title: N80_SC-Ura_Y8203_R11

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 8
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: ChIP2 input

status: Public on Dec 23 2021

type: SRA

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

country: USA

institute: Virginia Polytechnic Institute and State University

library_source: genomic

data_processing:
Adapters were trimmed using Trimmomatic
Trimmed sequencs were aligned to the bovine genome assembly using Hisat2
The aligned reads were sorted and merged using SAMtools
Peak calling of the aligned reads was made using MACS3 (3.0.0a5)
Genome_build: ARS-UCD 1.2 BosTau 9
Supplementary_files_format_and_content: peak files in BigWig

molecule: genomic DNA

organism: Bos taurus

source_name: skeletal muscle

growth_protocol: Bovine satellite cells were cultured in growth medium containing 10% fetal bovine serum for about a week.

extract_protocol:
Cells were lysed to release nuclei; nuclei were sonicated; and histone-DNA complexes were immunoprecipitated with H3K27ac antibody.
ChIP-seq libraries were prepared using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs), according to the supplier’s instructions.

treatment_protocol: Bovine satelltie cells cultured in growth medium were induced to differentiate into myotubes by replacing the growth medium with differentiation medium containing 2% horse serum.

tag: breed

value: Angus-crossbred

tag: cell type

value: muscle satellite cells

tag: antibody


title: wt18mb2

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

library_source: transcriptomic

data_processing:
FASTP: fastp -i R1-file.fastq.gz -I R2-file.fastq.gz -o processedfile_R1.fq.gz -O processedfile_R2.fq.gz -w 8 -h paste0(outDir,"QC/","fastp_",metaDF$Sample[i],".html") -j paste0(outDir,"QC/","fastp_",metaDF$Sample[i],".json")
Salmon: salmon quant -i salmonIndex -p 14 --numBootstraps 30 -1 paste0(filesDir,sampleData$ppR1[i]) -2 paste0(filesDir,sampleData$ppR2[i]) -l sampleData$libType[i] -o paste0(outMainDir,sampleData$Sample[i])
tximport: tximport(files, type="salmon", tx2gene = tx2gene, ignoreTxVersion = TRUE, dropInfReps=TRUE, txOut = TRUE)
DESeq2: DESeqDataSetFromTximport(txi, colData = samples, design = ~ Geno * Age * APpos)
count matrix export: write.csv(counts(dds1norm, normalized=TRUE),"DESeqDataSetFromTximport-ddsTxi1-NORMALIZED-geneLevel.csv")
Genome_build: mm10
Supplementary_files_format_and_content: .csv

molecule: total RNA

organism: Mus musculus

source_name: dissected embryonic CNS, midbrain

growth_protocol: Pregnant females under standard mouse housing conditions.

extract_protocol:
CNS dissected, forebrain and spinal cord kept at -80°C until RNA extraction with Qiagen Rneasy kit
NEBNext
RNA-seq Illumina HT2500 ~50M reads SE/PE 50-150bp unstranded

treatment_protocol: Embryos dissected at Embryonic day (E) 13.5 or 15.5.

tag: strain

tag: genotype

value: ctrl

tag: age

tag: ap-position

value: MB


title: wt18fb2

source_name: dissected embryonic CNS, forebrain

value: FB


title: WT LPS_PSA_6

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

country: Germany

institute: University Hospital of Bonn

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and base call file conversion.
Sequenced reads were corrected for low-quality sequence, then mapped to mm10 whole genome with the ensembl gene annotation version 101 using STAR v2.7.3a with standard parameters.
Read count generation was performed using featureCounts/Subread v2.0.0 ignoring multimapping reads.
Batch effects were removed with R [v4.0.4 (R Core Team, 2021)] in RStudio [v1.3.1093 (RStudio Team, 2020) using the RUVSeq package [v1.22.0 (Risso et al, 2014)].
Differential expression analysis was performed using DESeq2 [v1.28.1 (Love et al, 2014)] with the individual groups as contrasts. The log2‐fold change (log2FC) shrinkage was performed using apeglm to preserve large effects of true positives [v1.10.0 (Zhu et al, 2019)]. Transcript annotations were retrieved using the Bioconductor package org.Mm.eg.db [v3.11.4 (Carlson, 2020)] and plots were created using ggplot2 [v3.3.3 (Wickham, 2016)]. Pathway enrichment analyses were performed using clusterProfiler [v3.16.1 (Yu et al, 2012)] and reactomePA [v1.34.0 (Yu & He, 2016)] with log2FC ≥ 0.5 and adjusted p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Brains were collected and divided into two halves. Left hemispheres were immediately homogenized in 1 ml QIAzol (QIAGEN) and RNA was isolated using the RNeasy RNA isolation kit (Quiagen GmbH).
Library preparation was performed using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) with an input of 100 ng total RNA according to manufacturer's instructions.

treatment_protocol: Mice were intraperitoneally injected daily, and repeatedly over 4 consecutive days, with either 100 µl lipopolysaccharides (LPS) (1 µg/gbw/day, Enzo Life Science, Salmonella abortus equi S-form, Cat # ALX-581-009-002) or 100 µl PBS/day as vehicle control together with either 10 μg/gbw low molecular weight polysialic acid (polySia avDP20) or PBS as vehicle control.

tag: tissue

value: Brain

value: 3 months

value: wild type

tag: treatment

value: LPS injection

tag: treatment 2

value: PolySia avDP20 injection


title: wt18fb1


title: WT LPS_PSA_5


title: ChIP2 DD bovine satellite cells

value: during differentiation


title: BM cells, Case14_SNParray

type: genomic

city: Perugia

first: Danika

last: Di Giacomo

state: Perugia

address: S.Andrea delle fratte

department: Medicine and Surgery

country: Italy

institute: University of Perugia

description: Case_14 (UPN#546)

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis (ChAS) software with filters set at 400 Kb dimension for Copy Number Alterations (CNAs) and 10 Mb dimensions for copy neutral loss of heterozygosity (cnLOH). Our data refer to NetAffx Build 32.3 (hg19) database.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
LOG2 RATIO

label: Biotin

organism: Homo sapiens

source_name: Unsorted Bone Marrow Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells or periferal blood cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis.

value: Unsorted Bone Marrow Cells

tag: cytogenetics


title: WT LPS_PSA_4


title: BM cells, Case13_SNParray

description: Case_13 (UPN#606)


title: ChIP2 BD bovine satellite cells

value: before differentiation


title: ko15hb2

source_name: dissected embryonic CNS, hindbrain

value: cKO

value: HB


title: ChIP1 DD bovine satellite cells


title: ko15sc2

source_name: dissected embryonic CNS, spinal cord

value: SC


title: ko15sc1


title: WT LPS_PSA_3


title: WT LPS_PSA_2


title: dUTP strand-specific RNA-seq log-phase cells of Yarrowia lipolytica grown in BMW

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
For each of the 11 Ascomycota yeast species described above, the reads were merged and assembled using Trinity (Grabherr et al., 2011) (version ‘trinityrnaseq_r2012-05-18’) and mapped onto the assemblies to the respective genomes using GMAP (Wu and Watanabe, 2005). The Jaccard coefficient was used to join adjacent assemblies given enough connecting reads (a Jaccard cutoff of 0.35, the default in Trinity was used). Finally, upon mapping all of the reads to all of the merged assemblies, the Jaccard coefficient was used to clip assemblies which did not have enough support over a certain region. For each of the species, the reads were mapped to the genome sequence (Wapinski et al., 2007) using BLAT (Kent, 2002).
The RPKM used in the analysis described below were calculated for each transcript using RSEM (Li and Dewey, 2011), and only reads mapping to the sense mRNA strand were considered. Orthology between genes in different species was used as determined previously (Wapinski et al., 2007).
Genome_build: Various (from Wapinski et al, 2007, Nature)
Supplementary_files_format_and_content: tab delimited text containing all RPKM values for genes with S. cerevisiae orthologs

organism: Yarrowia lipolytica

source_name: log-phase cells

growth_protocol: We conducted RNA-seq on the following 11 Ascomycota yeast species: Candida albicans, Candida glabrata, Kluyveromyces lactis, Kluyveromyces waltii, Saccharomyces bayanus, Naumovozyma castellii, Saccharomyces cerevisiae, Schizosaccharomyces japonicus, Schizosaccharomyces octosporus, Schizosaccharomyces pombe, Yarrowia lipolytica. Each of the 11 species was grown in BMW medium, chosen to minimize cross-species growth differences, as previously described (Thompson et al., 2013). N. castellii was grown at 25℃ while the rest of the species were grown at 30℃.

extract_protocol:
RNeasy Midi or Mini Kits (Qiagen, Valencia, CA) were used to isolate total RNA from log-phase cells by mechanical lysis using the manufacturer instructions as previously described (Thompson et al., 2013).
dUTP strand-specific RNA-seq libraries were constructed as previously described (Yassour et al., 2010) with the following modifications. (1) The polyA+-selected RNA was fragmented in a 40 µl reaction containing 1x Fragmentation Buffer (Affymetrix) by heating at 80℃ for 4 minutes followed by cleanup via ethanol precipitation for all libraries (except Y. lipolytica, S. pombe, S. japonicus, and S. octosporus; for these species, the conditions described previously were used (Yassour et al., 2010)), followed by cleanup via 1.8x RNAClean XP beads (Beckman Coulter Genomics). (2) For C. glabrata, K. lactis, S. bayanus, S. pombe, S. japonicus, and S. octosporus libraries, the adapter ligation was performed overnight at 16℃. For the rest, this was done at 16 degrees for 2 hours as described previously (Yassour et al., 2010). (3) Normalization was carried out based on the cDNA input and pooling of selected Illumina barcoded-adaptor-ligated cDNA products followed by gel size selection occurred as follows: range of 275 to 575 bp for pooled C. albicans, K. polysporus, K. waltii, and N. castellii libraries, and 375 to 575 bp for C. glabrata, K. lactis, and S. bayanus libraries. For the other libraries, no pooling was performed before gel size-selection – range of 310 to 510 bp for Y. lipolytica and 350 to 550 bp for S. pombe, S. japonicus, and S. octosporus. (4) The final PCR product was purified by 1.8x AMPure XP beads (Beckman Coulter Genomics) followed by a second gel size-selection for the range of 300 to 575 bp for C. albicans, K. polysporus, K. waltii, and S. castellii libraries, but no gel size-selection was performed for the other libraries. The pooled final library was sequenced on one to four lanes of HiSeq2000 (Illumina) with 68 base (Y. lipolytica had 76 base) paired-end reads and 8 base index reads.

