title: PFPC3


title: ATAC-seq_TH2_ODC_KO_3

status: Public on Jul 07 2021

type: SRA

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

country: USA

institute: Johns Hopkins University

description:
processed data file:
TH2_ODC_KO.bw

library_source: genomic

data_processing:
Sequenced samples were trimmed with Trimmomatic and mapped using Bowtie2. Only fragments with less than 150bp were kept.
Open chromatin was detected with MACS2, while differences between treatments was determined using DiffBind with at lest 2 fold change in accessibility and a false discovery rate lower than 0.05.
For visualization only, replicate mapped files were merged with SAM tools and coverage files were generated with deepTools and visualized alongside coverage files on IGV.
Bed files were analyzed with Bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files showing normalized filtered mapped reads.

molecule: genomic DNA

organism: Mus musculus

source_name: Spleen and Lymph node

growth_protocol: CD4+ T cells from the spleen and lymph nodes were isolated by negative selection using a Stem Cell kit according to the manufacturers instructions (Stem Cell, Cat: 19852). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 55 μM β- mercaptoethanol. All activations were done with 5 ug/mL anti-CD3 and 2 ug/mL anti- CD28 and 100 U/mL IL-2. TH polarizations were performed as follows: TH1 – 4 μg/mL anti-IL-4, 10 ng/mL IL-12, 10 ng/mL IL-2. TH2 – 4 μg/mL anti-IFN- , 10 ng/mL IL-4, 10 ng/mL IL-2. TH17 – 10 μg/mL anti-IFN- , 10 μg/mL anti-IL-4, 5 ng/mL IL-6, 5 ng/mL TGF- , 10 μg/mL IL-1 . Treg – 4 μg/ mL anti-IFN- , 4 μg/mL anti-IL-4, 10 ng/mL TGF-B, 10 ng/mL IL-2. Cells were analyzed on day 4 of polarization.

extract_protocol:
5x10^4 T cells treated as described were washed in PBS and then lysed in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630 (all Sigma). Nuclei were then spun down and then resuspend in 25 l TD (2x reaction buffer), 2.5 L TDE1 (Nextera Tn5 Transposase) and 22.5 L nuclease-free water, incubated for 30 min at 37°C. DNA was purified with the Qiagen MinElute PCR Purification Kit (Thermo Fisher Scientific).
Libraries were prepared using the Nextera DNA library Prep Kit (Illumina) adapting a published protocol (Buenrostro et al., 2015). PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol.

treatment_protocol: CD4 T cells were isolated from the spleen and lymphnode of mice expressing Cre recombinase (CD4Cre) under the control of the CD4 promoter crossed with Dohh flox/flox and Odc flox/flox mice.

tag: tissue

value: Spleen and Lymph node

tag: cell type

value: CD4 T cell

tag: genotype

tag: strain

tag: polarization


title: ATAC-seq_Treg_ODC_KO_3

description:
processed data file:
Treg_ODC_KO.bw

value: Treg


title: RR0370807.042120.TR#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Tregs were magnetically isolated from thawed PBMCs as CD4+CD25hiCD127lo

library_source: transcriptomic

data_processing:
Reads were mapped to the human reference genome (GRCh38) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (v27)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Homo sapiens

source_name: CD4 TReg Cell

extract_protocol:
Human Tregs and Tconvs from COVID-19 patients and healthy donors were magnetically isolated from frozen PBMCs using a Stem Cell kit, as CD4+CD25hiCD127lo and CD4+CD25–, respectively. Around 1,000 isolated cells were directly into lysis buffer for RNA-seq (Smart-seq2)  library preparation following the standard ImmGen low-input protocol (www.immgen.org). Samples were collected and sequenced in two cohorts.
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

tag: disease

value: Blood

tag: processing batch

tag: severity

value: Recovered

tag: donor

value: CD4 TReg Cell


title: ATAC-seq_TH1_ODC_KO_3

description:
processed data file:
TH1_ODC_KO.bw


title: PF3

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

country: South Korea

institute: Inha university hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: HUMAN PD tunica albuginea (TA)

growth_protocol: DMEM contained with 10% fetal bovine serum (FBS), penicillin (100 U/mL), and streptomycin (100 μg/mL)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: NF and PF no treatment, PFPC treatment at 1ug/ml for 24 hours.

value: PD tunica albuginea (TA) fibroblasts

tag: agent


title: ATAC-seq_TH17_ODC_KO_3

description:
processed data file:
TH17_ODC_KO.bw


title: PF2


title: ATAC-seq_Treg_DOHH_WT_3

description:
processed data file:
Treg_DOHH_WT.bw


title: ATAC-seq_Treg_DOHH_KO_3

description:
processed data file:
Treg_DOHH_KO.bw


title: RR0931294.060520.TR#1


title: RR0243818.071420.TR#1


title: ATAC-seq_TH2_DOHH_KO_3

description:
processed data file:
TH2_DOHH_KO.bw


title: ATAC-seq_Treg_ODC_WT_3

description:
processed data file:
Treg_ODC_WT.bw


title: ATAC-seq_TH1_DOHH_WT_3

description:
processed data file:
TH1_DOHH_WT.bw


title: ATAC-seq_TH1_DOHH_KO_3

description:
processed data file:
TH1_DOHH_KO.bw


title: ATAC-seq_TH17_DOHH_WT_3

description:
processed data file:
TH17_DOHH_WT.bw


title: PF1


title: NF4

source_name: HUMAN tunica albuginea (TA)

value: tunica albuginea (TA) fibroblasts


title: ATAC-seq_TH17_DOHH_KO_3

description:
processed data file:
TH17_DOHH_KO.bw


title: ATAC-seq_Naive_DOHH_WT_3

description:
processed data file:
Naive_DOHH_WT.bw

value: Naive


title: NF2


title: ATAC-seq_Naive_DOHH_KO_3

description:
processed data file:
Naive_DOHH_KO.bw


title: NF3


title: RR0857858.042720.TR#1


title: ATAC-seq_Treg_ODC_KO_2

description:
processed data file:
Treg_ODC_KO.bw


title: ATAC-seq_TH2_DOHH_WT_3

description:
processed data file:
TH2_DOHH_WT.bw


title: RR0830593.041320.TR#1


title: ATAC-seq_TH2_ODC_WT_2

description:
processed data file:
TH2_ODC_WT.bw


title: RR0823855.041320.TR#1


title: RR0941176.041720.TR#1


title: ATAC-seq_Treg_ODC_WT_2

description:
processed data file:
Treg_ODC_WT.bw


title: ATAC-seq_TH2_ODC_KO_2

description:
processed data file:
TH2_ODC_KO.bw


title: ATAC-seq_TH1_ODC_WT_2

description:
processed data file:
TH1_ODC_WT.bw


title: NF1


title: AR-V7 ChIP-exo

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
ChIP-exo sequence reads were aligned to the hg19 genome assembly using bowtie2 using default parameters. All reads mapping with two or fewer mismatches were retained and only uniquely mapped reads were kept for further analysis.
Peaks were called using Model-based Analysis of ChIP-Seq (MACS2) algorithm (http://liulab.dfci.harvard.edu/MACS/) with a fold change > 5.
Genome_build: hg19
Supplementary_files_format_and_content: Average aligned reads for consecutive windows of 10bp were then quantified using bamCoverage feature in Deeptools. bigWig files are generated and visualized in IGV genome viewer using reference for the hg19 genome build (V24).

growth_protocol: LNCaP AR-V7 and VCaP AR-V7 cells grown in their corresponding medium were supplemented with 10% FBS and maintained under constant G418 antibiotic selection. Cells were ligand starved in 10% CSS medium for 24 hours before treatment.

extract_protocol:
Biological replicates of LNCaP AR-V7 cells treated with 10uM R1881 or 20ng/mL for 24 hours were formaldehyde fixed and and pooled together.  Nuclear extracts were prepared in a water bath sonicator and DNA-protein complexes were isolated with AR antibody and Protein A/G Magnetic Agarose. ChIP-exo libraries were prepared using ChIP-exo Kit from ActiveMotif following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq 2500 following the manufacturer's protocols.
Libraries were constructed using ChIP-exo library preparation kit (ActiveMotif, USA) following the manufacturer’s instructions. cDNA libraries were sequenced on the Illumina HiSeq 2500 platform by ActiveMotif, USA.

treatment_protocol: Cells were treated with 10nM R1881 for hormone response and 20ng/mL Doxycycline for AR-V7 response.

tag: cell line background

value: LNCaP

value: Immortalised prostate cancer cell line

tag: passages

tag: genotype/variation

value: expressing AR-V7 in response to doxycycline (LNCaP AR-V7)

tag: treatment

value: 20ng/mL Doxycycline for 24hrs

tag: chip antibody

value: AR antibody (RRID:AB_2793341)


title: ATAC-seq_TH1_ODC_KO_2

description:
processed data file:
TH1_ODC_KO.bw


title: AR ChIP-exo

value: 10uM R1881 for 24 hrs


title: ATAC-seq_TH17_ODC_WT_2

description:
processed data file:
TH17_ODC_WT.bw


title: RR0579992.041720.TR#1


title: ATAC-seq_TH17_ODC_KO_2

description:
processed data file:
TH17_ODC_KO.bw


title: RR0685229.041620.TR#1


title: ATAC-seq_Treg_DOHH_WT_2

description:
processed data file:
Treg_DOHH_WT.bw


title: RR0234740.072320.TR#1


title: RR0417079.041520.TR#1


title: Heart CTL rep 2

city: New York

first: Andrea

last: Ventura

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were aligned to the standard mouse genome (mm10) using the STAR aligner (v2.5.3a).
Mapped reads were counted at each gene locus and differential gene expression was calculated using DESeq2 V1.20.0
Log2Fold Change and adjusted pvalues were calculated by comparing T6B vs control tissues.
Genome_build: mm10
Supplementary_files_format_and_content: single csv file containing log2Foldand statistics for all expressed genes.

source_name: Heart

growth_protocol: Mice were bred and housed in the pathogen-free animal facility at Memorial Sloan-Kettering Cancer Center and were used in accordance with institutional guidelines. Mouse experiments were approved by the Institutional Animal Care and Use Committee of Memorial Sloan-Kettering Cancer Center.

extract_protocol:
Total RNA was extracted from homogenyzed tissues using the TRIzol reagent (Invitrogen) according to  manufacturer's instructions
After Ribogreen quantification and quality control, 500 ng of total RNA with RIN values of 7.0-10 underwent polyA selection and TruSeq library preparation according to instructions  provided by Illumina (TruSeq Stranded mRNA LT Kit). An Average of 34 million paired reads was generated per samples. Libraries generated from the colon were run on an Illumina HiSeq  2500 machine and generated using the HiSeq SBS Kit v4 generating single reads 50 bp long.

