26spt4_UV_0hr


title: rad26spt4_UV_2hr

source_name: rad26spt4_UV_2hr_yeast cells


title: control rep3

description: control

tag: genotype

value: mid-third instar larvae


title: Atoh1_P2_rep1


title: LCP_D0_rep2


title: Rad26_K328R_UV_1hr

source_name: Rad26_K328R_UV_1hr_yeast cells

value: Rad26 ATPase-dead mutant


title: Hepatocytes, ParaTSA 24hr Rep4

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were demulitplexed using the bcl2fastq tool, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Reads were then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

source_name: Hepatocytes

extract_protocol:
[Tissue harvesting] Mice were sacrificed by CO2 inhalation, then liver tissue was harvested and stored at -80 degrees celcius before use.
Poly-A mRNA was extracted using a Qiagen RNeasy Mini kit with on-column Dnase1 digestion, according to the manufacturer’s protocol.
mRNA libraries were prepared using the TruSeq Stranded LT kit according to the manufacturer’s protocol (Illumina)

treatment_protocol: [Mouse treatment protocol]  Nine-week-old C57BL/6 mice were given either 0.5 mg/kg Trichostatin A (TSA) or 10% DMSO (vehicle) via intraperitoneal injection, one day prior to paracetamol administration, for 4 days. Paracetamol was delivered at 350mg/kg where appropriate by single IP injection after a 10 hr fast.

tag: strain

tag: time point

tag: drug treatment

value: TSA/Paracetamol

tag: cell type

value: Hepatocytes


title: Rad26_K328R_UV_2hr

source_name: Rad26_K328R_UV_2hr_yeast cells


title: LCP_D4_rep1

tag: tissue


title: Rad26_K328R_UV_0hr

source_name: Rad26_K328R_UV_0hr_yeast cells


title: rad26spt4_UV_2hr_repeat


title: Hepatocytes, ParaTSA 24hr Rep3


title: Lgr5_P2_rep1


title: WT_UV_2hr

source_name: WT_UV_2hr_yeast cells

value: wild type


title: Hepatocytes, ParaTSA 24hr Rep1


title: WM983ASPH

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Expression Console was used for primary analysis, RMA algorithm with default settings.

source_name: melamoma spheoid

label_protocol: Labeling, hybridization and image scan were performed according to the recent laboratory protocol of UD-GenoMed Medical Genomic Technologies Ltd.

growth_protocol: Human melanoma cell lines were maintained in RPMI 1640 medium supplemented with 10% foetal bovine serum, 300 mg/l L-glutamine and antibiotics. Resistant melanoma cell lines were maintained in the same medium containing PLX4720.

extract_protocol: Total RNA was isolated using Qiagen Rneasy Plus Mini kit.

treatment_protocol: Spheroid cultures were established by seeding 1.8x10^4 cells/well into Corning® Costar® Ultra-Low Attachment 6 plate. After 72 hours the medium was complemented with 10% FBS and the spheroids were grown for a week in complete medium. The visible spheroids were transfer then into a cell culture flask and leave them to attach.

tag: cell line source

value: WM983A primary melanoma cell line

value: melamoma spheoid

tag: growth phase

value: VGP

tag: histologic type

value: NM

tag: braf mutation status


title: rad26_UV_2hr_repeat

source_name: rad26_UV_2hr_yeast cells

value: RAD26 deletion


title: RA-FLS_sample4_control_for_FasL

city: Kobe

first: Koji

last: Fukuda

address: 7-5-1 Kusunoki, Chuo

department: Department of Orthopaedic Surgery

institute: Kobe University Graduate School of Medicine

description: Gene expression data from non-stimulated RA-FLS sample4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT PLUS Kit User Manual, 2013, Affymetrix).

growth_protocol: RA-FLS were cultured in DMEM supplemented with 10% fetal bovine serum (FBS; BioWhittaker, Walkersville, MD, USA) and 100 units/ml of penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the QIAshredder and RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacture’s protocol.

treatment_protocol: RA-FLS were incubated with either 1.0 μg/ml recombinant human FasL protein (FasL; R&D Systems, Minneapolis, MN, USA) or phosphate buffered saline (PBS) diluted with serum-free Opti-MEM medium as non-stimulated control for 12 hours at 37°C with 5% CO2.

value: Fibroblast like synoviocytes


title: WT_UV_0hr

source_name: WT_UV_0hr_yeast cells


title: RA-FLS_sample3_FasL-stimulated

description: Gene expression data from FasL-stimulated RA-FLS sample3

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3, FasL-stimulated


title: WM983BSPH

value: WM983B metastatic melanoma cell line


title: WM983ARES-SPH

value: BRAFi resistant WM983A primary melanoma cell line


title: RA-FLS_sample3_control_for_FasL

description: Gene expression data from non-stimulated RA-FLS sample3

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3


title: RA-FLS_sample2_control_for_FasL

description: Gene expression data from non-stimulated RA-FLS sample2

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2


title: RA-FLS_sample2_FasL-stimulated

description: Gene expression data from FasL-stimulated RA-FLS sample2

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2, FasL-stimulated


title: RA-FLS_sample4_FasL-stimulated

description: Gene expression data from FasL-stimulated RA-FLS sample4

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4, FasL-stimulated


title: WM983BRES-SPH

value: BRAFi resistant WM983B metastatic melanoma cell line


title: Hepatocytes, ParaDMSO 24hr Rep3

value: DMSO/Paracetamol


title: RA-FLS_sample1_FasL-stimulated

description: Gene expression data from FasL-stimulated RA-FLS sample1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1, FasL-stimulated


title: Hepatocytes, ParaDMSO 24hr Rep4


title: RA-FLS_sample1_control_for_FasL

description: Gene expression data from non-stimulated RA-FLS sample1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1


title: rad26_UV_2hr

value: UV irradiated 125 J/m2


title: Hepatocytes, ParaDMSO 24hr Rep2


title: Hepatocytes, ParaTSA 24hr Rep2


title: Hepatocytes, ParaDMSO 24hr Rep1


title: no UV

source_name: no UV_yeast cells

value: no


title: rad26_UV_0hr

source_name: rad26_UV_0hr_yeast cells


title: Hepatocytes, ParaTSA 14hr Rep4

source_name: Hepatocytes


title: Hepatocytes, ParaTSA 14hr Rep2


title: rad26_UV_0hr_repeat


title: Hepatocytes, ParaDMSO 14hr Rep3


title: Hepatocytes, ParaDMSO 14hr Rep2