tag: media

value: BMW

tag: growth temperature (celcius)

tag: growth phase

value: log phase


title: WT LPS_PSA_1


title: WT LPS_6

value: PBS injection


title: ko15mb2


title: ko15mb1


title: WT LPS_5


title: ko15hb1


title: BM cells, Case9_SNParray

description: Case_9 (UPN#544)


title: MCF-3-24

city: Gdańsk

first: Marcin

last: Jakalski

address: Dębinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdańsk

description: MCF-3-24, replicate 1

data_processing:
Sequenced reads obtained from the sequencing facilty were quality-controlled with FastQC and mapped to H. sapiens genome (GRCh38, GENCODE release 30) using STAR aligner (version 2.6.0a)
Significantly differentially expressed genes (DEGs) were detected using R library edgeR. TMM normalization was applied to the raw count matrix after removing all genes not fulfilling the following criteria - at least 1 count per million in at least 2 samples
GLM statistics were applied duirng DEG testing, and the Benjamini-Hochberg correction of p-values was applied.
To select significant DEGs two filters were applied, i.e. FDR <0.05 and log2 fold change >=1
Genome_build: GRCh38 (GENCODE release 30)
Supplementary_files_format_and_content: tab-delimited text file including raw counts as generated by the STAR aligner

source_name: MCF-7 cell line treated with 3 µg/ml of 2b derivative, sampled after 24 hours

growth_protocol: Monolayer culture of MCF-7 cells was maintained in RPMI 1640 supplemented with 10% fetal bovine serum and penicillin-streptomycin mixture at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated using High Pure RNA Isolation Kit (Roche Diagnostics, Poland) according to manufacturer’s instruction. The concentration and quality of isolated RNA was determined using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Performed by RNA-seq Service (Macrogen, Seoul, Rep. of Korea)

treatment_protocol: Cells were seeded in 10 cm plates (1 x 106) and treated with 3 µg/ml 2b or DMSO for 6 or 24 h

tag: cell line

value: MCF-7 breast cancer cell line

tag: time

value: 2b treated


title: MCF-3-24b

description: MCF-3-24, replicate 2


title: MCF-3-6b

description: MCF-3-6, replicate 2

source_name: MCF-7 cell line treated with 3 µg/ml of 2b derivative, sampled after 6 hours


title: WT LPS_4


title: MCF-K24b

description: MCF-K24, replicate 2

source_name: MCF-7 cell line treated with DMSO (control), sampled after 24 hours

value: untreated (control)


title: WT LPS_2

value: Brain


title: MCF-3-6

description: MCF-3-6, replicate 1


title: BM cells, Case5_SNParray

description: Case_5 (UPN#605)


title: ko15fb2

value: FB


title: BM cells, Case3_SNParray

description: Case_3 (UPN#541)


title: MCF-K24

description: MCF-K24, replicate 1


title: BM cells, Case6_SNParray

description: Case_6 (UPN#543)


title: BM cells, Case4_SNParray

description: Case_4 (UPN#542)


title: ko15fb1


title: wt15hb2

value: ctrl


title: wt15sc2


title: wt15hb1


title: WT PSA_6

value: 3 months

value: wild type


title: BM cells, Case1_SNParray

description: Case_1 (UPN#540)


title: WT PSA_5

value: PolySia avDP20 injection


title: wt15sc1


title: wt15mb2

value: MB


title: wt15mb1


title: WT PSA_4


title: WT LPS_3

value: LPS injection


title: WT LPS_1


title: MCF-K6

description: MCF-K6, replicate 1

source_name: MCF-7 cell line treated with DMSO (control), sampled after 6 hours


title: WT PSA_3


title: WT PSA_2


title: wt15fb2


title: wt15fb1


title: WT PSA_1


title: MCF-K6b

description: MCF-K6, replicate 2


title: ChIP1 input

value: Angus-crossbred

value: muscle satellite cells


title: wt13sc2

value: SC


title: BM cells, Case10_SNParray

description: Case_10 (UPN#547)

value: Unsorted Bone Marrow Cells


title: WT PBS_5


title: WT PBS_6


title: NON_REP1_L002

city: Berkeley

first: Jamie

middle: H D

last: Cate

state: CA

address: 2151 Berkeley Way

department: Molecular and Cell Biology/Chemistry

institute: University of California

description: Samples EIF3D/L, EIF3F/E and EIF3G/E/F PAR-CLIP, nonactivated Jurkat, replicate 1

data_processing:
Library strategy: PAR-CLIP
PAR-CLIP replicate 1 library adaptors have 3' sequence TCGTATGCCGTCTTCTGCTTG. This is preceded by a 5-nt UMI barcode for PCR deduplication. Finally, each eIF3 subunit sample is indicated by a 5-nt barcode.
Barcoding for PAR-CLIP samples: PA=TCACTNNNNN  PB=TCATCNNNNN  PD=TCCACNNNNN  P1=TCCGTNNNNN  P2=TCACTNNNNN where NNNNN is the UMI for PCR deduplication
Clusters of overlapping sequence reads mapped against the human genome version hg38 were generated using the PARalyzer software (Pubmed ID: 21851591) incorporated into the PARpipe pipeline (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/, (Pubmed ID: 30517751) with the settings below. Binding sites were categorized using the Gencode GRCh38.p12 GTF annotations (gencode.v21.annotation.gtf), https://www.gencodegenes.org/human/.
Settings used for PARpipe: Conversion = T>C;   Minimum read count per group = 5;   Minimum read count per cluster = 7;   Minimum read count for kde = 3;   Minimum cluster size = 11;   Minimum conversion locations for cluster = 2;   Minimum conversion count for cluster = 2;   Minimum read count for cluster inclusion = 1;   Minimum read length = 20;   Maximum number of non conversion mismatches = 1;
Genome_build: hg38
Supplementary_files_format_and_content: Excel spreadsheets with tabulated data from the PAR-CLIP experiment or RNA-Seq experiment.

growth_protocol: Cells were maintained in RPMI 1640 Medium (ATCC modification) with 10% FBS (VWR Life Science Seradigm) and 0.01% Penicillin-Streptomycin (10,000 U/mL) (ThermoFisher).

extract_protocol:
The cells were pelleted by centrifugation at 100 x g for 15 min at 4 °C, and the pellet was resuspended in three volumes of NP40 lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM KCl, 2 mM EDTA, 0.5% Nonidet P-40 alternative, 0.5 mM dithiothreitol (DTT), 1 Complete Mini EDTA-free Protease Inhibitor Cocktail tablet (Roche)). The cell suspension was then incubated on ice for 10 min, passed through an 18G needle five times, and centrifuged at 13,000 x g for 15 min at 4 °C and RNAs were lightly digested by treatment with MNase (Thermo Scientific) at a final concentration of 0.05 U μl-1 for 20 min at 16 °C. For each PAR-CLIP assay 1000 μL of Dynabeads (Invitrogen) and 800 μL of anti-EIF3B antibody (Bethyl A301-761A) were used. The remaining steps of the PAR-CLIP analysis were performed exactly as described in (Pubmed ID: 25849773, 26463383) with the exception of using MNase at 5 U μL-1 for the on-bead digestion step.
PAR-CLIP cDNA libraries were sequenced on an Illumina HiSeq 2500 platform. To eliminate potential PCR biases during PAR-CLIP library preparation, a random bar code was introduced into the 3’ adapter and all the reads that matched the random barcode were collapsed into single reads.

treatment_protocol: 50 µM of 4-thiouridine was determined as non-toxic to Jurkat cells over the time course of the PAR-CLIP experiments. Jurkat cells seeded at 8 x 10^5 cells ml-1 were treated with 50 µM of 4-thiouridine for 7 hours. Then, the cells were treated with or without 1X Cell Stimulation Cocktail, containing PMA and IONO (ThermoFisher, Cat. #: 00-4970-93) for 5 hours. Cells were then crosslinked on ice with 365 nm UV irradiation at an energy dose of 0.2 J cm-2.

value: T cell leukemia

value: Jurkat Clone E6-1

tag: molecule

value: RNA crosslinked to eIF3


title: wt13hb1

value: HB


title: wt13mb2


title: WT PBS_2

value: PBS injection


title: wt13hb2


title: WT PBS_4

value: Brain


title: WT PBS_1


title: ACT_REP1_L001

description: Samples EIF3A/C/B  and EIF3B/C PAR-CLIP, activated Jurkat, replicate 1


title: wt13fb2

value: FB


title: WT PBS_3


title: Lung Basal cells DNp63 WT 3

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

description:
Basal_WT_3
SJW-RNA_WT-3

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample

source_name: ΔNp63fl/fl and ΔNp63Δ/Δ mice

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Sequencing libraries were prepared using the Illumina Truseq stranded total RNA kit using 1000 ng of RNA per sample.

treatment_protocol: Basal cells were isolated and grown on J2-3T3 feeders in MTEC-plus media. AT2 cells were isolated and grown with lung endothelial cells in BASC media. Cells were treated with either adenoviral-empty or adenoviral-cre for deletion of ΔNp63

value: lung

value: basal cells

value: DNp63 WT


title: R1593

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

data_processing:
The raw data was filtered with cutadapt (Martin, 2011) to remove adapter sequences, ambiguous (N) and low quality bases (Phred score < 25).
The filtered reads were mapped to a customized version of human reference genome (GRCh38 release 99) with STAR aligner (Dobin et al., 2013). The backbone of the plasmid sequences (pCXLE-gw) and gene annotations to the reference genome were added as a separate chromosome.
Gene expression was counted from read pairs mapping to exons using featureCount in Rsubreads (Liao, Smyth and Shi, 2019). Duplicates, chimeric and multi mapping reads were excluded, as well as reads with low mapping score (MAPQ < 10). The read count data were analyzed with DESeq2 (Love, Huber and Anders, 2014).
Genome_build: GRCh38.99
Supplementary_files_format_and_content: csv, read counts

molecule: polyA RNA

source_name: iPSC

growth_protocol: LCL cells were cultured in LCL medium (RPMI 1640 with GlutaMAX (Thermo Fisher Scientific) supplemented with 15% fetal bovine serum (FBS) (Life Technologies) and 1 µM sodium pyruvate). Human fibroblasts were cultured in fibroblast medium (Dulbecco’s Modified Eagle Medium (DMEM, Sigma-Aldrich, D6546) supplemented with 10% FBS, 2 mM GlutaMAX (Gibco) and 100 µl/ml penicillin-streptomycin (Sigma-Aldrich)). Human induced pluripotent stem cells (iPSC) were cultured in plates coated with Matrigel (Corning) in E8 (Gibco) or E8 Flex (Gibco) medium. The medium was changed every other day. All cells were kept in an incubator at 37 °C and 5% CO2 and were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted from 15 iPSC lines (Supplementary Table 6), and purified by NucleoSpin RNA Plus kit (Macherey-Nagel).
mRNA was enriched using oligo(dT) beads, fragmented, and converted to cDNA using random hexamers, followed by second-strand synthesis (Illumina), with terminal repair, ligation of A and adaptor sequences, and size selection and PCR enrichment. Library preparation and sequencing (RNA-seq, using Illumina PE150) was performed at Novogene as a service.