treatment_protocol: Mice were fed chow containing doxycycline (625mg/Kg)

value: CAG-rtTA

value: doxycycline


title: Heart CTL rep 3


title: RR0997256.051220.TR#1


title: ATAC-seq_TH2_DOHH_KO_2

description:
processed data file:
TH2_DOHH_KO.bw

value: Spleen and Lymph node


title: Heart CTL rep 1


title: ATAC-seq_TH1_DOHH_WT_2

description:
processed data file:
TH1_DOHH_WT.bw

value: CD4 T cell


title: Heart T6B rep 3

value: CAG-rtTA; T6B


title: ATAC-seq_TH17_DOHH_KO_2

description:
processed data file:
TH17_DOHH_KO.bw


title: RR0907841.051820.TR#1

value: Blood


title: ATAC-seq_TH17_DOHH_WT_2

description:
processed data file:
TH17_DOHH_WT.bw


title: ATAC-seq_Naive_DOHH_WT_2

description:
processed data file:
Naive_DOHH_WT.bw


title: RR0469109.051920.TR#1

value: Recovered


title: Heart T6B rep 1


title: Heart T6B rep 2


title: ATAC-seq_TH2_ODC_WT_1

description:
processed data file:
TH2_ODC_WT.bw


title: RR0424088.041520.TR#1

value: mild outpatients

value: CD4 TReg Cell


title: ATAC-seq_TH2_ODC_KO_1

description:
processed data file:
TH2_ODC_KO.bw


title: Skeletal Muscle CTL rep 3

source_name: Quadriceps


title: ATAC-seq_TH1_DOHH_KO_2

description:
processed data file:
TH1_DOHH_KO.bw


title: ATAC-seq_Naive_DOHH_KO_2

description:
processed data file:
Naive_DOHH_KO.bw


title: ATAC-seq_Treg_ODC_KO_1

description:
processed data file:
Treg_ODC_KO.bw

value: Treg


title: Skeletal Muscle CTL rep 2


title: RR0602232.050120.TR#1


title: ATAC-seq_Treg_DOHH_KO_2

description:
processed data file:
Treg_DOHH_KO.bw


title: ATAC-seq_TH1_ODC_WT_1

description:
processed data file:
TH1_ODC_WT.bw


title: ATAC-seq_TH1_ODC_KO_1

description:
processed data file:
TH1_ODC_KO.bw


title: ATAC-seq_TH2_DOHH_WT_2

description:
processed data file:
TH2_DOHH_WT.bw


title: Skeletal Muscle CTL rep 1


title: ATAC-seq_TH17_ODC_WT_1

description:
processed data file:
TH17_ODC_WT.bw


title: Skeletal Muscle T6B rep 3


title: ATAC-seq_Treg_DOHH_WT_1

description:
processed data file:
Treg_DOHH_WT.bw


title: RR0467460.050520.TR#1


title: RR0157115.051220.TR#1


title: ATAC-seq_TH17_ODC_KO_1

description:
processed data file:
TH17_ODC_KO.bw


title: ATAC-seq_Treg_ODC_WT_1

description:
processed data file:
Treg_ODC_WT.bw


title: BDXNY-Xen-mitotic-controlIGG-H3H4-R2-T1

city: Worcester

first: Bastiaan

last: Dekker

state: Massachusetts

address: 368 Plantation street

department: Systems Biology

institute: University of Massachusetts Medical School

description: Egg extract added to demembranated sperm nuclei to make reconstituted mitotic chromosomes.

data_processing:
Hi-C FASTQ sequencing files were mapped to the Xenopus Leavis 9.2 Genome
publicly available distiller-nf mapping pipeline (https://github.com/mirnylab/distiller-nf) and downstream
analysis tools pairtools (https://github.com/mirnylab/pairtools) and cooltools
(https://github.com/mirnylab/cooltools).
Genome_build: Xenopus Laevis 9.2
Supplementary_files_format_and_content: multicooler files (.mcool) for all interactions

organism: Xenopus laevis

source_name: Individual Xenopus

growth_protocol: Egg extract was isolated from Xenopus Eggs

extract_protocol:
half million sperm was used as input for reconstituting chromosomes
Hi-C was performed as described in detail in supplemental methods.

treatment_protocol: Extract was either depleted with specific antibody or with control IGG

tag: protocol

value: Hi-C

tag: enzyme

value: DpnII

tag: cell line

value: Xenopus sperm

tag: antibody

value: IGG

value: Depletion of protein in Egg extract with described antibody


title: ATAC-seq_Treg_DOHH_KO_1

description:
processed data file:
Treg_DOHH_KO.bw

tag: tissue

tag: cell type

tag: genotype


title: RR0236312.051220.TR#1

tag: disease


title: BDXNY-Xen-mitotic-Dilution-H1-dep-R2-T1


title: ATAC-seq_TH2_DOHH_WT_1

description:
processed data file:
TH2_DOHH_WT.bw

tag: strain

tag: polarization


title: Skeletal Muscle T6B rep 1


title: RR0951931.042820.TR#1

tag: processing batch

tag: severity

value: hospitalized moderate to severe

tag: donor


title: ATAC-seq_TH2_DOHH_KO_1

description:
processed data file:
TH2_DOHH_KO.bw


title: Skeletal Muscle T6B rep 2


title: RR0248668.050520.TR#1


title: Liver CTL rep 2

source_name: Liver


title: RR0511931.040820.TR#1


title: BDXNY-Xen-mitotic-H3H4-dep-R2-T1

value: H3 and H4


title: Liver CTL rep 1


title: BDXNY-Xen-mitotic-dilution-IGG-R2-T1


title: ATAC-seq_TH1_DOHH_KO_1

description:
processed data file:
TH1_DOHH_KO.bw


title: BDXNY-Xen-mitotic-wildtype-mockIgg-S1

data_processing:
Hi-C FASTQ sequencing files were mapped to the Xenopus Leavis 9.2 Genome
publicly available distiller-nf mapping pipeline (https://github.com/mirnylab/distiller-nf) and downstream
analysis tools pairtools (https://github.com/mirnylab/pairtools) and cooltools
(https://github.com/mirnylab/cooltools).
Genome_build: Xenopus laevis 9.2
Supplementary_files_format_and_content: multicooler files (.mcool) for all interactions

extract_protocol:
half million sperm was used as input for reconstituting chromosomes
Hi-C was performed as described in detail in supplemental methods, DpnII enzyme.

value: Egg extract added to demembranated sperm nuclei to make reconstituted mitotic chromosomes.


title: RR0783978.051820.TR#1


title: RR0318907.051220.TR#1


title: ATAC-seq_TH17_DOHH_WT_1

description:
processed data file:
TH17_DOHH_WT.bw


title: Liver T6B rep 3

value: R26-rtTA; T6B

value: doxycycline


title: RR0183111.051520.TR#1


title: BDXNY-Xen-mitotic-H1-dep-S2


title: Liver T6B rep 2


title: RR0915093.033120.TR#1


title: BDXNY-Xen-mitotic-CondI-dep-S3

value: CAPG


title: Liver CTL rep 3


title: Liver T6B rep 1


title: ATAC-seq_Naive_DOHH_WT_1

description:
processed data file:
Naive_DOHH_WT.bw

value: Spleen and Lymph node

value: CD4 T cell

value: Naive


title: BDXNY-Xen-mitotic-CondII-dep-S4


title: RNA-seq_Treg_ODC_KO_4

description:
processed data file:
ODC_counts.tsv

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a matrix with raw counts for features in samples, obtained with featureCounts.

extract_protocol:
RNA was extracted using RNeasy Kit (QIAGEN) following the manufacturer’s instructions with an additional on-column DNase treatment using the RNAse-Free DNase set (Qiagen). RNA was quantified using Qubit 2.0 (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina)


title: MSCs - 6-OHDA treated 5

city: Lisboa

first: Ana

middle: Filipa Ribeiro

last: Cardoso

state: Lisboa

address: Avenida  Brasília, Fundação champalimaud, Immunophysiology lab

country: Portugal

institute: Fundação Champalimaud

description: 6-OHDA treated 5

data_processing:
Global quality of FASTQ files with raw RNA-sequencing reads was analysed using FastQC (version 0.11.9)52.
Trimmomatic-0.39 was used to remove the first 10 base pairs (HEADCROP=10)53.
Aligning and read processing were performed using STAR 2.7.3a (https://github.com/alexdobin/STAR/releases)54, sequences were aligned to the reference file of Mus musculus genome assembly GRCm38.p6 and the corresponding genome annotation file (http://www.ensembl.org/Mus_musculus/Info/Index).
Volcano plot of differentially expressed genes was obtained using EdgeR (version 3.30.3) (https://bioconductor.org/packages/release/bioc/html/edgeR.html)55.
DeSeq2 (version 1.28.1) (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) was used to obtain the statistics of all genes56. Genes with lower than 10 average reads, false discovery rate (FDR) above 0.05, and a log2 (difference between groups) above -2 and below 2, were excluded from further analysis.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: Tab-delimited text files including read counts values for each sample, and statistics.

source_name: Gonadal adipose tissue

extract_protocol:
For the isolation of adipose tissue cells, tissue was collected into PBS, cut into small pieces and incubated with Liberase TM (2.5µg/ml, Roche) and DNase I (20U/ml; Roche) for 1h at 37°C under gentle agitation. A single cell suspension was obtained by passage through a 100μm cell strainer (Thermo Fisher Scientific) and centrifugation was used to separate the stromal vascular fraction from the adipocyte fraction. Erythrocytes were lysed with red blood cell lysis buffer (eBioscience) and removed by centrifugation. Cell suspensions were stained and populations were gated on live cells and defined as MSCs: CD45- Sca-1+ CD31- Pdgfra+. Cells were sorted using FACSFusion (BD Biosciences). Total RNA from sorted cells was extracted using RNeasy micro kit or RNeasy mini kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gonadal adipose tissue

value: MSCs


title: RR0415843.060920.TR#1

value: Blood

value: CD4 TReg Cell


title: RNA-seq_Treg_ODC_WT_4

description:
processed data file:
ODC_counts.tsv

value: Treg


title: MSCs - 6-OHDA treated 4

description: 6-OHDA treated 4


title: ATAC-seq_TH1_DOHH_WT_1

description:
processed data file:
TH1_DOHH_WT.bw


title: ATAC-seq_Naive_DOHH_KO_1

description:
processed data file:
Naive_DOHH_KO.bw


title: RR0650386.033120.TR#1


title: BDXNY-Xen-mitotic-H1-CondI-dep-S5

value: Hi-C

value: DpnII

value: Xenopus sperm

value: H1 and CAPG


title: RR0270554.040720.TR#1

value: hospitalized moderate to severe


title: RNA-seq_TH2_ODC_KO_4

description:
processed data file:
ODC_counts.tsv


title: BDXNY-Xen-mitotic-CondI-CondII-dep-S7

value: CAPG, and CAPD3

value: Depletion of protein in Egg extract with described antibody

value: Egg extract added to demembranated sperm nuclei to make reconstituted mitotic chromosomes.