treatment_protocol: LCL were passaged the day before reprogramming. On the day of reprogramming (day 0), LCL were dissociated into single cells by trituration and washed in PBS (Thermo Fisher Scientific). Cells were electroporated with the Neon transfection system (Invitrogen) using R buffer. A total of 106 cells and 6 µg of plasmid mixture, containing 1.5 µg of dCas9-activator plasmid (Addgene #69535) and 4.5 µg of guide plasmids, were electroporated in a 100 µl tip using 1300 V, 10 ms and 3x pulses conditions. For conventional reprogramming, plasmid mixture containing 2 µg of each ectopic expression plasmids (Addgene #27077, #27078, #27080) (Okita et al. 2011) was transfected with the same electroporation conditions as CRISPRa. Electroporated LCL were then plated onto cell culture dishes in LCL growth medium supplemented with 0.25 mM sodium butyrate (NaB). The GFP expression from the episomal dCas9 activator-plasmid was visualized on the next day to verify a successful electroporation. After 3 days, the cells were passaged onto Matrigel coated plates. On day 4 after the transfections, the medium was changed to hES medium (DMEM/F12 with GlutaMAX (Life Technologies) supplemented with 20% KnockOut Serum Replacement (Life technologies), 0.0915 mM 2-mercaptoethanol (Life Technologies), 1x Non-Essential Amino Acids (Life Technologies) and 6 ng/mL bFGF (Sigma or Life Technologies)) supplemented with 0.25 mM NaB. The cell growth medium was changed to E8 medium at day 10 of reprogramming, and the unattached LCL were removed at this point. The cells were cultured until day 21, when the colonies were large enough so that they could be picked manually and plated on Matrigel coated wells in E8 medium. Media was changed every other day. Fibroblasts were seeded four days prior to the start of reprogramming. On the day of reprogramming (day 0) cells were detached as single cells from the culture plates with TrypLE Select (Gibco) and washed with PBS. Cells were electroporated using the Neon transfection system (Invitrogen) and reprogrammed by CRISPRa as described previously (Weltner et al. 2018). Conventional reprogramming was performed with the same transfection conditions as CRISPRa, only instead using the three ectopic expression plasmids mentioned previously (Addgene #27077, #27078, #27080). Electroporated fibroblasts were plated on Matrigel coated plates immediately after the transfections. Medium was changed every other day, and on day 4, the fibroblast medium was changed to a 50:50 ratio of fibroblast medium and hES medium, supplemented with 0.25 mM NaB. The cells were kept growing with medium changes every other day, until the formed iPSC colonies were picked manually and plated on Matrigel coated wells in E8 medium on day 21.

value: lymphoblastoid

tag: donor


title: R1599

tag: cell type


title: wt13mb1

value: ctrl

value: MB


title: R1639


title: wt13fb1


title: Lung Basal cells DNp63 WT 2

description:
Basal_WT_2
SJW-RNA_WT-2


title: R1638


title: ko13sc2

value: cKO


title: Lung Basal cells DNp63 WT 1

description:
Basal_WT_1
SJW-RNA_WT-1


title: Lung Basal cells DNp63 CRE 3

description:
Basal_CRE_3
SJW-RNA_CRE-3

value: DNp63 CRE


title: R1629


title: wt13sc1

value: SC


title: Lung Basal cells DNp63 CRE 2

description:
Basal_CRE_2
SJW-RNA_CRE-2


title: R1628


title: ko13hb2


title: R1604


title: NON_REP1_L001

description: Samples EIF3A/C/B  and EIF3B/C PAR-CLIP, nonactivated Jurkat, replicate 1


title: ko13hb1


title: ko13mb2


title: ko13sc1


title: ko13fb2


title: R16012


title: ACT_REP1_L002

description: Samples EIF3D/L, EIF3F/E and EIF3G/E/F PAR-CLIP, activated Jurkat, replicate 1


title: ko13fb1


title: R16117


title: R1614


title: ko13mb1


title: ChIP1 BD bovine satellite cells

tag: breed

value: Angus-crossbred

value: muscle satellite cells

value: before differentiation

tag: antibody


title: R1401

value: fibroblast

value: HFF


title: R141


title: ko11sc1

tag: strain

tag: genotype


title: ko11hb2

tag: age

tag: ap-position

value: HB


title: ko11sc2


title: R1398


title: ko11hb1


title: R1392


title: R1395


title: ko11mb1


title: SH-SY5Y cells expressing mCherry protein_Rep2 - mCherry2

city: Klong-luang

first: Jeeraphong

last: Thanongsaksrikul

state: Patumthani

country: Thailand

institute: Thammasat University

description: Background control

data_processing:
Illumina CASAVA v1.8 was used for base-calling
Sequencing reads were trimmed for adaptor sequence, low-quality sequences, then mapped to GRCh38 human reference genome using TopHat2 v2.0.12/Bowtie v2.2.3. Final transcriptome was reconstructed using Cufflink v2.2.1 and blasted using NCBI BLAST v2.2.28
Sequencing reads fell onto each trasncripts were counted using HTSeq v0.6.1 and normalized abundance measurements by fragment per kilibase per million reads (FPKM)
Genome_build: GRCh38
Supplementary_files_format_and_content: Individual *.txt file includes gene ID, chromosome, strand, start position, end position, length, FPKM values, and associated gene name for each sample

source_name: SH-SY5Y cells culture

growth_protocol: SH-SY5Y cells were seeded in 6-well plate (5x10^5 cells/well) and maintained in DMEM/F-12 supplemented with 10% FBS, L-glutamine, and penicillin/streptomycin until reaching 50-60% cell confluent.

extract_protocol:
RNA samples were havested and extracted at 6 hours post-transfection using RNeasy mini kit (QIAGEN).
Libraries were constructed according to NEBNext® Ultra™ RNA library prep kit for Illumina®

treatment_protocol: SH-SY5Y cells were transfected with pLVX::FLAG-2B-mCherry, or pLV-mCherry using Lipofectamine 3000 transfection kit.

value: ATCC CRL-2266

tag: stain/plasmid

value: Addgene plasmid #36084

tag: transfection

value: pLV-mCherry transfection


title: SH-SY5Y cells expressing mCherry protein_Rep3 - mCherry3

description: Background control


title: Untransfected SH-SY5Y cells_Rep2 - SHSY5Y2

description: Normal control

value: Normal growth


title: SH-SY5Y cells expressing EV-A71 2B protein fused with mCherry and FLAG tag protein_Rep2 - 2BmCherry2

description: Experiment

value: EV-A71 subgenotype B5

value: pLVX::FLAG-2B-mCherry transfection


title: SH-SY5Y cells expressing mCherry protein_Rep1 - mCherry1

description: Background control


title: Untransfected SH-SY5Y cells_Rep1 - SHSY5Y1

description: Normal control


title: Untransfected SH-SY5Y cells_Rep3 - SHSY5Y3

description: Normal control


title: SH-SY5Y cells expressing EV-A71 2B protein fused with mCherry and FLAG tag protein_Rep3 - 2BmCherry3

description: Experiment


title: ko11fb2

value: FB


title: SH-SY5Y cells expressing EV-A71 2B protein fused with mCherry and FLAG tag protein_Rep1 - 2BmCherry1

description: Experiment


title: ko11mb2

value: MB


title: ko11fb1

value: cKO


title: RNA_kdlr_pos_3_TAA

city: Warsaw

first: Michal

last: Pawlak

address: Trojdena 4

institute: International Institute of Molecular and Cell Biology

data_processing:
Raw RNA-seq and ATAC-seq reads were quality checked using Fastqc (0.11.8)
Adapters were removed using Cutadapt (1.18)
Reads quality filtering was performed using SAMtools (1.9)
RNA-seq reads were aligned to the zebrafish reference genome (GRCz11) using STAR (2.6)
Gene counts were calculated by using R (GenomicRanges Bioconductor package) and tranformed to regularized-logarithm (DESeq2 Bioconductor package)
Genome_build: GRCz11
Supplementary_files_format_and_content: comma-separated file containing normalized read counts (rlog) of Ensembl-annotated genes organized in columns for each sample separately

organism: Danio rerio

source_name: FACS-sorted liver cells

growth_protocol: Zebrafish transgenic lines Tg(fabp10a:dsRed), Tg(hand2:EGFP) and Tg(kdrl:ras-mCherry)  in AB wild-type background were maintained in the IIMCB zebrafish facility (License no. PL14656251) according to standard procedures.

extract_protocol:
For RNA sequencing 100,000 of fluorescent liver cells were sorted directly to TRIzol LS (Thermo Fisher Scientific, USA). After ethanol precipitation RNA was depleted of DNA by using DNase I treatment and purified on columns by using RNA Clean & Concentrator™-5 (Zymo Research, USA)
Sequencing libraries were performed from total RNA by using SMARTer low input RNA Kit (Clontech), according to manufacturer protocol.

treatment_protocol: Adult females were anesthetized with MS-222 (Sigma-Aldrich, Germany) as previously described  and injected intraperitoneally with 500 mg/kg thioacetamide (TAA) or sterile water as a control 6 times over the course of 2 weeks.