title: MSCs - 6-OHDA treated 3

description: 6-OHDA treated 3


title: BDXNY-Xen-mitotic-H1-CondI-CondII-dep-S8

value: H1, CAPG, and CAPD3


title: RR0919381.050520.TR#1


title: MSCs - 6-OHDA treated 2

description: 6-OHDA treated 2


title: ATAC-seq_TH17_DOHH_KO_1

description:
processed data file:
TH17_DOHH_KO.bw

value: Spleen and Lymph node


title: RNA-seq_TH2_ODC_WT_4

description:
processed data file:
ODC_counts.tsv

value: CD4 T cell


title: BDXNY-Xen-mitotic-dilution-IGG-R1-T1

value: IGG

value: Depletion of protein in Egg extract with described antibody, before fixation samples were diluted


title: MSCs - 6-OHDA treated 1

description: 6-OHDA treated 1

value: Gonadal adipose tissue

value: MSCs


title: RR0866687.050720.TR#1

value: Blood

value: CD4 TReg Cell


title: RNA-seq_TH1_ODC_KO_4

description:
processed data file:
ODC_counts.tsv


title: RR0921314.060320.TR#1


title: MSCs - Vehicle treated 4

description: Vehicle treated 4

value: Vehicle


title: RR0277045.050520.TR#1


title: BDXNY-Xen-mitotic-CondI-CondII-dep-R2-T1

value: Hi-C

value: DpnII


title: BDXNY-Xen-mitotic-H1-CondII-dep-S6

value: Xenopus sperm

value: H1 and CAPD3


title: RNA-seq_TH1_ODC_WT_4

description:
processed data file:
ODC_counts.tsv


title: MSCs - Vehicle treated 3

description: Vehicle treated 3


title: RR0615993.052220.TR#1

value: mild outpatients


title: HH0000003.082520.TR#1

value: HD

value: Healthy


title: RNA-seq_TH17_ODC_KO_4

description:
processed data file:
ODC_counts.tsv


title: BDXNY-Xen-mitotic-CondI-dep-R2-T1

value: CAPG

value: Depletion of protein in Egg extract with described antibody

value: Egg extract added to demembranated sperm nuclei to make reconstituted mitotic chromosomes.


title: HH0000002.072820.TR#1


title: BDXNY-Xen-mitotic-Dilution-H1-dep-R1-T1


title: BDXNY-Xen-mitotic-CondII-dep-R2-T1


title: RNA-seq_TH17_ODC_WT_4

description:
processed data file:
ODC_counts.tsv

value: Spleen and Lymph node

value: CD4 T cell


title: RNA-seq_Treg_ODC_KO_3

description:
processed data file:
ODC_counts.tsv

value: Treg


title: RNA-seq_Treg_ODC_WT_3

description:
processed data file:
ODC_counts.tsv


title: AC3032552.092619.TR#1


title: Try03_P10

city: Vienna

first: Sylvia

last: Knapp

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

description: Lavage Pool 2, Passage 10

data_processing:
Demultiplexing of the raw data, mapping to the mouse genome GRCm38 (mm10) and removing of PCR duplicates with identical mapping and UMI sequences was done by the Bluebee® software (version Quantseq 2.3.6 FWD UMI)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ex vivo cultured alveolar macrophages

extract_protocol:
Total RNA from indicated cell types was isolated using RNeasy Micro kit (Qiagen).
QuantSeq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina together with the PCR Add-on Kit for Illumina and the UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 015.96, 020.96, 081.96), according to the manufacturer’s instructions. Libraries for all cell types were prepared from 150 ng total RNA input and 15 cycles of library amplification were performed. Sample integrity was assessed using a Bioanalyzer 2100 (Agilent Technologies). Pooled libraries were 65 bp single-end sequenced on the HiSeq4000 (Illumina).

tag: "strain"

tag: "genptype"

value: wild type

tag: "tissue"

value: Ex vivo cultured alveolar macrophages


title: AC3034431.110619.TR#1

value: Blood

value: CD4 TReg Cell


title: RR0611936.010220.TR#1


title: Try03_P5

description: Lavage Pool 2, Passage 5


title: MSCs - Vehicle treated 1

description: Vehicle treated 1

value: Gonadal adipose tissue

value: MSCs

tag: treatment

value: Vehicle


title: BDXNY-Xen-mitotic-H1-CondI-dep-R2-T1

tag: protocol

value: Hi-C

value: DpnII

value: Xenopus sperm

value: H1 and CAPG


title: Try02_P13

description: Lavage Pool 1, Passage 13


title: BDXNY-Xen-mitotic-H1-CondII-dep-R2-T1

tag: enzyme

value: H1 and CAPD3


title: RR0947025.020520.TR#1

value: HD

value: Healthy


title: RNA-seq_TH2_ODC_WT_3

description:
processed data file:
ODC_counts.tsv

value: Spleen and Lymph node


title: RR0438670.020620.TR#1


title: BDXNY-Xen-mitotic-H1-dep-R2-T1

tag: cell line

value: Depletion of protein in Egg extract with described antibody

value: Egg extract added to demembranated sperm nuclei to make reconstituted mitotic chromosomes.


title: Try02_P8

description: Lavage Pool 1, Passage 8

value: wild type


title: RNA-seq_TH1_ODC_KO_3

description:
processed data file:
ODC_counts.tsv

value: CD4 T cell


title: PLF_M4

description: Mouse 4

source_name: Peritoneal lavage cells

value: Peritoneal lavage cells


title: MSCs - Vehicle treated 2

description: Vehicle treated 2


title: BDXNY-Xen-mitotic-controlIGG-H3H4-R1-T1

tag: antibody

value: IGG


title: RNA-seq_TH1_ODC_WT_3

description:
processed data file:
ODC_counts.tsv

tag: tissue


title: BDXNY-Xen-mitotic-H3H4-dep-R1-T1

value: H3 and H4


title: D35PrTzF_Via (3)

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

institute: UT Southwestern Medical Center

description: re-analysis of GSM4337428

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 4.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 4.0.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Viable human prostate transition zone

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)
scRNA-seq

treatment_protocol: Populations of single-cells dissociated from health prostates from organ donors were isolated by FACS

tag: patient phenotype

value: Donor (Normal)

tag: prostatic zone

value: Transition Zone + Urethra

tag: digestion enzyme

value: 5mg/mL Collagenase I 4hr

tag: facs ab profile

value: Via-

tag: 10x library type


title: D35PrPzF_Via (3)

description: re-analysis of GSM4337427

source_name: Viable human prostate peripheral zone

value: Peripheral Zone


title: PLF_M2

description: Mouse 2


title: RNA-seq_TH17_ODC_KO_3

description:
processed data file:
ODC_counts.tsv

tag: cell type

tag: genotype

tag: strain

tag: polarization


title: BDXNY-Xen-mitotic-H1-CondI-CondII-dep-R2-T1

value: Hi-C

value: DpnII

value: Xenopus sperm

value: H1, CAPG, and CAPD3


title: BDXNY-Xen-mitotic-control-IGG-R2-T1


title: D27PrTzF_Via (3)

description: re-analysis of GSM4337426


title: mexAM_M4

description: Mouse 4

tag: "strain"

tag: "genptype"

value: Ex vivo cultured alveolar macrophages


title: RNA-seq_TH2_ODC_KO_3

description:
processed data file:
ODC_counts.tsv

value: Spleen and Lymph node


title: D27PrPzF_Via (3)

description: re-analysis of GSM4337425


title: RNA-seq_Treg_DOHH_KO_3

description:
processed data file:
DOHH_counts.tsv

value: Treg


title: BDXNY-Xen-mitotic-Separose-H3H4-R1-T1

value: Separose

tag: treatment

value: Depletion of protein in Egg extract with described antibody

value: Egg extract added to demembranated sperm nuclei to make reconstituted mitotic chromosomes.


title: RNA-seq_Treg_DOHH_WT_3

description:
processed data file:
DOHH_counts.tsv

value: CD4 T cell


title: D17PrTzF_Via (3)

description: re-analysis of GSM4337424


title: mexAM_M1

description: Mouse 1

value: wild type

tag: "tissue"


title: RNA-seq_TH2_DOHH_KO_3

description:
processed data file:
DOHH_counts.tsv


title: D17PrPzF_Via (3)

description: re-analysis of GSM4337423

value: Donor (Normal)


title: BMDM_M4

description: Mouse 4

source_name: Bone marrow derived macrophages

value: Bone marrow derived macrophages


title: RNA-seq_TH2_DOHH_WT_3

description:
processed data file:
DOHH_counts.tsv


title: BPH389PrSF

source_name: Human prostate transition zone

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 and v3 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)

treatment_protocol: Populations of single-cells dissociated from diseased prostates from BPH patients were isolated by FACS

value: BPH Stromal Nodule

value: Transition Zone

value: 5mg/mL Collagenase I 4hr


title: PLF_M1

description: Mouse 1

value: Peritoneal lavage cells


title: BPH389PrGF

value: BPH Glandular Nodule


title: BMDM_M2

description: Mouse 2


title: BMDM_M1

description: Mouse 1


title: RNA-seq_TH1_DOHH_WT_3

description:
processed data file:
DOHH_counts.tsv


title: BPH340PrSF_Via

value: Via-


title: RNA-seq_TH17_ODC_WT_3

description:
processed data file:
ODC_counts.tsv


title: BALF_M4

description: Mouse 4

source_name: Bronchoalveolar lavage cells

value: Bronchoalveolar lavage cells


title: mexAM_M2

description: Mouse 2

value: Ex vivo cultured alveolar macrophages


title: BPH340PrGF_Via [re-analysis]

description: re-analysis of GSM4337070


title: BPH327PrSF_Via


title: BALF_M2

description: Mouse 2


title: RNA-seq_TH17_DOHH_KO_3

description:
processed data file:
DOHH_counts.tsv

value: Spleen and Lymph node


title: RNA-seq_TH17_DOHH_WT_3

description:
processed data file:
DOHH_counts.tsv


title: BALF_M1

description: Mouse 1


title: BPH327PrGF_Via [re-analysis]

description: re-analysis of GSM4337069


title: RNA-seq_Treg_ODC_KO_2

description:
processed data file:
ODC_counts.tsv

value: Treg


title: RNA-seq_TH1_DOHH_KO_3

description:
processed data file:
DOHH_counts.tsv


title: RNA-seq_Treg_ODC_WT_2

description:
processed data file:
ODC_counts.tsv


title: BPH283PrSF_Via


title: BPH283PrGF_Via


title: KI_4

city: ILLKIRCH

first: Jocelyn

last: Laporte

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description: Tibilias anterior KI_4 (raw)

data_processing:
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped to spike sequences using bowtie version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1
Genome_build: mm10

molecule: polyA RNA

source_name: Tibilias anterior

extract_protocol: RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Tibilias anterior


title: KI_2

description: Tibilias anterior KI_2 (raw)


title: KI_3

description: Tibilias anterior KI_3 (raw)


title: KI_1

description: Tibilias anterior KI_1 (raw)


title: Sleep distubance(male7)

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using BaseSpace Small RNA v1.0.
Expression count were calculated using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: serum

extract_protocol:
Total RNA was isolated from 1.5 ml of serum, using the Mirvana Paris kit (Ambion), then miRNAs were isolated using a Bioanalyzer (Agilent Technologies).
cDNA library based on 10 ng of small RNAs was prepared using the NEBNext® Multiplex Small RNA Library Prep Set.

tag: group

value: SD

tag: Sex

value: Male


title: OXNAC33_Shiraz_rep1

type: RNA

city: Verona

first: Sara

last: Zenoni

address: Strada Le Grazie 15

country: Italy

institute: Università degli Studi di Verona

description:
OXNAC33_1
Vitis vinifera cv. Shiraz
Shiraz OX

hyb_protocol: For microarray analysis on Shiraz leaves stably overexpressing VviNAC33, the hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

scan_protocol: Scanning and Feature Extraction were performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual.

data_processing: A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe. The data were normalized on the 75th percentile and a correlation analysis was then performed to assess the consistency of the biological triplicates.

organism: Vitis vinifera

source_name: OXNAC33 leaves of Vitis vinifera cv. Shiraz

label_protocol: For microarray analysis on Shiraz leaves stably overexpressing VviNAC33, the cDNA synthesis and labeling reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

growth_protocol: Grapevine plants (Vitis vinifera cv. Shiraz, BVRC12 clone) were grown at the University of Verona greenhouse, starting from calli developed from anthers collected during the 2009 seasons in Coombe Vineyard (University of Adelaide, Urrbrae, South Australia). For the microarray analysis performed on grapevine, three biological replicates of young leaves were collected from control and transgenic plants at the onset of the phenotypic manifestation.

extract_protocol: Total RNA was isolated from ~100 mg of the ground grapevine leaves tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich).

tag: cultivar

value: Shiraz

tag: genotype/variation

value: VviNAC33 overexpression

value: Young leaves


title: CTRL_Shiraz_rep3 [OXNAC33]

description:
CTRL_3
Vitis vinifera cv. Shiraz
Shiraz control

source_name: Control leaves of Vitis vinifera cv. Shiraz

value: Control

tag: tissue


title: OXNAC33_Shiraz_rep3

description:
OXNAC33_3
Vitis vinifera cv. Shiraz
Shiraz OX


title: OXNAC33_Shiraz_rep2

description:
OXNAC33_2
Vitis vinifera cv. Shiraz
Shiraz OX


title: Sleep distubance(male6)


title: OXNAC33_Sultana_rep3

hyb_protocol: For microarray analysis on Sultana leaves transiently overexpressing VviNAC33, the hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

data_processing: A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe. The data were normalized on the 75th percentile and a correlation analysis was then performed to assess the consistency of the biological quadruplicates.

source_name: OXNAC33 leaves of Vitis vinifera cv. Sultana

label_protocol: For microarray analysis on Sultana leaves transiently overexpressing VviNAC33, the cDNA synthesis and labeling reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

growth_protocol: For the transient overexpression of VviNAC33 in grapevine, plantlets of Vitis vinifera cv. Sultana were in vitro micropropagated and cultivated in growth chamber at 25°C with a 16-h photoperiod.

treatment_protocol: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VviNAC33 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty pK7WG2 containing a non-coding sequence. Eight in vitro six-week-old plants of grapevine cv. Sultana for overexpression and seven for the control were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa).

value: cv Sultana


title: CTRL_Shiraz_rep1 [OXNAC33]

description:
CTRL_1
Vitis vinifera cv. Shiraz
Shiraz control


title: RNA-seq_TH2_ODC_WT_2

description:
processed data file:
ODC_counts.tsv

source_name: Spleen and Lymph node

value: CD4 T cell


title: OXNAC33_Sultana_rep4


title: OXNAC33_Sultana_rep2


title: RNA-seq_TH1_ODC_KO_2

description:
processed data file:
ODC_counts.tsv


title: Sleep distubance(male5)


title: WT_4

description: Tibilias anterior WT_4 (raw)

value: WT


title: CTRL_Shiraz_rep2 [OXNAC33]

description:
CTRL_2
Vitis vinifera cv. Shiraz
Shiraz control


title: RNA-seq_TH1_ODC_WT_2

description:
processed data file:
ODC_counts.tsv


title: WT_3

description: Tibilias anterior WT_3 (raw)


title: CTRL_Sultana_rep4 [OXNAC33]

source_name: Control leaves of Vitis vinifera cv. Sultana

value: empty pK7WG2 containing a non-coding sequence


title: RNA-seq_TH2_ODC_KO_2

description:
processed data file:
ODC_counts.tsv


title: Sleep distubance(male3)


title: RNA-seq_TH17_ODC_KO_2

description:
processed data file:
ODC_counts.tsv


title: CTRL_Sultana_rep2 [OXNAC33]


title: WT_2

description: Tibilias anterior WT_2 (raw)


title: RNA-seq_TH17_ODC_WT_2

description:
processed data file:
ODC_counts.tsv


title: Sleep distubance(male2)


title: OXNAC33_Sultana_rep1


title: WT_1

description: Tibilias anterior WT_1 (raw)


title: Sleep control(male5)

value: SC


title: CTRL_Sultana_rep1 [OXNAC33]


title: WT treated 3

city: New Delhi

first: Soumen

last: Basak

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

data_processing:
Paired-end reads in FASTQ files were mapped to mouse genome build GRCm38/mm10 using STAR alignment software v2.5.2b.
Counts of mapped reads were summarized to gene level using featureCounts v1.5.0-P1 software and with GENCODE M7 gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: txt, Read count

source_name: IECs

extract_protocol:
Colons were surgically removed from the indicated mice subsequent to euthanization, longitudinally cut open, washed with PBS, and then cut into 2-5 mm small pieces. These pieces were rocked on a shaker platform submerging in HBSS containing 30mM EDTA that led to the detachment of IECs. IECs were collected by centrifugation and subjected to biochemical analyses. The purity of isolated IECs, determined as CD45.2-EpCAM+ cells, was found to be typically ~ 90% in flow cytometric analyses.
Total RNA from mouse colonic epithelial cells was isolated following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific) followed by a Qiagen RNeasy Micro clean-up procedure according to the manufacturer's protocol. All RNAs were analyzed using an Agilent Bioanalyser (Agilent, Santa Clara, CA, USA) for quality assessment with RNA Integrity Number (RIN) ranging from 7.2-9.2 and a median RIN of 8.8. cDNA libraries were prepared from 2 ng total RNA starting material and 1 ml of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific) using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1. Use of 20 mM TSO; 2. Use of 250 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA).

treatment_protocol: Mice were either left untreated or treated with DSS for 48h.

value: Colon

value: wild type

tag: age

value: 7-9 weeks


title: RNA-seq_Treg_DOHH_KO_2

description:
processed data file:
DOHH_counts.tsv

value: Spleen and Lymph node


title: RNA-seq_Treg_DOHH_WT_2

description:
processed data file:
DOHH_counts.tsv

value: Treg


title: RNA-seq_TH2_DOHH_KO_2

description:
processed data file:
DOHH_counts.tsv


title: WT treated 2


title: Sleep control(male3)


title: CTRL_Sultana_rep3 [OXNAC33]


title: Sleep control(male4)


title: RNA-seq_TH2_DOHH_WT_2

description:
processed data file:
DOHH_counts.tsv


title: Sleep control(male1)


title: Sleep control(male2)


title: WT treated 1


title: WT untreated 3


title: papillary thyroid carcinoma tissue_rep3

city: Ghuangzhou

first: Yushuang

last: Sun

address: NO.2 Zhongshan Road

department: Institute of Precision Medicine

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

description: CircRNA expression  in papillary thyroid carcinoma tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8×15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After the slides were washed, the arrays were scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Statistical differences in circRNA expression between the two groups were determined with Volcano Plot filtering. Differentially expressed circRNAs between the two sample sets were identified through Fold Change filtering. Hierarchical Clustering was performed to show distinguishable circRNAs expression patterns among samples.

source_name: papillary thyroid carcinoma tissue,rep3

label_protocol: Total RNA from each sample was treated with RNase R (Epicentre, Inc.) to remove linear RNAs and to enrich for circRNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA from papillary thyroid carcinoma samples and paracancerous tissues was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The RNA extractions were stored at 80°C. Total RNA from each sample was quantified using a NanoDrop ND-1000. Sample preparation and microarray hybridization were performed based on Arraystar’s standard protocols.

treatment_protocol: Three fresh-frozenpapillary thyroid carcinoma samples and three paracancerous tissues were collected from the First, Second and Fourth Clinical Hospitals affiliated with Harbin Medical University. The paracancerous samples were obtained from the same patient. All tissue samples were stored in liquid nitrogen, and pathologists from the Department of Pathology in the Fourth Clinical Hospitals affiliated with Harbin Medical University performed pathologic diagnosis.