tag: treatment

value: TAA

tag: genetic background

value: AB

tag: fluorescence

value: mCherry positive

tag: Sex

value: female

value: FACS-sorted liver cells


title: wt11sc2

value: ctrl

value: SC


title: RHLA 2

type: RNA

city: Rio de Janeiro

first: Michele

middle: Rocha

last: Castro

state: Rio de Janeiro

address: Av. Athos da Silveira Ramos, nº 149, A537 and A541 - Technology Center, University City - Rio de Janeiro - RJ

department: Department of Biochemistry - Institute of Chemistry

country: Brazil

institute: Federal University of Rio de Janeiro (UFRJ) - Rio de Janeiro - Brazil

description: RMA expression value derived from Expression Console software

hyb_protocol: The biotinylated cRNA was subsequently hybridized to a GeneChip® P. aeruginosa Genome Array (Affymetrix, CA, USA).

scan_protocol: The GeneChip arrays were washed and stained according to the manufacturer’s protocols and scanned using a GeneChip® Scanner 3000 (Affymetrix)

data_processing: Affymetrix Expression Console Software version 1.0 was used to create summarized expression values (CHP-files). The Robust Multichip Analysis (RMA) algorithm was applied. The data were analyzed with TAC software.

label: biotin

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa strain (PAO1) rhlA-knockout derivative (ΔrhlA::GmR)

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

growth_protocol: P. aeruginosa strains used in the study were stored at -80 °C in Lysogeny Broth medium (LB; 10.0 g/L Tryptone, 5.0 g/L Yeast Extract, 5.0 g/L NaCl; Sigma-Aldrich, St. Louis, USA). The strains were grown in 250 mL erlenmeyer flasks containing 100 mL of LB medium, until the stationary growth phase was reached (OD600 2.0), with shaking (170 rpm), at 30 °C. An aliquot of the culture was collected for total RNA extraction.

extract_protocol: Total RNA from all cell lines used in this study was obtained using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions.

treatment_protocol: not applicable


title: RHLA 1


title: App[NL-G-F/NL-G-F]•Mutyh-/- mouse, Biological replicate 2

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
CEL files were imported into the Transcriptome Analysis Console (TAC) Software 4.0 and CHP files were generated.
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

source_name: Hippocampus of 6-month-old App[NL-G-F/NL-G-F]•Mutyh-/- mouse

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 6 months of age.

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene) according to the manufacturers’ instructions.

treatment_protocol: Each mouse was anesthetized, transcardially perfused with saline, and hippocamppus was isolated quickly, preserved at –80°C until RNA preparation.

tag: genotype/variation

value: App[NL-G-F/NL-G-F]•Mutyh-/-

value: Female

value: 6 months

tag: tissue

value: Hippocampus


title: App[NL-G-F/NL-G-F]•Mutyh-/- mouse, Biological replicate 1


title: RNA_kdlr_pos_3_ctrl

value: sterile water


title: RHLA


title: PAO 1-2

source_name: wild-type P. aeruginosa strain (PAO1)

value: wild-type


title: wt11hb2

value: HB


title: RNA_kdlr_pos_2_ctrl


title: RNA_kdlr_pos_2_TAA


title: App[NL-G-F/NL-G-F]•Mutyh-/- mouse, Biological replicate 3


title: wt11sc1


title: RNA_kdlr_pos_1_ctrl


title: wt11mb2

source_name: dissected embryonic CNS, midbrain


title: wt11hb1


title: 36O_2

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

description:
Mature plants standard growth conditions
306.R2.bed

data_processing:
Raw sequences cleaned with CutAdapt and mapped to TAIR10 Arabidopsis genome with Bowtie2 (Langmead and Salzberg, 2012).
Data were sorted and indexed with SAMtools (Li et al., 2009).
MACS2 (Zhang et al., 2008) was used for peak-calling and to calculate fold enrichments and q values using inputs as control to detect enriched peaks in the IPs.
Peaks from two biological replicates with an FDR < 0.01 were intersected using BEDTools (Quinlan and Hall, 2010), and only peaks that exhibited intersection beyond the two replicates were selected.
Peaks were then attributed to gene models within 1 kb upstream the TSS using PAVIS2 (Huang W et al., 2013).
Genome_build: TAIR10 (Araport11 annotation)
Supplementary_files_format_and_content: BED files with peak location, peak summit, p value and q value of the identified peaks

organism: Arabidopsis thaliana

source_name: L306 Replica 2 Output

growth_protocol: Arabidopsis plants were grown in standard condition to maturity in soil (a 2:1:1 mix of peat moss, vermiculite, and perlite) at 22°C in a long-day photoperiod (16/8 h).

extract_protocol: The chromatin extraction and in vitro double crosslinking were performed as previously described (Milhindos et al., 2019). Chromatin was then sonicated using a Bioruptor (Diagenode) for 9 cycles (30’’on/30’’off each). A 100 µL aliquot of each sample and replicate were kept as input. For immunoprecipitation, samples were incubated wit anti-GFP antibody (ab290; Abcam) and magnetic DynabeadsTM Protein A (ThermoFisher Scientific). Finally, chromatin was eluted, proteins were digested with Proteinase K, and DNA was purified with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.

treatment_protocol: Inflorescences were collected from the main stem when it developed 5-10 flowers. Open/anthesis flowers as well as 2-3 older floral buds were removed before flash freeze in liquid nitrogen. Two independent biological replicates (Rep 1 and Rep2) for each genotype were recollected (1.8 g each) from pGAI:gai∆17-3xYPet, pGAI:gai∆17-3xYPet cuc2-1, and non-transgenic

tag: ecotype

value: Landsberg erecta (Ler)

value: Inflorescences

value: anti-GFP antibody


title: RNA_kdlr_neg_3_ctrl

value: mCherry negative


title: wt11fb1

source_name: dissected embryonic CNS, forebrain

value: FB


title: wt11fb2


title: 36I_2

source_name: L306 Replica 2 Input


title: LEO_2

description:
Mature plants standard growth conditions
Ler.R2.bed

source_name: Ler Replica 2 Output

value: Ler


title: RNA_kdlr_neg_2_ctrl

value: AB

value: female


title: RNA_kdlr_neg_1_ctrl

value: FACS-sorted liver cells


title: CCO_1

description:
Mature plants standard growth conditions
306.cuc2.R1.bed

source_name: L306 cuc2-1 Replica 1 Output

value: pGAI:gaidelta17-3xYPet cuc2-1


title: CCO_2

description:
Mature plants standard growth conditions
306.cuc2.R2.bed

source_name: L306 cuc2-1 Replica 2 Output


title: RNA_hand_pos_3_TAA

value: TAA

value: EGFP positive


title: CCI_2

source_name: L306 cuc2-1 Replica 2 Input


title: 96ET3

city: Nashville

first: Ian

last: Macara

address: 465 21st Ave South

institute: Vanderbilt University

data_processing:
Sample 1-10
Illumina HiSeq 3000 for basecalling
reads were filtered, sorted and aligned to the mm9 genome assembly
Data filtered with a p-value of either <.05, and FC >2 or <0.005
Sample 11-12
Illumina Nextseq 500 for basecalling
reads were filtered, sorted and aligned to the mm9 genome assembly using inDrop pipeline
Data filtered with a p-value of either <.05
Genome_build: mm9
Supplementary_files_format_and_content: h5ad
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Myoepithelial cells

growth_protocol: All cells were freshly sorted except for sample 12 - cultured for 72 hours

extract_protocol:
Mammary tissue was processed with Collagenase and Trypsin for single cells, stained with antibodies and FACS sorted.
Sample 1-Sample 10: libraries constructed using Illumina TruSeq RNA v2 Sample preparation protocol, Sample 11 and 12: libraries constructed as per Kelin et al 2015's CEL-Seq workflow.

treatment_protocol: Sample 12 was cultured for 72 hours

tag: developmental stage

value: untreated


title: 36O_1

description:
Mature plants standard growth conditions
306.R1.bed

source_name: L306 Replica 1 Output


title: wt11mb1

value: ctrl

value: MB


title: PAO1

value: wild-type


title: LEI_2

source_name: Ler Replica 2 Input


title: PAO 1-1


title: CCI_1

source_name: L306 cuc2-1 Replica 1 Input


title: 96ET2

source_name: s-shipGFP+ cap cells


title: RNA_hand_pos_3_ctrl

source_name: FACS-sorted liver cells

value: sterile water

tag: cell type


title: RNA_hand_pos_2_TAA


title: 96ET1


title: 36I_1

source_name: L306 Replica 1 Input

value: Landsberg erecta (Ler)


title: RNA_kdlr_pos_1_TAA

value: mCherry positive


title: RNA_hand_pos_2_ctrl


title: LEO_1

description:
Mature plants standard growth conditions
Ler.R1.bed

source_name: Ler Replica 1 Output

value: Inflorescences

value: anti-GFP antibody


title: RNA_hand_pos_1_TAA


title: LEI_1

source_name: Ler Replica 1 Input


title: 3261IGM23


title: RNA_hand_pos_1_ctrl


title: 3261IGM22


title: 96ET4


title: RNA_hand_neg_2_ctrl

value: EGFP negative


title: 3261IGM21


title: 3261IGM20


title: dMyc OE rep 2

city: Providence

first: Jackson

middle: R

last: Taylor

state: RI

address: 185 Meeting St, MCB G-L 163

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

description:
Direct-zol RNA MicroPrep Kit (Zymo)
TruSeq RNA Library Prep Kit v2 (Illumina)
MYC.2

data_processing:
Illumina Casava1.7 software used for basecalling.
Transcript abundance was quantified using Salmon and the tximport Bioconductor package was used to summarize by gene.
Genome_build: dm6
Supplementary_files_format_and_content: comma-delimited text files include TPM (transcripts per million) values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: Flies were collected within 24 hours of eclosion and aged and maintained on 15% dextrose/15% yeast/2% agar food at 25 °C on a 12-h light/dark cycle at 60% relative humidity.

extract_protocol:
Fat bodies were dissected in ice-cold PBS, flash frozen on dry ice, and RNA was harvested using RNAqueous™-Micro Total RNA Isolation Kit (Ambion) , with optional DNase treatment performed. Ovation Universal RNA-seq System (Nuegen) was used with 50 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Tecan and Illumina protocols. Library preparations with Illumina TruSeq RNA Library Prep Kit were performed by GENEWIZ.