value: papillary thyroid carcinoma tissue

tag: gender

value: female


title: RNA-seq_TH1_DOHH_KO_2

description:
processed data file:
DOHH_counts.tsv


title: WT untreated 2


title: Sleep distubance(female7)

value: SD

value: Female


title: WT untreated 1


title: paracancerous tissue_rep1

description: CircRNA expression  in paracancerous tissue

source_name: paracancerous tissue,rep1

value: paracancerous tissue


title: Sleep distubance(female6)


title: papillary thyroid carcinoma tissue_rep2

source_name: papillary thyroid carcinoma tissue,rep2


title: paracancerous tissue_rep3

source_name: paracancerous tissue,rep3


title: MSL2vir DIP 9

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

data_processing:
Sequencing reads were aligned to the dm6 version of the D. melanogaster genome using bowtie2 (version 2.3.5) allowing only unique matches
Coverage vectors were generated by counting overlapping fragments at each genomic position
Genome_build: dm6 (mel) and caf1 (vir)
Supplementary_files_format_and_content: bigwig files with coverage

organism: Drosophila virilis

source_name: sheared genomic DNA from D. virilis flies

growth_protocol: D. melanogaster embryonic Kc167 cell line was obtained from the Drosophila Genomic Resource Center (https://dgrc.bio.indiana.edu/Home). D. melanogaster S2 (subclone L2-4) cell line was a kind gift of P Heun (Villa et al., 2016). D. virilis 79f7Dv3 cell line was a kind gift of BV Adrianov (Albig et al., 2019). The identity of cell lines was verified by high-throughput sequencing. Cells were subjected to mycoplasma testing. Cells were maintained at 26°C in Schneider’s Drosophila Medium (Thermo-Fischer, Cat. No 21720024) supplemented with 10% FBS (Kc167 and S2) or 5% FBS (79f7Dv3) and 1% Penicillin-Streptomycin solution (Sigma-Aldrich, Cat No P-4333). Spodoptera frugiperda 21 (SF21) cells (Gibco) were used for amplification of recombinant baculoviruses and baculovirus-driven expression of recombinant proteins. SF21 cells were cultured at 26°C in Sf-900 II medium (Gibco) supplemented with 10% fetal calf serum and gentamycin.

extract_protocol:
Pellet from 6 × 107 S2 or virilis cells was suspended in 1.2 ml of lysis buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA pH 8, 0.5% SDS, 0.15 mg/ml of proteinase K) and incubated at 56°C overnight. After addition of sodium acetate to a final concentration of 0.3 M, the nucleic acids were extracted with phenol–chloroform and precipitated with an equal volume of isopropanol at −20°C for 1 h. Precipitated nucleic acids were centrifuged and washed with 70% ethanol. Dried pellets were resuspended in TE buffer and sonicated with Covaris AFA S220 (microTUBEs, Peak Incident Power 175 W, Duty Factor 10%, Cycles per Burst 200, 430 s) to generate 200 bp fragments. After RNAse digestion (0.1 mg/ml, 1 h at 37°C), DNA was purified with the GenElute kit (Sigma-Aldrich). DNA immunoprecipitation (DIP) experiments were performed as in (Villa et al. 2016) with few modifications. Briefly, 400 ng of genomic DNA (gDNA) was incubated with 80nM of recombinant proteins at 26°C for 30 min in 100 μl of binding buffer (100 mM KCl, 2 mM MgCl2, 2 mM Tris–HCl pH 7.5, 10% Glycerol, 10 μM ZnCl2). Ten percent of the reaction was taken as input material. DNA–protein complexes were immunoprecipitated using 30 μl of anti-FLAG M2 beads (SIGMA) and washed twice with 100 μl of binding buffer to eliminate unbound DNA. After proteinase K digestion (0.5 mg/ml, 1 h at 56°C), DNA was purified with AMPure beads (Beckman Coulter).
Libraries for sequencing were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465).

treatment_protocol: Cells were transfected with the plasmid of interest plus 1:20 of pCoBlast (Thermo Fischer, Cat. No K5150-01) using Effectene transfection reagent (QIAgen, Cat. No 301425). 72h after transfection cells were diluted 2-3 times and Blasticidin was added to the medium at a final concentration of 50ng/ul for 7 or 10 days. For the DIP experiments in presence of RNA we pre-incubated the recombinant proteins with different amount of RB4 (GGUUAACGUUAUACAAGCCGAG) or ctrl (GACGUUGUAAUAUGUACGGGAU) RNA oligos and proceeded with the normal DIP protocol.

tag: ip target

value: MSL2 Drosophila virilis

tag: assay type

value: DIP

tag: experimental series


title: RNA-seq_TH17_DOHH_KO_2

description:
processed data file:
DOHH_counts.tsv

tag: cell type

tag: genotype


title: RNA-seq_TH1_DOHH_WT_2

description:
processed data file:
DOHH_counts.tsv

tag: strain

tag: polarization


title: Nfkb2 knockout treated 3


title: papillary thyroid carcinoma tissue_rep1

source_name: papillary thyroid carcinoma tissue,rep1


title: Nfkb2 knockout treated 2


title: Sleep distubance(female4)


title: MSl2mel DIP1

value: MSL2 Drosophila melanogaster


title: RNA-seq_Treg_ODC_KO_1

description:
processed data file:
ODC_counts.tsv

value: CD4 T cell


title: Nfkb2 knockout treated 1


title: Sleep distubance(female1)


title: Nfkb2 knockout untreated 3


title: Sleep control(female7)


title: paracancerous tissue_rep2

source_name: paracancerous tissue,rep2


title: MSL2vir DIP 8


title: Nfkb2 knockout untreated 2


title: RNA-seq_TH2_ODC_KO_1

description:
processed data file:
ODC_counts.tsv


title: RNA-seq_TH2_ODC_WT_1

description:
processed data file:
ODC_counts.tsv


title: DIP input 4

value: input control


title: RNA-seq_TH17_DOHH_WT_2

description:
processed data file:
DOHH_counts.tsv


title: RNA-seq_TH1_ODC_KO_1

description:
processed data file:
ODC_counts.tsv


title: Nfkb2 knockout untreated 1


title: Sleep control(female5)


title: F4

city: Hangzhou

first: Jiayue

last: Zhou

state: Zhejiang

address: Number 88 Jiefang Road

department: The Eye Center, Second Affiliated Hospital of School of Medicine

institute: Zhejiang University

data_processing:
Clean data were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from the raw data of fastq format. Q20, Q30 and GC content of the clean data were calculated at the same time.
Paired-end clean reads were aligned to the rat reference genome Rnor_6.0 using Hisat2 v2.0.5, featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene.
FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using DESeq2 v1.16.1. P-values were adjusted using Benjamini and Hochbergʼs approach. Genes with | log2FoldChange | > 1 compared with Normal Control group and adjusted P value < 0.05 were considered as DEGs for transcriptomic analysis.

organism: Rattus norvegicus

source_name: Lens capsules

extract_protocol:
Total RNA of the Hypothermia Group (n = 5) and the Nomal Control Group (n = 5) were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Agarose gel electrophoresis, NanoPhotometer spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) were used for total RNA qualification. RNA samples with RIN ≥ 5.8 were select for sequencing.
A total amount of 0.8 μg RNA per sample was used as input material for the library preparation. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Rats were divided randomly into the Normal Group and the Hypothermia Group and subsequently euthanized. The lens capsules of rats in the Normal Group were collected directly after euthanasia. The lens of rats in Hypothermia Group were isolated and incubated in Hibernate-A medium (Thermofisher Scientific, MA, USA) at 4°C for 8 hours. The lens capsules were separated from the lens cortex after being washed in 4°C phosphate-buffered solution (PBS).

value: Lens capsules

value: normal control


title: F5


title: Sleep control(female3)

value: SC


title: Sleep distubance(female2)


title: Non_icteric07

city: Bangkok

first: Natthaya

last: Chuaypen

state: Select a State or Province

address: 1873 Rama 4 road, Pathumwan

department: Biochemistry

country: Thailand

institute: Chulalongkorn University, Faculty of Medicine

hyb_protocol: nCounter miRNA Hybridization Assay Standard nanostring miRNA hybridization protocol (10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot  from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet).

scan_protocol: nSolverTM software (v4.0; NanoString)

data_processing:
nSolverTM software (v4.0; NanoString)
Normalized signal intensity (fold-change)

source_name: Serum

label_protocol: Standard nanostring miRNA protocols

extract_protocol:
Serum samples (200 µl) were used for total RNA extraction using the miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s instruction.
100ng total RNA per sample normalized to 33ng/µL

value: Male

tag: condition

value: anicteric leptospirosis

tag: sample type

value: Serum


title: Sleep control(female1)


title: Non_icteric09


title: RNA-seq_Treg_ODC_WT_1

city: Baltimore

first: Immunometabolism

last: Department

institute: Johns Hopkins University

description:
processed data file:
ODC_counts.tsv

value: Spleen and Lymph node

value: Treg


title: Non_icteric06


title: RNA-seq_TH17_ODC_KO_1

description:
processed data file:
ODC_counts.tsv


title: Icteric03

value: icteric leptospirosis


title: Non_icteric08


title: F3

value: SD

tag: treatment


title: Icteric02


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 4

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

institute: University of Louisville

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.

data_processing:
Trimgalore was used to trim, and quality filter the newly generated reads.
Trimmed reads were mapped to the human reference genome hg19 (NCBI build 37.1 released 2009) using mirDeep2
mirDeep2 and mirBase annotation information for human and orthologous species was used to identify and quantify miRNAs
Genome_build: hg19
Supplementary_files_format_and_content: MirDeep2 and mirBase annotation information for human and orthologous species was used to identify and quantify miRNAs

source_name: HaCaT

growth_protocol: HaCaT cells were cultured in 4 biological replicates in MEM alpha modification media supplemented with 10% fetal bovine serum, penicillin/streptomycin and glutamine. Cultures were maintained at 37°C in a humidified 5% CO2 atmosphere with 20% oxygen and were maintained separately for 3 and 7 weeks. A set of HaCaT cells maintained for 28 weeks (1 biological replicate) were obtained form Dr. Michael P. Waalkes.

extract_protocol:
Total RNA was purified from the cells using the mirVana™ miRNA Isolation Kit.
The Truseq Stranded mRNA kit was used to prepare mRNA libraries from 1 μg total RNA. Libraries were validated on the Agilent 2100 Bioanalyzer and quantitated using the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems and the ABI7900HT real-time PCR instrument. All samples were pooled and run simultaneously on 4 flow cells, using 2x150 paired end sequencing with the 500 High-output v2 (300 cycles) sequencing kit on the Illumina NextSeq500 instrument.

treatment_protocol: cells maintained with and without 100 nM sodium arsenite from day 1 of plating.

tag: cell line

value: HaCaT

value: Immortalized Human Keratinocytes (HaCaT)

value: The cells were maintained for 28 weeks with 100 nM sodium arsenite


title: RNA-seq_TH17_ODC_WT_1

address: 1650 Orleans Street

description:
processed data file:
ODC_counts.tsv


title: Sleep control(female6)

source_name: serum

tag: group

tag: Sex

value: Female


title: F2


title: Non_icteric05


title: RNA-seq_Treg_DOHH_KO_1

description:
processed data file:
DOHH_counts.tsv


title: Non_icteric04


title: RNA-seq_TH1_ODC_WT_1

description:
processed data file:
ODC_counts.tsv


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 3


title: RNA-seq_Treg_DOHH_WT_1

description:
processed data file:
DOHH_counts.tsv


title: F1


title: Icteric01


title: E5

value: 4degC 8h


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 2


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 1


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 4

value: The cells were maintained for 19 weeks with 100 nM sodium arsenite


title: Non_icteric03


title: RNA-seq_TH1_DOHH_KO_1

description:
processed data file:
DOHH_counts.tsv

value: CD4 T cell


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 3


title: E2

value: Lens capsules


title: RNA-seq_TH2_DOHH_WT_1

description:
processed data file:
DOHH_counts.tsv


title: RNA-seq_TH2_DOHH_KO_1

description:
processed data file:
DOHH_counts.tsv


title: RNA-seq_TH1_DOHH_WT_1

description:
processed data file:
DOHH_counts.tsv


title: E3


title: Non_icteric02


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 2


title: NC

city: guilin

first: qiu

last: fxiaofen

state: sz

address: Guangxi Normal University, Guilin, Guangxi

institute: Guangxi Normal University

data_processing:
Barcode processing: To improve data quality, a ‘whitelist’ of correct barcode sequences was applied to fix the occasional sequencing error in barcodes obtained from the ‘I2’ index read
Genome alignment: Reference-based analysis was performed using the Cell Ranger ATAC pipeline. BWA-MEM was applied with default parameters to align the trimmed read pairs that were greater than 25 bp to GRCh38
Filteing: We filtered scATAC-seq data using cut-offs of 1,000 unique nuclear fragments per cell and a transcription start site (TSS) enrichment score of 8 to exclude low-quality cells in 10x genomic Cell Ranger ATAC platform
Peak calling: First, the number of transposition events at each base pair along the genome was counted. Next, a smoothed profile of these events with a 401 bp moving window around each base pair and fitting a ZINBA-like mixture model was generated. Then, a signal threshold was set to determine whether a region was a peak signal or noise based on an odds ratio of 1/5. Finally, peaks within 500 bp of each other were merged to produce a position-sorted BED file.
Cell calling and peak-barcode matrix: For each barcode, the mapped high-quality fragments that passed all filters were recorded, and the number of fragments that overlapped any peak regions was used to separate the signal from noise. To capture the signal and noise, a mixture model of two negative binomial distributions was set, and barcodes that corresponded to real cells from the non-cell barcodes were separated by setting an odds ratio of 1000. Subsequently, a raw peak-barcode matrix consisting of the counts of fragment ends within each peak region for each barcode was produced. After filtering to contain only cell barcodes, the matrix was used in subsequent analyses, such as dimensionality reduction, clustering and visualization.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files for barcodes; mtx files for matrix; bed files for peaks

source_name: Umbilical Cord Blood mononuclear cells

extract_protocol:
CBMCs were separated using an equal proportion of Ficoll-Paque Plus. Nuclei suspensions were obtained by adding lysis buffer (10 mM Tris-HCl, 3 mM MgCl2, 10 mM NaCl , 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 1% BSA). The final libraries were constructed via PCR with P5 and P7 primers in Illumina® bridge amplification.
scATAC-seq libraries were generated according to the Chromium Single Cell ATAC protocol (10x GENOMICS)

value: Umbilical Cord Blood mononuclear cells

value: CBMCs

tag: disease state

value: Natural control


title: E1

tag: tissue


title: ES

value: ES patients


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 1


title: RNA-seq_TH17_DOHH_KO_1

description:
processed data file:
DOHH_counts.tsv


title: Str_S_3

city: WuXi

first: Tao

last: Zheng

address: No. 69, Xue Jiali, Nanquan Town

institute: NanJing Agricutural university

description: skin samples 3 under  transport 16h

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Tachysurus fulvidraco x Tachysurus vachelli

source_name: (Tachysurus fulvidraco♀ × P. vachellii♂)

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: juvenile

value: transport 16h

value: left side skin of each fish in the posterior of the dorsal fin


title: RNA-seq_TH17_DOHH_WT_1

description:
processed data file:
DOHH_counts.tsv

value: Spleen and Lymph node


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 4

value: The cells were maintained for 7 weeks with 100 nM sodium arsenite


title: Str_S_2

description: skin samples 2 under  transport 16h


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 3

value: HaCaT


title: E4

value: SD


title: Primary lens cells - IgG_rep2

city: Boca Raton

first: Marc

last: Kantorow

state: FL

address: 777 Glades Road

institute: Florida Atlantic University

description: IgG.bedgraph

data_processing:
Library strategy: CUT&RUN
Reads were trimmed with Trimmomatic  with the following settings (ILLUMINACLIP: 2:15:4:4:true SLIDINGWINDOW:4:15 MINLEN:25) and aligned to the galgal6 genome (ensemble version 96) using Bowtie2  with the following settings: (--end-to-end,--dove-tail,--phred33)
Samtools  was used to retain fragments <120bp, and to remove reads in mitochondrial DNA and remove reads overlapping low-complexity regions in the Galgal6 genome as defined by the RepeatMasker  track in the UCSC genome browser
HIF1α-DNA binding complexes were identified using MACS2  by pooling the HIF1α BAM files versus the pooled IgG BAM files using the following settings: (narrowPeak setting, q value cutoff 0.05, --SPMR, --keep-dup auto)
Genome_build: galgal6
Supplementary_files_format_and_content: peak text files: MACS2 on CUT&RUN samples identified 8,375 HIF1α-DNA binding complexes in the primary chick lens cells

organism: Gallus gallus

source_name: Primary lens cells

growth_protocol: Primary chick lens epithelial cell cultures were prepared from the lenses of Embryonic day 10 (E10) White Leghorn embryonated chicken eggs (Charles River Laboratories, Storrs, CT). Briefly, primary lens cells were isolated from chicken lenses by trypsinization and agitation. Cells were plated onto dishes coated with mouse laminin (Invitrogen, prod no: 23017-015) and cultured in Medium 199 (Invitrogen, prod no: 11150) supplemented with 10% FBS (Invitrogen, prod no: 16140-071) and penicillin-streptomycin antibiotic mix (50 units/ml; Invitrogen, prod no: 15140-122)

extract_protocol:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) was performed on unfixed permeabilized primary lens cells incubated with a HIF1α-specific  ChIP grade antibody (Abcam, ab2185) and an IgG negative control antibody (Invitrogen, prod no: 10500c) to elucidate genome-wide HIF1α-DNA binding complexes. Briefly, primary lens cells were harvested, counted, and pooled into biological duplicates of 500,000 cells each and resuspended in 1.5 ml Wash Buffer without Digitonin (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, Protease Inhibitor). After three rounds of washing and centrifuging for 3 minutes at 600 g, the resuspended cells were washed in 1 ml wash buffer and ConA-coated magnetic beads (Bangs Labroatories, prod no: BP531, 10μl per sample) were added followed by gentle rotation at room temperature for 10 minutes. Each sample was divided into two equal volumes and the supernatants removed using a magnet stand. 150 μl of antibody buffer with 0.1% final concentration digitonin was added to each aliquot with gentle agitation to permeabilize the cells. For each biological sample, one aliquot of ConA-bound cells was incubated with ChIP-grade HIF1α antibody and the other aliquot was incubated with IgG antibody at a 1:100 dilution and rotated at 4 °C overnight. Antibody-bound ConA-bound cells were washed twice with 1 ml wash buffer with 0.1% digitonin. The supernatant was removed and 150 μl of Protein A-MNase (700ng/mL final concentration, Addgene #123461) in wash buffer with digitonin was added to the pellet with gentle agitation and the mix rotated at 4 °C for 1 hour. Cells were washed twice with 1 ml of digitonin wash buffer and once with 1ml low salt rinse buffer (20mM HEPES pH 7.5, 0.5mM Spermidine, 0.05% Digitonin). The supernatant was removed and 200 µl of ice-cold incubation buffer (3.5mM HEPES pH 7.5, 10mM CaCl2, 0.05% Digitonin) added with gentle agitation. The resulting samples were incubated on ice for 5 minutes before removing the supernatant using the magnet stand followed by the addition of 200 µl STOP buffer (170mM NaCl, 20mM EGTA, 0.05% Digitonin, 50ug/mL RNAse A, 25μg/mL Glycogen) with gentle agitation. The samples were incubated for 30 minutes at 37 °C to release CUT&RUN fragments. Following incubation, the supernatant containing CUT&RUN fragments was transferred to a fresh microcentrifuge tube. CUT&RUN fragments were treated with 2 µl 10% SDS and 2.5 µl Proteinase K (20 mg/ml) for 1 hour at 50 °C. DNA was isolated by standard Phenol-Chloroform extraction using Qiagen MaXtract tubes, and the DNA pellet resuspended in 30 µl 1 mM Tris-HCl pH 8 0.1 mM EDTA
Library prep was carried out using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) following the manufacturer’s instructions

treatment_protocol: Primary lens cells were treated with the HIF1α activator dimethyloxalllyl glycine (DMOG, Santa Cruz Biotechnology, prod no: sc200755) (1 mM) for 4 hours at 37 °C

value: Embryonic day 10 primary lens cells

value: White leghorn

tag: cut&run antibody

value: IgG (Invitrogen, prod no:10500c)

value: treated with 1mM DMOG for 4 hours


title: Primary lens cells - IgG_rep1

description: IgG.bedgraph


title: Str_S_1

description: skin samples 1 under  transport 16h


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 1

value: Immortalized Human Keratinocytes (HaCaT)


title: Con_S_3

description: skin control sample 3

value: untreated


title: Non_icteric01

tag: gender

value: Male

tag: age

value: anicteric leptospirosis

value: Serum


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 4

value: The cells were maintained for 28 weeks without 100 nM sodium arsenite


title: miRNA HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 2


title: Primary lens cells - HIF1a_rep2

description:
HIF1a_peaks.txt
HIF1a.bedgraph

value: HIF1a (Abcam, ab2185)


title: Con_S_1

description: skin control sample 1

value: juvenile


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 3


title: Con_S_2

description: skin control sample 2

value: left side skin of each fish in the posterior of the dorsal fin


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 2


title: MOLM13-RES cells, G16

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

description: Gilt.bw

data_processing:
Sequenced on HiSeq 4000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Rsubread align function
Read counts for each transcript were obtained using featureCounts (Liao 2014).
Raw count data were directly analyzed for differential peak enrichment using csaw to identify FDR corrected peaks
Genome_build: hg38
Supplementary_files_format_and_content: wig files

source_name: Bone marrow,  AML

extract_protocol:
Bone marrow was harvested and enriched for AML using MACS (Milteny Biotec) separation of human CD45+ cells. Genomic DNA was isolated and purified using MinElute spin columns (Qiagen). Nextera index adapters (i7 and i5) were used to amplify transposed DNA fragments per the manufacturer’s protocol (Illumina) for high-throughput DNA sequencing.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment cohort

value: Gilteritinib 30mg/kg


title: 10-11-21_C

city: Rehovot

first: Robert

last: Fluhr

address: hertzl 234, 17

department: Plant and environmental sciences

country: Israel

institute: Weizmann institute of science

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6H

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using cutadapt, (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to the barley genome (Mascher et al. 2017) using STAR,  v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Araport annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis is done for genes having minimum 5 read in at least one sample.
Genome_build: barley genome (Mascher et al. 2017)
Supplementary_files_format_and_content: Normalization of the counts and differential expression analysis was performed using DESeq2 , with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.