treatment_protocol: dSirt6 and dMyc were overexpressed using the GAL4-UAS system

value: Fat body

value: Adult day 10

value: tubulinGeneSwitch>w1118; UAS-dMyc

value: dMyc overexpression


title: dMyc + S6 OE rep 1

description:
Direct-zol RNA MicroPrep Kit (Zymo)
TruSeq RNA Library Prep Kit v2 (Illumina)
MYC.S6.1

value: tubulinGeneSwitch> UAS-dSirt6; UAS-dMyc

value: dMyc + dSirt6 overexpression


title: Control for dMyc OE rep 2

description:
Direct-zol RNA MicroPrep Kit (Zymo)
TruSeq RNA Library Prep Kit v2 (Illumina)
C.2

value: tubulinGeneSwitch>w1118; w1118

value: Control


title: RNA_hand_neg_1_ctrl

value: AB

value: female

value: FACS-sorted liver cells


title: 3261IGM19

value: untreated


title: RNA_fabp_pos_3_ctrl

value: sterile water

value: dsRed positive


title: si-MCC-2

city: Nanjing

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

country: China

institute: Jinling Hospital, Nanjing University School of Medicine

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.4) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.4).
Stringtie was used to count the reads numbers mapped to each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human podocyte cell line

growth_protocol: Immortalized human podocytes from Dr. Saleem M’s laboratory (University of Bristol, Bristol, UK) were cultured with RPMI1640 medium supplemented with 10% FBS, 1% Pen/Strep and 1% ITS at 33°C in 5% CO2 incubator for growth, followed by trypsinization, replating and culture at 37°C for 10 days to obtain differentiated cells.

extract_protocol:
The cells were homogenized with Trizol (Invitrogen) and the total RNA was extracted following the manual instruction.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated.

treatment_protocol: Then the differentiated podocytes were transfected with siRNA against MCC or left untreated with only vehicle for 24 hours.

value: Human podocyte cell line

value: si-MCC


title: Control for dMyc OE rep 1

description:
Direct-zol RNA MicroPrep Kit (Zymo)
TruSeq RNA Library Prep Kit v2 (Illumina)
C.1


title: si-MCC-3


title: RNA_fabp_pos_2_TAA

value: TAA


title: si-MCC-1


title: 3261IGM24


title: RNA_fabp_pos_2_ctrl


title: 40 day S6 OE rep 3

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
O.S6.3

value: Fat body

value: Adult day 40

value: Aged (40 days) + dSirt6 overexpression


title: 40 day S6 OE rep 2

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
O.S6.2

value: Adult day 10


title: dMyc + S6 OE rep 2

description:
Direct-zol RNA MicroPrep Kit (Zymo)
TruSeq RNA Library Prep Kit v2 (Illumina)
MYC.S6.2

value: tubulinGeneSwitch> UAS-dSirt6; UAS-dMyc


title: scramble-3

value: scramble


title: RNA_fabp_pos_1_TAA


title: RNA_hand_neg_3_ctrl

value: EGFP negative


title: 40 day S6 OE rep 1

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
O.S6.1


title: scramble-2


title: RNA_fabp_pos_1_ctrl


title: scramble-1


title: RNA_fabp_neg_3_ctrl

value: dsRed negative


title: dMyc OE rep 1

description:
Direct-zol RNA MicroPrep Kit (Zymo)
TruSeq RNA Library Prep Kit v2 (Illumina)
MYC.1

value: tubulinGeneSwitch>w1118; UAS-dMyc

value: dMyc overexpression


title: RNA_fabp_pos_3_TAA

value: AB

value: female

value: FACS-sorted liver cells


title: 40 day Control rep 1

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
O.C.1

value: tub-gal4>w1118 (background control for dSirt6 overexpression)

value: Aged (40 days)


title: RNA_fabp_neg_2_ctrl

value: sterile water


title: 40 day Control rep 3

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
O.C.3


title: sample 2 in Imper group

city: Quzhou

first: Minchao

last: Lv

state: Zhejiang

address: No. 100, Mingjiang Avenue

department: Department of Orthopedics

institute: The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital

data_processing:
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min.
the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）.
An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.
Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.
The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Genome_build: Ensembl_v96(ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/)
Supplementary_files_format_and_content: text files including FPKM values of each sample

source_name: 143B_125 μM imperatorin for 24 h

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: human osteosarcoma cell-line 143B

value: 125 μM IMP 24h


title: 40 day Control rep 2

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
O.C.2

value: Fat body

value: Adult day 40


title: sample 3 in Imper group


title: RNA_fabp_neg_1_ctrl


title: sample 1 in Imper group


title: ATAC_kdlr_pos_3_TAA

description: tagmented genomic DNA

data_processing:
Raw ATAC-seq reads were quality checked using Fastqc (0.11.8)
Adapters were removed using Cutadapt (1.18)
Bowtie2 (2.3.4.3) was used to map ATAC-seq reads to the genome
Peaks of chromatin open regions were called by using MACS2 (2.1.0.2) (Zhang et al. 2008) with parameters --nomodel --shift -100 --extsize 200 --broad -g 1.21e9 -q 0.05 -B --keep-dup all. Nucleosome free regions were identified as previously described (Buenrostro et al. 2013).
For each of the three replicates per base enrichment p-value track was calculated using Poisson test. Than p-values tracks from replicates were combined using Fisher method yielding track of per base Χ2 statistics that was used to calculate combined p-values. After Benjamini - Hochberg multiple testing correction, peaks were called on obtained tracks with q-value cutoff of 1e-5. Further obtained BED files were manipulated  using Bedtools (2.27.1) to construct reference peak list.
Genome_build: GRCz11
Supplementary_files_format_and_content: bedGRAPH files from MACS2; Peak bed files from MACS2

extract_protocol:
For ATAC-seq 60,000  cells from zebrafish FACS-sorted liver cells were sorted to Hank’s solution (1X HBSS, 2mg/mL BSA, 10 mM Hepes pH 8.0), centrifuged for 5 minutes at 500x g and prepared for chromatin tagmentation as previously described (Buenrostro et al. 2013).
NEBNext High-Fidelity 2 × PCR Master Mix (New England Biolabs, USA) and custom HPLC-purified primers containing Illumina-compatible indexes were used to prepare DNA sequencing libraries. DNA libraries were purified with Agencourt AMPure XP PCR purification beads (Beckman Coulter, USA) and DNA fragment distribution was assessed by using D1000 ScreenTape and Agilent 2200 TapeStation system (Agilent Technologies, USA). KAPA library quantification kit (Kapa Biosystems, USA) was used for qPCR-based quantification of the libraries obtained. Paired-end sequencing (2×75bp reads) was performed with NextSeq500 sequencing system (Illumina, USA).

value: TAA

value: endothelial cells

value: mCherry positive


title: 10 day S6 OE rep 4

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.S6.4

value: dSirt6 overexpression


title: sample 3 in Control group

value: non (control)


title: 10 day S6 OE rep 3

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.S6.3


title: 10 day S6 OE rep 2

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.S6.2

value: Adult day 10


title: ATAC_kdlr_pos_2_ctrl

description: tagmented genomic DNA


title: 10 day S6 OE rep 1

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.S6.1


title: 10 day Control rep 4

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.C.4

value: Control


title: 10 day Control rep 3

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.C.3


title: ATAC_kdlr_pos_1_TAA

description: tagmented genomic DNA

value: AB


title: ATAC_kdlr_pos_2_TAA

description: tagmented genomic DNA

value: female


title: J60-1

city: Beijing

first: Yan

last: WU

state: Beijing

address: No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

data_processing:
Sequencing reads were trimmed and filtered by Trimmomatic.
Sequencing reads were aligned with STAR to genome reference GRCh38.p13 for human.
Intron-level and exon-level read count of each gene were calculated with TPMCalculator for each sample.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tsv files containing intron-level and exon-level read counts of all genes from TPMCalculator.

source_name: Jurkat T-cells

growth_protocol: Cells were cultivated in RPMI-1640 Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at the concentration between 5x10^5 and 5x10^6 cells/mL and incubated under 37 °C and 5% CO2.

extract_protocol:
Cells were centrifuged at 300 xg for 1 min and the supernatant was replaced by 1 mL Trizol. Gently mixed cell lysate was then flash-frozen in liquid nitrogen and MagZol Reagent Kit was used for RNA extraction.
VAHTS mRNA-seq V3 Library Prep Kit for Illumina was used for library construction. Sequencing was performed on Illumina NovaSeq 6000 instrument in PE150 mode.

treatment_protocol: Cells were re-plated at the density of 5x10^6 cells/mL in 1 mL media and rested for 30 min before stimulation. Then cells were stimulated with 50 ng/mL PMA and 1 uM Ionomycin for different durations, namely 3, 6, 9, 12, 15, 30, 45, and 60 min. Note that cells without stimulation were also collected and annotated as 0 min.

value: Jurkat, Clone E6-1

value: PMA + Ionomycin

tag: treatment time

value: 60 min

tag: replicate


title: ATAC_hand_pos_3_TAA

description: tagmented genomic DNA

tag: genotype

value: hepatic stellate cells

value: EGFP positive

value: FACS-sorted liver cells


title: J60-2


title: 10 day Control rep 2

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.C.2

tag: strain

value: Fat body

tag: age

value: tub-gal4>w1118 (background control for dSirt6 overexpression)


title: 10 day Control rep 1

description:
RNAqueous™-Micro Total RNA Isolation Kit (Ambion)
Ovation Universal RNA-seq System (Tecan)
Y.C.1


title: ATAC_kdlr_pos_1_ctrl

description: tagmented genomic DNA

value: sterile water


title: ATAC_hand_pos_3_ctrl

description: tagmented genomic DNA


title: ATAC_hand_pos_2_ctrl

description: tagmented genomic DNA


title: dUTP strand-specific RNA-seq log-phase cells of Schizosaccharomyces pombe grown in BMW

organism: Schizosaccharomyces pombe

source_name: log-phase cells

tag: media

value: BMW

tag: growth temperature (celcius)

tag: growth phase

value: log phase


title: IR8C3

city: Ann Arbor

first: Paul

last: Tang

state: MI

address: 2800 Plymouth Road

department: Cardiac surgery

institute: University of Michigan

data_processing:
The transcript abundance was quantified using Kallisto with default parameters. The kallisto index was generated using RN6 cDNA fasta file from ensembl.
Genome_build: rn6

organism: Rattus norvegicus

source_name: heart tissue

extract_protocol:
Total RNA was isolated using Trizol followed the manufactor's protocol. RNA was then examined by Bioanalyzer RNA nano chip.
RNA with RIN>8 was used for library contrusction. RNA libraries were prepared using NEB Ultra II RNA library prep kit and amplified with single end primers. Libraries were sequenced with illumina H4K (50SE).