organism: Hordeum vulgare

source_name: flag leaf

growth_protocol: plants were grown in a small randomized block design in a glasshouse. Plants were kept at ~22 °C during the day and ~18 °C during the night; days were extended to a 16-hour photoperiod when required, using GE Multi-Vapor MVR1000/C/U lights (General Electric, Cleveland, OH, USA). Plants in potting soil were fertilized with 250 ml Peter's Professional General Purpose fertilizer (4 g l-1; Scotts-Sierra Horticultural Products Company, Marysville, OH, USA) per 4-liter pot with three plants. Fertilizer was applied every alternate week until anthesis, starting at 2 weeks after germination. Additionally, a treatment with 100 ml 16 mM KNO3 (Sigma-Aldrich, St. Louis, MO, USA) was applied twice per week, per pot, from germination to anthesis.

extract_protocol:
Each sample/replicate consisted of at least 10 flag leaves, and three independent samples/replicates were harvested for both 'Karl' and '10_11' at each time point. the samples were immediately shock-frozen in liquid nitrogen and RNA was extracted separately from frozen tissues using a standard Trizol extraction method (Sigma-Aldrich).
Libraries were prepared with the MARS-seq protocol (Diego Adhemar Jaitin, 2017) and sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Once plants reached anthesis, each shoot utilized for further experimentation was tagged with its exact anthesis date. Flag leaves were harvested at 7, 14, and 21 days past anthesis and immediately shock-frozen in liquid nitrogen

tag: cultivar

value: flag leaf

value: 21 days post anthesis


title: Primary lens cells - HIF1a_rep1

description:
HIF1a_peaks.txt
HIF1a.bedgraph

tag: cell type


title: MOLM13-RES cells, G10

description: Gilt.bw


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 1

value: HaCaT


title: MOLM13-RES cells, V11

description: Veh.bw

value: Vehicle


title: Paraxial, biological rep 3

city: Istanbul

first: Emre Can

last: Tüysüz

address: Ibrahimaga Mah.

country: Turkey

institute: Yeditepe University

description: miRNA expression data from differentiated mESC (Flk1-PDGFaR+)

hyb_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA

scan_protocol: miRNA 4.1 strips were scanned using the GeneAtlas Array scanner

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software and IPA

label: biotin

source_name: Differentiated mESCs

label_protocol: biotin

growth_protocol: mESCs were plated onto low-adherent 100 mm petri dish on a swirling rotator (50 rpmi/min) in IMDM (Thermo Fisher, Cat No: 12440053) supplemented with %15 FBS, 200 µg/ml Holotransferrin (Millipore, Cat No: 616424), 50 µg/ml Ascorbic Acid (Sigma, Cat No: A4403), 4.5 mM Monothioglycerol.  (Sigma, Cat No: M1753) at 37 °C in humidified atmosphere containing %5 CO2.

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

treatment_protocol: Not Applicable

tag: genotype/variation


title: Paraxial, biological rep 2


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 3

value: The cells were maintained for 19 weeks without 100 nM sodium arsenite


title: MOLM13-RES cells, V6

description: Veh.bw


title: Paraxial, biological rep 1


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 2


title: MOLM13-RES cells, V3

description: Veh.bw


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 1


title: Resting Disease TPCs

city: Stanford

first: Christopher

last: Still

state: California

address: 443 Via Ortega, Room 376

institute: Stanford

description: No mechanical stimulus applied

data_processing:
10X Chromium libraries processed by Cellranger version 3.0.2.
Drop-seq libraries processed using the Drop-seq alignment cookbook. Hisat2 was used instead of the standard STAR aligner.
Cell hashing data was processed using CITE-seq-Count python package version 1.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Drop-seq processed files are tab-delimited text files
Supplementary_files_format_and_content: Cell hashing processed files are csv files
Supplementary_files_format_and_content: 10X Chromium libraries are contained in standard cellranger output filtered_feature_bc_matrix

source_name: Tendon progenitor cells

growth_protocol: Following extraction of cells from tendon samples, cells were plated at low density (500 cells per cm^2) until confluent. All cells used in experiments started at passage 2. Cells were grown in low-glucose DMEM with 10% FBS, 50ug/ml ascorbic acid, and antibiotics.

extract_protocol:
Peritendous connective tissue was removed. Tendon tissue was then broken down by digestion with 0.1% type IV collagenase at 37°C with gentle agitation. Cells were then passed through a 70-micron filter to obtain a single cell suspension.
Drop-seq libraries were constructed as detailed in Macosko et al. 2015 with minor exceptions. A glass dolomite chip was used instead of the traditional PDMS chip. 10X Chromium Single Cell 3' V3 libraries were generated according to the standard protocol by the Stanford Functional Genomics Facility (SFGF). Cell Hashing libraries were generated according to the standard protocol by the SFGF.

treatment_protocol: Moderate strength cyclic stetch (6% end-to-end) for 12 hours a day, 3 days in a row followed by 1 day of rest.

value: Patellar Tendon

tag: disease status

value: Tendinopathy


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 4

value: Immortalized Human Keratinocytes (HaCaT)

value: The cells were maintained for 7 weeks without 100 nM sodium arsenite


title: MOLM13-RES cells, G5

description: Gilt.bw


title: frog_oocyte_eGFP_eGFP_HA_PALTRAP_eluate

city: Cambridge

first: David

last: Bartel

address: 455 Main Street

institute: Whitehead Institute

description:
C12
no rRNA depletion

data_processing:
Library strategy: PAL-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq); *hits.txt files are raw signal intensities from Hiseq 2000 sequencing which are used with a custom algorithm to call poly(A) tail lengths

source_name: Xenopus laevis stage VI oocyte

growth_protocol: All mammalian cells were cultured at 37°C with 5% CO2. HeLa cells were cultured in DMEM (VWR, 45000-304) with 10% FBS (TaKaRa, 631106). HCT116 OsTIR1 cells were cultured in McCoy’s 5A media (Thermo Fisher, 16600082) supplemented with 10% FBS, 2mM L-glutamine (Thermo Fisher, 25030081). NIH3T3 cells were cultured in DMEM with 10% BCS (Sigma, 12133C).

extract_protocol:
To prepare lysate from mammalian cells, cycloheximide (CHX) was added to each plate at final concentration 100 µg/ml. Plates were immediately moved to a cold room and culture media were removed. Cells were washed twice with ice-cold PBS supplemented with 100 µg/ml CHX. After the last wash, 1 ml buffer RLL (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% (v/v) Triton X-100, 100 µg/ml cycloheximide, 500 unit/ml RNasin Plus (Promega, N2615), 2 mM DTT, cOmplete protease inhibitor cocktail (Sigma, 11836170001, 1 tablet per 10ml buffer)) was added to each 15 cm plate, and cells were scraped off and incubated on ice for 10 min. The resulting lysates were passed through a 26-gauge needle six times and cleared by centrifugation at 1300g at 4°C for 10 min. To prepare lysate from frog oocytes, injected oocytes were washed once with complete OR-2 buffer and three times with buffer RLL. After removing all wash buffer, oocytes were lysed in buffer RLL (10 µl/oocyte) by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5,000g at 4°C for 10 min. One tenth of each cleared lysate was added to 10 volumes of Tri Reagent for total-RNA preparation, following the manufacturer’s protocol. Another small portion (~10 µl) was taken for western analysis. The remainder was aliquoted, flash frozen in liquid nitrogen, and stored at –80°C.
Sequencing libraries were prepared as described previously (Subtelny et al., 2014) and (Eisen et.al, 2020)
Library strategies were as described previously (Subtelny et al., 2014) and (Eisen et.al, 2020)

treatment_protocol: For 5EU labeling: 48 h after siRNA transfection, HeLa cells were incubated with pre-warmed fresh media with 400 µM 5-ethynyl uridine (5EU, Jena Biosciences) for 1, 2, 4, and 8 h. For IAA-indcued degradation, HCT116 cells were incubated with 1 µg/ml doxycycline and 0.2 mM auxinole (Aobious, AOB8812), an inhibitor of OsTIR1 for 6 h, after which fresh media with 1 µg/ml doxycycline and 0.5 mM IAA were added. Cells were collected after 0.5, 1, and 3 h of induction.

value: oocyte

tag: Stage

value: VI

tag: manipulation

value: express eGFP and eGFP-HA

tag: time after 5eu labeling (h)

tag: time after iaa addition (h)

tag: rna population

value: cytoplasmic RNA, HA IP eluate (beads)

tag: library type

value: PAL-seq v3


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 4

tag: cell line

tag: treatment


title: DU 145 Control Replicate 3

city: Selangor

first: Nurul Azwa

last: Abd. Wahab

state: Not US or Canada

address: Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor

department: Jeffrey Cheah School of Medicine and Health Sciences

country: Malaysia

institute: Monash university Malaysia

description:
DU145 C3
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring

hyb_protocol: nCounter XT CodeSet Gene Expression  Assays

scan_protocol: Nanostring nCounter platform

data_processing: nSolver 4.0 software

source_name: DU 145 Control

growth_protocol: DU 145 were cultured in Eagle’s Minimum Essential Medium (EMEM) meanwhile, PC-3 cells were cultured in Ham’s F-12 medium (F-12K). These cells were incubated at 37 oC in a humidified atmosphere of 5% CO2.

extract_protocol: total RNA by Qiagen RNeasy - total RNA

treatment_protocol: DU 145 and PC-3 cells were incubated with 16 µM of MS13 for 24 h based on the EC50 values.