value: heart

tag: treatment

value: ischemic reperfusion + sodium octanoate (8C)


title: ATAC_kdlr_pos_3_ctrl

description: tagmented genomic DNA

tag: genetic background

value: endothelial cells

tag: fluorescence

value: mCherry positive


title: J45-1

value: 45 min


title: dUTP strand-specific RNA-seq log-phase cells of Saccharomyces cerevisiae grown in BMW

data_processing:
For each of the 11 Ascomycota yeast species described above, the reads were merged and assembled using Trinity (Grabherr et al., 2011) (version ‘trinityrnaseq_r2012-05-18’) and mapped onto the assemblies to the respective genomes using GMAP (Wu and Watanabe, 2005). The Jaccard coefficient was used to join adjacent assemblies given enough connecting reads (a Jaccard cutoff of 0.35, the default in Trinity was used). Finally, upon mapping all of the reads to all of the merged assemblies, the Jaccard coefficient was used to clip assemblies which did not have enough support over a certain region. For each of the species, the reads were mapped to the genome sequence (Wapinski et al., 2007) using BLAT (Kent, 2002).
The RPKM used in the analysis described below were calculated for each transcript using RSEM (Li and Dewey, 2011), and only reads mapping to the sense mRNA strand were considered. Orthology between genes in different species was used as determined previously (Wapinski et al., 2007).
Genome_build: Various (from Wapinski et al, 2007, Nature)
Supplementary_files_format_and_content: tab delimited text containing all RPKM values for genes with S. cerevisiae orthologs

organism: Saccharomyces cerevisiae

extract_protocol:
RNeasy Midi or Mini Kits (Qiagen, Valencia, CA) were used to isolate total RNA from log-phase cells by mechanical lysis using the manufacturer instructions as previously described (Thompson et al., 2013).
dUTP strand-specific RNA-seq libraries were constructed as previously described (Yassour et al., 2010) with the following modifications. (1) The polyA+-selected RNA was fragmented in a 40 µl reaction containing 1x Fragmentation Buffer (Affymetrix) by heating at 80℃ for 4 minutes followed by cleanup via ethanol precipitation for all libraries (except Y. lipolytica, S. pombe, S. japonicus, and S. octosporus; for these species, the conditions described previously were used (Yassour et al., 2010)), followed by cleanup via 1.8x RNAClean XP beads (Beckman Coulter Genomics). (2) For C. glabrata, K. lactis, S. bayanus, S. pombe, S. japonicus, and S. octosporus libraries, the adapter ligation was performed overnight at 16℃. For the rest, this was done at 16 degrees for 2 hours as described previously (Yassour et al., 2010). (3) Normalization was carried out based on the cDNA input and pooling of selected Illumina barcoded-adaptor-ligated cDNA products followed by gel size selection occurred as follows: range of 275 to 575 bp for pooled C. albicans, K. polysporus, K. waltii, and N. castellii libraries, and 375 to 575 bp for C. glabrata, K. lactis, and S. bayanus libraries. For the other libraries, no pooling was performed before gel size-selection – range of 310 to 510 bp for Y. lipolytica and 350 to 550 bp for S. pombe, S. japonicus, and S. octosporus. (4) The final PCR product was purified by 1.8x AMPure XP beads (Beckman Coulter Genomics) followed by a second gel size-selection for the range of 300 to 575 bp for C. albicans, K. polysporus, K. waltii, and S. castellii libraries, but no gel size-selection was performed for the other libraries. The pooled final library was sequenced on one to four lanes of HiSeq2000 (Illumina) with 68 base (Y. lipolytica had 76 base) paired-end reads and 8 base index reads.


title: IR8C1


title: J30-1

value: 30 min


title: IR8C2


title: J15-1

value: Jurkat, Clone E6-1

value: 15 min


title: sample 2 in Control group

value: human osteosarcoma cell-line 143B

value: non (control)


title: ATAC_hand_pos_1_ctrl

description: tagmented genomic DNA

value: AB

value: hepatic stellate cells

value: EGFP positive

tag: Sex

value: female


title: J12-2

value: PMA + Ionomycin

value: 12 min


title: ATAC_hand_pos_1_TAA

description: tagmented genomic DNA

value: TAA

tag: tissue

value: FACS-sorted liver cells


title: J45-2


title: J12-1


title: ATAC_fabp_pos_3_TAA

description: tagmented genomic DNA

value: hepatocytes

value: dsRed positive


title: PTG WT ZT8 rep2 [#49 ctrl 14:30]

city: Copenhagen

first: Søren

last: Egstrand

address: Blegdamsvej 9

department: Depart. of Nephrology

country: Denmark

institute: Rigshospitalet

data_processing:
NovaSeq System Software generated base calls
Sequenced reads were alligned to the mm10 genome using STAR (version 2.7.8a+galaxy0)
Unambigously alligned reads were counted by featureCounts (version 2.0.1+galaxy1)
Genes with less then 10 counts in total were excluded
Counts were then normalized for sequencing depth and RNA composition using the median of ratios method employed in DESeq2 (version 1.30.1).
Counts were transformed using the rlog transformation function employed in DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Parathyroid glands

growth_protocol: Mice with parathyroid gland-specific deletion of Bmal1 (Arntl) was generated using the Cre-LoxP recombination system by crossing B6.129S4(Cg)-Arntltm1Weit/J mice in which LoxP sequences are inserted into the flanking regions of exon 8 of the Bmal1 gene (Bmal1flox/flox) with 129;FVB-Tg(PTH-cre)4167Slib/J (PTHcre). This novel genotype: PTHcre;Bmal1flox/flox is the "Knockout" which have human PTH promoter controlled Cre-recombinase activity, resulting in excision of the Bmal1 exon 8, restricted to the parathyroid glands. The Bmal1flox/flox littermates without recombinase activity constitutes the "Wildtype".

extract_protocol:
Parathyroid glands were harvested, flash frozen in liquid nitrogen and store at -80 degrees. Samples are pooled from two male mice. Total RNA was isolated using Allprep DNA/RNA minikit (Qiagen, Hilden, Germany) and purified using Qiagen RNase-Free DNase Set (Qiagen, Hilden, Germany) on a QIAcube Connect (Qiagen, Hilden, Germany). RNA quality was examined using an Agilent Technologies 2100 Bioanalyzer. Library preparation was done using a TruSeq Stranded Total RNA Gold kit with dual adaptor indexing strategy; IDT for Illumina – TruSeq RNA UD Indexes (Illumina, San Diego, USA). The library was diluted and pooled to a concentration of 2 nM according to the procedure of “Denature and Dilute Libraries Guide of Illumina Novaseq 6000” and final loading concentration was 400 pM.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples from each genotype was harvested at 4-hour interval over 24h as indicated.

value: Bma1 Wildtype

tag: zeitgebertime

value: Male

value: 11 weeks

value: Parathyroid glands


title: PTG KO ZT8 rep3 [#46 KO 14:30]

value: Bma1 Knockout


title: IR3

value: heart

value: ischemic reperfusion


title: J30-2

value: Jurkat, Clone E6-1

value: 30 min


title: PTG KO ZT4 rep3 [#45 KO 10:30]


title: IR1


title: ATAC_hand_pos_2_TAA

description: tagmented genomic DNA

value: AB

value: hepatic stellate cells

value: EGFP positive


title: J9-2

value: PMA + Ionomycin

value: 9 min


title: IR2


title: Sham3

value: sham


title: ATAC_fabp_pos_2_TAA

description: tagmented genomic DNA

value: TAA

value: hepatocytes

value: female

value: FACS-sorted liver cells


title: PTG WT ZT16 rep5 [#43 ctrl 22:30]

value: Bma1 Wildtype

value: Male

value: 11 weeks


title: Sham2

value: heart


title: sample 1 in Control group

value: human osteosarcoma cell-line 143B

value: non (control)


title: ATAC_fabp_pos_2_ctrl

description: tagmented genomic DNA

value: sterile water

value: dsRed positive


title: ATAC_fabp_pos_3_ctrl

description: tagmented genomic DNA

value: AB


title: PTG KO ZT16 rep1 [#44 KO 22:30]

value: Bma1 Knockout

value: Parathyroid glands


title: Sham1


title: J6-1

value: Jurkat, Clone E6-1

value: PMA + Ionomycin

value: 6 min


title: PTG WT ZT16 rep4 [#42 ctrl 22:30]


title: ATAC_fabp_pos_1_TAA

description: tagmented genomic DNA

value: TAA

value: hepatocytes


title: PTG WT ZT0 rep3 [#40 ctrl 06:30]


title: J6-2


title: dUTP strand-specific RNA-seq log-phase cells of Saccharomyces bayanus grown in BMW

city: Cambridge

first: Carl

last: de Boer

institute: The Broad Institute

organism: Saccharomyces bayanus

value: BMW

value: log phase


title: J3-2

value: 3 min


title: ATAC_fabp_pos_1_ctrl

description: tagmented genomic DNA

value: female

value: FACS-sorted liver cells


title: PTG KO ZT20 rep4 [#39 KO 02:30]

value: Male

value: 11 weeks


title: PTG WT ZT20 rep4 [#38 ctrl 02:30]

value: Bma1 Wildtype


title: J0-2

value: 0 min


title: OsSRT1-RNAi_RNA_8h

city: Wuhan

first: Baibai

last: Gao

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

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

organism: Oryza sativa

source_name: OsSRT1-RNAi mature leaf

growth_protocol: Rice [Oryza sativa L. ssp. indica cv. Minghui 63 (MH63)] seeds were sown on May 19, 2017 in a paddy field. At 20 days after germination, the seedlings were transplanted into a paddy field of Huazhong Agricultural University at Wuhan, China, and grown under normal agricultural conditions. In the paddy field, the plants were transplanted at a density of one plant per 15 × 30 cm area.

extract_protocol:
Total RNA was isolated from OsSRT1-RNAi mature leaves at 8:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.

treatment_protocol: Samples for RNA isolation were immediately frozen in liquid nitrogen and stored at -80°C until use.

tag: tissues

value: mature leaf

value: mature leaves were flag leaf at floral induction phase

tag: time point


title: OsSRT1-RNAi_RNA_20h

extract_protocol:
Total RNA was isolated from OsSRT1-RNAi mature leaves at 20:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.


title: PTG WT ZT20 rep3 [#37 ctrl 02:30]

value: Parathyroid glands


title: MH63_RNA_20h

source_name: MH63 mature leaf

extract_protocol:
Total RNA was isolated from MH63 mature leaves at 20:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.

value: Minghui 63


title: J9-1

tag: cell line

value: Jurkat, Clone E6-1

value: PMA + Ionomycin

value: 9 min


title: J0-1

tag: treatment time


title: MH63_RNA_8h

extract_protocol:
Total RNA was isolated from MH63 mature leaves at 8:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.


title: PTG WT ZT20 rep2 [#36 ctrl 02:30]


title: PTG KO ZT12 rep2 [#34 KO 18:30]

value: Bma1 Knockout


title: PTG WT ZT20 rep1 [#35 ctrl 02:30]


title: Living Donor biopsies [Sample_1162-EO-1]

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

data_processing:
The sequencing data is pre-processed using the 10X Genomics software Cell Ranger. Downstream analysis is performed with the Seurat3 R package (Satija Lab). Combined analysis of the single-cell datasets generated from the different sample sources (LD and Surveillance biopsies) using Seurat (v3) included the following steps: filtering out of cells with <500 genes or >50% mitochondrial content default normalization, scaling based on sample mRNA count and mitochondrial RNA content, dimensionality reduction PCA (Principal component analysis) and UMAP (Uniform Manifold Approximation and Projection), sample integration using Harmony algorithm, standard unsupervised clustering, and the discovery of differentially expressed cell type-specific markers.
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix files in tab delimited format

source_name: Kidney biopsy

extract_protocol:
We leveraged the surveillance biopsy program at the University of Michigan, where biopsies are performed at time 0, 3-,6- and 12 months. For this study the time 0 biopsies from healthy living donors (controls) were obtained at the back table prior to perfusion. While surveillance biopsies were performed at 3- and 12 months.. As part of our established Human Kidney Transplant Transcriptomic Atlas (HKTTA) workflow Along with standard of care biopsy cores, patients consent for a single research core obtained with a 16-gauge needle. The research core was collected following a standardized protocol.12,13 The research core is then cut into three pieces (1-2 mg each) with Piece#1 stored in RNA laterTM solution for bulk transcriptome analysis, Piece #2 and Piece #3 put into in Cryostor CS10 Freeze Media solution (Biolife Solutions) for scRNA-seq analysis, and for future use including single nuclear studies respectively.  All clinical and research activities being reported are consistent with the Principles of the Declaration of Istanbul.
The generation of single-cell preparations was accomplished by enzymatic (Liberase TL) and mechanical dissociation for 12 minutes at 37˚C following our protocol previously published.12 Cells are filtered through a 50µm strainer, counted, and up to 10,000 viable cells are submitted to the Genomics Core facility for droplet-based high-throughput 10X GenomicsTM Chromium TM platform arrays. After droplet encapsulation, the 10X Genomics approach allows cell lysis, individual cell RNA molecular barcoding, and reverse transcription. Subsequently, cDNA libraries are generated and sequenced on an Illumina NovaSeq6000 platform as asymmetric paired-end runs (26X1paired-end generating more than 200 million raw sequence reads per sample

value: biopsy from the donor kidney before transplantation

tag: biopsy

value: Living Donor biopsies


title: FAIRE_20h_rep2

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

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

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

tag: development stage

value: mature leaves harvested at 20:00 at floral induction stage

tag: cultivar


title: FAIRE_16h_rep2

value: mature leaves harvested at 16:00 at floral induction stage


title: PTG WT ZT8 rep1 [#33 ctrl 14:30]

tag: genotype

tag: age


title: FAIRE_20h_rep1


title: Living Donor biopsies [Sample_1162-EO-2]


title: Living Donor biopsies [Sample_1158-EO-3]


title: Living Donor biopsies [Sample_1158-EO-2]


title: J3-1

value: 3 min

tag: replicate


title: Jaml KO IRI 24h Renal - 3

city: Jinan

first: Wei

middle: Jinan

last: Huang

address: 44# Wenhua Xi Road

department: Department of Pharmacology

institute: School of Basic Medical Sciences, Shandong University

description: Gene expression in renal of mice with IRI 24h

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Jaml KO IRI 24h Renal

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: All mice (3-5 mice per cage) were housed under standard laboratory conditions (12 h on/off; lights on at 7:00 a.m.) and temperature (24℃) in the specific-pathogen-free experimental animal center.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: Bilateral renal aortas were ligatured with surgical suture,thirty minutes later, reperfusion was performed by unfastening the ligations.

value: kidney

tag: gender

value: male

value: KO

value: IRI 24h


title: Jaml KO Sham Renal - 3

description: Gene expression in renal of mice with sham-operation

source_name: Jaml KO Sham Renal

tag: treatment

value: sham-operation


title: Living Donor biopsies [Sample_1158-EO-1]


title: Jaml KO Sham Renal - 2


title: FAIRE_16h_rep1

value: mature leaf


title: PTG KO ZT8 rep1 [#31 KO 14:30]

value: Male

value: 11 weeks

value: Parathyroid glands


title: Living Donor biopsies [Sample_1157-EO-2]


title: Jaml KO IRI 24h Renal - 2


title: FAIRE_12h_rep2

value: mature leaves harvested at 12:00 at floral induction stage

value: Minghui 63


title: PTG WT ZT0 rep2 [#28 ctrl 06:30]

value: Bma1 Wildtype


title: FAIRE_8h_rep2

value: mature leaves harvested at 8:00 at floral induction stage


title: PTG KO ZT8 rep2 [#30 KO 14:30]

value: Bma1 Knockout


title: FAIRE_4h_rep2

value: mature leaves harvested at 4:00 at floral induction stage


title: FAIRE_12h_rep1


title: Living Donor biopsies [Sample_1153-EO-3]

value: biopsy from the donor kidney before transplantation

value: Living Donor biopsies


title: FAIRE_8h_rep1


title: PTG WT ZT0 rep1 [#27 ctrl 06:30]


title: Living Donor biopsies [Sample_1153-EO-2]


title: Living Donor biopsies [Sample_1157-EO-1]


title: FAIRE_4h_rep1


title: WT IRI 24h Renal - 1

source_name: WT IRI 24h Renal

value: kidney

value: WT


title: PTG KO ZT0 rep3 [#26 KO 06:30]


title: WT Sham Renal - 3

source_name: WT Sham Renal

value: male


title: Jaml KO IRI 24h Renal - 1

value: KO

value: IRI 24h


title: WT Sham Renal - 2

value: sham-operation


title: FAIRE_0h_rep2

value: mature leaf

value: mature leaves harvested at 0:00 at floral induction stage


title: Jaml KO Sham Renal - 1


title: WT IRI 24h Renal - 2


title: PTG KO ZT0 rep2 [#25 KO 06:30]

value: Male

value: 11 weeks

value: Parathyroid glands


title: WT IRI 24h Renal - 3


title: Living Donor biopsies [PRE98-sc]


title: Living Donor biopsies [Sample_1157-EO-3]


title: PTG KO ZT0 rep1 [#24 KO 06:30]


title: PolrMT-E423P-mitoRNA-rep2

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

description: Total mitochodnrial RNA

data_processing:
Sequenced reads were trimmed for adapter contamination using Trim Galore version 0.6.7 with parameter  "--stringency 5", then mapped to BDG6 whole genome using HISAT2 v 2.2.1 with default settings.
Low mapping quality reads were filtered out using samtools with parameter "-q 30" and only reads mapping to mitochondria were used for further analysis.
FeatureCounts (subread v2.0.0) was used for gene counting with parameters "-p -s 0 " for unique counts  and "-p -s 0 -M -O -J -R CORE"  to obtain details for junctions.
Genome_build: BDGP6, Ensembl release 84
Supplementary_files_format_and_content: Excel spreadsheet RNA frequency Unprocessed and Junctions

source_name: E423P mitochondria

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Whole fly mitochondria were extracted and mitochondrial RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total mitochondrial RNA for the construction of sequencing libraries.

value: E423P RNA polymerase overexpression

value: Two weeks old


title: dUTP strand-specific RNA-seq log-phase cells of Naumovozyma castellii grown in BMW

address: 415 Main St

organism: Naumovozyma castellii

tag: media

value: BMW

tag: growth temperature (celcius)

tag: growth phase

value: log phase


title: PTG WT ZT16 rep3 [#21 ctrl 22:30]

value: Bma1 Wildtype

tag: Sex

tag: tissue


title: PTG WT ZT16 rep2 [#19 ctrl 22:30]

tag: zeitgebertime


title: WT Sham Renal - 1


title: PolrMT-E423P-mitoRNA-rep3

description: Total mitochodnrial RNA


title: Living Donor biopsies [Sample_1153-EO-1]

tag: time point

value: biopsy from the donor kidney before transplantation

value: Living Donor biopsies


title: FAIRE_0h_rep1

value: Minghui 63


title: PTG KO ZT16 rep3 [#23 KO 22:30]

value: Bma1 Knockout


title: PTG KO ZT16 rep2 [#20 KO 22:30]


title: PolrMT-E423P-mitoRNA-rep1

description: Total mitochondrial RNA


title: PolrMT-mitoRNA-rep3

description: Total mitochodnrial RNA

source_name: Wild type mitochondria

value: wild type RNA polymerase overexpression


title: Living Donor biopsies [PRE062-1]


title: Living Donor biopsies [PRE19-05]


title: Living Donor biopsies [PRE19-025]


title: RNAPII_ChIA_20h_rep1

data_processing:
Library strategy: ChIA-PET
ChIA-PET raw reads were processed using modified ChIA-PET Tool pipeline
Genome_build: MH63
Supplementary_files_format_and_content: bedpe