tag: metastatic

value: Brain

tag: disease

value: Carcinoma

value: androgen-independent prostate cancer cells

value: control


title: PC-3 Treated Replicate 3

description:
PC3 T3
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring

source_name: PC-3 Treated

value: Bone

value: Adenocarcinoma; Grade IV

value: 16 µM of MS13 for 24 h


title: PC-3 Control Replicate 2

description:
PC3 C2
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring

source_name: PC-3 Control


title: PC-3 Control Replicate 1

description:
PC3 C1
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 2

value: HaCaT

tag: tissue


title: PC-3 Treated Replicate 2

description:
PC3 T2
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: PC-3 Treated Replicate 1

description:
PC3 T1
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: DU 145 Treated Replicate 3

description:
DU145 T3
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring

source_name: DU 145 Treated


title: PC-3 Control Replicate 3

description:
PC3 C3
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: DU 145 Treated Replicate 2

description:
DU145 T2
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: DP, biological rep 1

description: miRNA expression data from differentiated mESC (Flk1+PDGFaR+)


title: DP, biological rep 3


title: DP, biological rep 2


title: Lateral, biological rep 3

description: miRNA expression data from differentiated mESC (Flk1+PDGFaR-)


title: frog_oocyte_eGFP_eGFP_HA_PALTRAP_input

description:
C11
no rRNA depletion

value: cytoplasmic RNA, HA IP input


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 1


title: frog_oocyte_ePAB_RPL3_HA_PALTRAP_eluate

description:
C10
no rRNA depletion

value: express ePAB and RPL3-HA


title: miRNA HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 3

value: Immortalized Human Keratinocytes (HaCaT)


title: Lateral, biological rep 2


title: Lateral, biological rep 1


title: Resting Normal TPCs

description: No mechanical stimulus applied

value: Patellar Tendon

value: Normal


title: DU 145 Control Replicate 2

description:
DU145 C2
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: frog_oocyte_ePAB_RPL3_HA_PALTRAP_flowthrough

description:
C09
no rRNA depletion

value: oocyte

value: VI

value: cytoplasmic RNA, HA IP flowthrough


title: DU 145 Treated Replicate 1

description:
DU145 T1
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: DU 145 Control Replicate 1

description:
DU145 C1
The total RNA of MS13 treated cell lines was extracted and analysed with Nanostring


title: ARv567.Veh.1

city: Houston

first: Nancy

middle: J

last: Weigel

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Fastq files were trimmed with TrimGalore!
Trimmed files were aligned to hg19 using HISAT2.
Aligned reads were quantified using featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: comma delimited count file

source_name: Empty lentiviral infected LNCaP cells.

growth_protocol: LNCaP-ARv567es were plated at 250,000 cells per well in a 6 well format in RPMI-1640 with 10% FBS.

extract_protocol:
mRNA was extracted with Qiagen's RNeasy mini kit and Qiashredder spin columns.
TruSeq Stranded mRNA was used following manufacturers guidelines.

treatment_protocol: The next day the media was changed to 10% charcoal stripped serum (CSS) followed by treatment with ethanol (0.1%) or doxycycline (30 ng/mL) for 24hrs.

value: LNCAP cell line

tag: genotype

value: LNCaP


title: DN, biological rep 3

description: miRNA expression data from differentiated mESC (Flk1-PDGFaR-)


title: ARv567.Dox.1

source_name: LNCaP cells were infected with lentiviral vector expressing ARv567 under doxycycline control.

value: LNCaP + Dox induced ARv567es


title: DN, biological rep 2


title: frog_oocyte_eGFP_RPL3_HA_PALTRAP_eluate

description:
C07
no rRNA depletion

value: express eGFP and RPL3-HA

value: cytoplasmic RNA, HA IP eluate (beads)

value: PAL-seq v3


title: Primary lens cells - Untreated_rep3

data_processing:
Cutadapt  was used to remove adaptor-contaminated reads, low quality bases and undetermined bases
Reads were mapped to galgal6 genome (ensemble version 96) using Bowtie2  and HISAT2
The mapped reads were assembled using StringTie
Comprehensive transcriptomes were generated using gffcompare and StringTie
The R package edgeR  was used to estimate the expression levels of all transcripts and to identify differentially expressed genes (log2 fold change FPKM > 0.6 or <-0.6) with parametric F-test comparing nested linear models (p < 0.05)
Genome_build: galgal6
Supplementary_files_format_and_content: DMOGvUntreated_RNAseq.txt file: 526 genes were found to be differentially expressed in DMOG-treated primary lens cells relative to untreated primary lens cell samples

extract_protocol:
Total RNA was isolated from primary lens cells using TRIZOL® reagent (Invitrogen, prod no: 15593018) according to the manufacturer’s instructions
Libraries were prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol

value: Embryonic day 10 primary lens cells

tag: strain

value: White leghorn

value: untreated


title: frog_oocyte_ePAB_RPL3_HA_PALTRAP_input

description:
C08
no rRNA depletion

value: cytoplasmic RNA, HA IP input


title: ARv567.Dox.2

value: LNCaP + Dox  induced ARv567es


title: frog_oocyte_eGFP_RPL3_HA_PALTRAP_input

description:
C05
no rRNA depletion


title: frog_oocyte_eGFP_RPL3_HA_PALTRAP_flowthrough

description:
C06
no rRNA depletion


title: Primary lens cells - Untreated_rep2


title: tRip-selected tRNAs - Free tRNAs - tRNA/tRip=10

city: Charleston

first: Renaud

last: Geslain

state: SC

address: 58 Coming Street

department: Biology

institute: College of Charleston

hyb_protocol: Extracted radioactive tRNA were hybridized onto in-house printed human tRNA arrays. Each chip consists of 48 different probes, repeated 8 times (for a complete and generic protocol please refer to Emetu et al., 2018). Those probes hybridize either to a unique tRNA species (Arg-3h, Asn-1h, Asp-1h, Gly-2h, His-1h, Leu-3h, Lys-1h, Lys-3h, Lys4H, Met-1h, Sec-1h, Thr-3h, Thr-4h, Val-4h), a group of tRNA isodecoders (Arg-1h, Arg-4h, Glu-2h, Ile-2h, Leu-2hn, Leu-4h, Leu-6h, Lys-2h, Met-2h, Phe-1h, Ser-1h, Ser-3h, Thr-1h, Thr-2h, Thr-5h, Tyr-2h), several isoacceptors specific to the same amino acid (Ala-2h, Arg-2h, Glu-1h, Gly-1h, Leu-1h, Pro-1h, Ser-2h, Val-1h), or tRNAs specific to different amino acids (Glu-3h, Ser-4h, Thr6h, Tyr-1h, Val3H). Arrays were placed inside a hybridization cassette and loaded with radiolabeled tRNA samples. All subsequent steps were performed on an automated hybridization-washing station (DigiLab, Hyb10022) for maximum reproducibility: 1. Gasket conditioning for 2 min at 75 °C, 2. Probe introduction at 60 °C, 3. Probes and samples denaturation for 5 min at 90 °C., 4. Sample hybridization for 3 h at 60 °C, 5. Slides washing at 50 °C twice with 2 X SSC, 0.1% (w/v) SDS (flow 10 s and hold 20 s), 6. Slides washing at 42 °C twice with 0.1 X SSC, 0.1% SDS (flow 10 s and hold 20 s), and 7. Slides washing at 42 °C twice with 0.1 X SSC (flow 10 s and hold 20 s). microarray hybridizer as described in (Emetu et al., 2018).

scan_protocol: Arrays were exposed onto a storage phosphor screen in an exposure cassette at room temperature for 10 to 24 h depending on signal strength and scanned at 50 µm resolution using a Typhoon FLA 7000 IP phosphorimager.

data_processing: Radioactivity intensities at each probe spot were quantified using the free Image J software upgraded with a microarray profiler and background subtracted.

source_name: Human transfer RNAs, tRip-excluded, tRNA/tRip=5

label_protocol: Radioactive labeling of the 3’ end of tRNAs was performed on 140 pmoles of tRNA/transcript with 20 µCi [32P]ATP in 50 mM Tris-HCl pH 8.0, 50 µM CTP, 10 mM MgCl2, 8 mM DTE and 6 ng/µl of yeast CCase for 20 min at 37°C according to Vlassov et al., 1980

growth_protocol: HeLa cells were washed in phosphate buffer sodium (PBS) and total RNA was extracted using Tri-Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. Further fractionation was performed on a gel filtration column (Superdex 200) in 50 mM HEPES-KOH pH 7.5, 150 mM NaCl in order to isolate tRNAs from mRNAs and ribosomal RNAs.

extract_protocol: tRNAs were gel extracted using the crush & soak method (300 mM sodium acetate, 1 mM EDTA, 0.1% SDS according to Petrov et al., 2013

treatment_protocol: Increasing amounts of total tRNA purified from HeLa cells (8 µM, 20 µM and 40 µM) were incubated 20 min at 4ºC with 2 µM tRip dimers in a total volume of 100 µl with EMSA buffer. These mixtures were loaded on a 6% native gel and separated for 4 h at 140 V (10 ºC). Bands were visualized by UV shadowing

value: Cultured HeLa cells

tag: separated on non-denaturing polyacrylamide gel

value: Yes

tag: complexed to trip

value: No

tag: trna/trip ratio

tag: molecule subtype

value: Transfer RNA


title: No selection - Total tRNA - replicate#1

source_name: Human transfer RNAs, total tRNA, experimental input, replicate#2

tag: cell type


title: tRip-selected tRNAs - Free tRNAs - tRNA/tRip=20

source_name: Human transfer RNAs, tRip-excluded, tRNA/tRip=20


title: No selection - Total tRNA - replicate#2


title: Primary lens cells - DMOG_rep3

value: treated with 1mM DMOG for 4 hours


title: frog_oocyte_ePAB_TAIL_seq

description:
C04
no rRNA depletion

data_processing:
Library strategy: TAIL-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq); *hits.txt files are raw signal intensities from Hiseq 2000 sequencing which are used with a custom algorithm to call poly(A) tail lengths

value: oocyte

tag: Stage

value: VI

tag: manipulation

value: ePAB-overexpressed

value: cytoplasmic RNA

value: TAIL-seq


title: Primary lens cells - Untreated_rep1


title: ARv567.Veh.2

value: LNCAP cell line

value: LNCaP


title: frog_oocyte_PABPC1_TAIL_seq

description:
C03
no rRNA depletion

tag: time after 5eu labeling (h)

tag: time after iaa addition (h)


title: tRip-selected tRNAs - Free tRNAs - tRNA/tRip=4

source_name: Human transfer RNAs, tRip-excluded, tRNA/tRip=10


title: tRip-selected tRNAs - Bound tRNAs - tRNA/tRip=20

source_name: Human transfer RNAs, tRip-bound, tRNA/tRip=20


title: frog_oocyte_eGFP_TAIL_seq

description:
C02
no rRNA depletion

value: eGFP-expressed

tag: rna population

tag: library type


title: Primary lens cells - DMOG_rep2

source_name: Primary lens cells

value: Embryonic day 10 primary lens cells

value: White leghorn

tag: treatment