extract_protocol:
Sample was ground in liquid nitrogen into a fine powder and resuspended in 100 ml of EB1 buffer. The mixture was then filtered through Miracloth, and the filtrate was centrifuged at 1,800 × g for 10 min at 4 °C. The pellet was washed three times in 5 ml of EB2 buffer and centrifuged at 2,000 × g for 10 min at 4 °C. Next, the pellet was washed in 2 ml of EB3 buffer and centrifuged at 2,000 × g for 1 h at 4 °C. The final pellet was resuspended in 1 ml of NLB buffer, and chromatin was fragmented into 1-3 kb by sonication. After centrifugation at 2,000 × g for 10 min at 4 °C, the supernatant was transferred to a new tube for chromatin immunoprecipitation (ChIP). The antibody (80 µg; RNAPII, BioLegend, 920102) was mixed with 800 µl suspended protein G magnetic beads, and incubated at 4°C for 8 h with rotation to coat the magnetic beads. All of the chromatin was extracted to the antibody-loaded beads in a new tube and incubated at 4°C overnight with rotation. The supernatant was discarded and the beads were sequentially washed with 5 mL 0.1% SDS FA cell lysis buffer (0.05 M HEPES-KOH, 0.15 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) for three times, 5 mL High salt ChIP buffer (0.05 M HEPES-KOH, 0.35 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) twice, 5 mL ChIP wash buffer (0.01 M Tris–HCl, 0.25 M LiCl, 0.001 M EDTA, 2.5% NP-40, and 0.5% sodium deoxycholate) once and 5 mL 1 × TE buffer (pH 8.0, Ambion, cat. no. AM9849) twice. ChIP DNA was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F) and Klenow enzyme (NEB, cat. no. M0212L). Proximity ligation of ChIP DNA was performed using biotinylated bridge-linker (forward strand: 5′-[5Phos] CGCGATATC/iBIOdT/TATCTGACT-3′, reverse strand: 5′-[5Phos]GTCAGATAAGATATCGCGT-3′).
Protein-DNA complex was reverse cross-linked and the ChIA-PET libraries were prepared by using Tn5 transposase (VAHTS; cat. no. TD501). The libraries were sequenced (2 × 150 bp) using Illumina Hiseq X-Ten (Beijing AnnoRoad Company).

treatment_protocol: Rice leaves were dual cross-linked with 1% formaldehyde for 20 min and quenched with 0.2 M glycine. Next, EGS was added to a final concentration of 1.5 mM in PBS buffer and incubated for another 40 min at room temperature.

value: mature leaves harvested at 20:00 at floral induction stage

tag: chip antibody

value: RNAPII


title: PolrMT-mitoRNA-rep1

description: Total mitochodnrial RNA


title: RNAPII_ChIA_8h_rep2

value: mature leaf

value: mature leaves harvested at 8:00 at floral induction stage


title: PolrMT-mitoRNA-rep2

description: Total mitochondrial RNA


title: Living Donor biopsies [PRE055-1]


title: RNAPII_ChIA_20h_rep2


title: PTG WT ZT16 rep1 [#18 ctrl 22:30]

value: Male


title: RNAPII_ChIA_8h_rep1


title: PTG WT ZT4 rep4 [#17 ctrl 10:30]

value: 11 weeks


title: PTG KO ZT4 rep2 [#16 KO 10:30]

value: Parathyroid glands


title: Input_rep1

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the duplication reads
peaks were called using MACS.2.2.1 with narrow parameters
Genome_build: MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

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

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 20 min and quenched with 0.2 M glycine at room temperature.


title: RNAPII_ChIP-20h_rep2


title: PTG WT ZT4 rep2 [#14 ctrl 10:30]


title: Living Donor biopsies [PRE019-4]


title: PTG WT ZT4 rep3 [#15 ctrl 10:30]


title: Living Donor biopsies [PRE027]


title: Living Donor biopsies [PRE018-1]


title: circCAMSAP1_Ana NAI rep1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: cDNA

data_processing:
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Analyses by CIRCshapemapper.
Genome_build: Target RNA sequence
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

organism: synthetic construct

source_name: circCAMSAP1_Ana NAI

extract_protocol:
For in vitro SHAPE-MaP, RNA are purified. About 50-100 μg of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for linear or circular RNAs (5S rRNA was used as a spike-in control). Mn2+ was removed using G-25 micro-spin columns (GE Healthcare) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase and nested PCR was performed to further improve DNA yield.
circSHAPE-MaP libraries were prepared from 1 ng of DNAs for circular (circSHAPE-MaP) RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina X Ten at CAS-MPG Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For in vitro circSHAPE-MaP, circular RNAs were refolded in 3.3× folding buffer (333 mM HEPES, pH 8.0; 333 mM NaCl; 33 mM MgCl2). After refolding, RNAs were incubated with10x SHAPE Chemical in DMSO with the final concentration of NAI (EMD Millipore) at 100 mM for 10 minutes at 37°C.

tag: sample type

value: in vitro

value: circCAMSAP1_Ana NAI samples modified by NAI in DMSO


title: circCAMSAP1_Ana DMSO

description: cDNA

source_name: circCAMSAP1_Ana DMSO

value: circCAMSAP1_Ana DMSO samples only treated with DMSO


title: circCAMSAP1_Ana NAI rep2

description: cDNA


title: PTG KO ZT20 rep3 [#12 KO 02:30]


title: circCAMSAP1_TD DC

description: cDNA

source_name: circCAMSAP1_TD DC

value: circCAMSAP1_TD DC samples denatured by formamide at 95C


title: RNAPII_ChIP_16h_rep2

value: mature leaves harvested at 16:00 at floral induction stage


title: RNAPII_ChIP_20h_rep1


title: circCAMSAP1_TD DMSO

description: cDNA

source_name: circCAMSAP1_TD DMSO

value: circCAMSAP1_TD DMSO samples only treated with DMSO


title: RNAPII_ChIP_16h_rep1


title: PTG KO ZT20 rep2 [#11 KO 02:30]


title: Living Donor biopsies [PRE038]

value: biopsy from the donor kidney before transplantation

tag: biopsy

value: Living Donor biopsies


title: RNAPII_ChIP_12h_rep2

tag: development stage

value: mature leaves harvested at 12:00 at floral induction stage

value: Minghui 63


title: circCAMSAP1_TD NAI rep2

description: cDNA

source_name: circCAMSAP1_TD NAI

value: circCAMSAP1_TD NAI samples modified by NAI in DMSO


title: PTG KO ZT20 rep1 [#10 KO 02:30]

value: Bma1 Knockout


title: RNAPII_ChIP_12h_rep1

value: mature leaf

tag: cultivar

value: RNAPII


title: circCAMSAP1_Ana DC

description: cDNA

source_name: circCAMSAP1_Ana DC

value: circCAMSAP1_Ana DC samples denatured by formamide at 95C


title: circCAMSAP1_Lig DC

description: cDNA

source_name: circCAMSAP1_Lig DC

value: circCAMSAP1_Lig DC samples denatured by formamide at 95C


title: circCAMSAP1_TD NAI rep1

description: cDNA


title: PTG KO ZT12 rep1 [#9 KO 18:30]

source_name: Parathyroid glands

tag: genotype

value: Male

value: 11 weeks

value: Parathyroid glands


title: RNAPII_ChIP_8h_rep1

value: mature leaves harvested at 8:00 at floral induction stage


title: RNAPII_ChIP_8h_rep2


title: PTG KO ZT4 rep1 [#13 KO 10:30]

tag: age


title: circCAMSAP1_Lig DMSO

description: cDNA

source_name: circCAMSAP1_Lig DMSO

value: in vitro

value: circCAMSAP1_Lig DMSO samples only treated with DMSO


title: PTG WT ZT12 rep2 [#6 ctrl 18:30]

value: Bma1 Wildtype


title: PTG WT ZT12 rep1 [#5 ctrl 18:30]


title: RNAPII_ChIP_4h_rep1

source_name: MH63 mature leaf

value: mature leaves harvested at 4:00 at floral induction stage


title: circCAMSAP1_Lig+RIG-I NAI rep2

description: cDNA

source_name: circCAMSAP1_Lig+RIG-I NAI

value: circCAMSAP1_Lig interact with RIG-I samples modified by NAI in DMSO


title: circCAMSAP1_Lig+RIG-I NAI rep1

description: cDNA


title: circCAMSAP1_Lig+PKR NAI rep1

description: cDNA

source_name: circCAMSAP1_Lig+PKR NAI

value: circCAMSAP1_Lig interact with PKR samples modified by NAI in DMSO


title: circCAMSAP1_Lig NAI rep2

description: cDNA

source_name: circCAMSAP1_Lig NAI

value: circCAMSAP1_Lig NAI samples modified by NAI in DMSO


title: circCAMSAP1_Lig+PKR NAI rep2

description: cDNA


title: circCAMSAP1_Lig NAI rep1

description: cDNA


title: RNA_20h_rep2

extract_protocol:
Total RNA was isolated from mature leaves at 20:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.

value: mature leaves were flag leaf at floral induction phase

value: Minghui 63


title: Lens homozygous rep2

city: GaungZhou

first: Minglei

last: Zhao

address: 7#, Jinsui Road

institute: Sun yat sen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lens

extract_protocol:
Lens were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lens

tag: strain

value: Lss mutant homozygous


title: RNAPII_ChIP_0h_rep2

value: mature leaf

value: mature leaves harvested at 0:00 at floral induction stage

value: RNAPII


title: Lens homozygous rep3


title: RNAPII_ChIP_0h_rep1


title: circPOLR2A_Ana DC

description: cDNA

source_name: circPOLR2A_Ana DC

value: circPOLR2A_Ana DC samples denatured by formamide at 95C


title: PTG WT ZT12 rep3 [#7 ctrl 18:30]

value: Male

value: 11 weeks

value: Parathyroid glands


title: RNA_20h_rep1


title: Lens homozygous rep1


title: RNA_16h_rep2

extract_protocol:
Total RNA was isolated from mature leaves at 16:00 using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
1.5 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.


title: RNA_16h_rep1


title: Lens WT rep3

value: WT


title: circPOLR2A_Ana DMSO

description: cDNA

source_name: circPOLR2A_Ana DMSO

value: in vitro

value: circPOLR2A_Ana DMSO samples only treated with DMSO